673 Matching Annotations
  1. Oct 2026
    1. In order toprovide final proof that SLC6A8 deficiency is caused by a de-fect of the creatine transporter, we transfected the wild-typeSLC6A8 open reading frame (ORF) into primary fibroblastsof a SLC6A8-deficient patient, and tested the creatine uptakecapacity

      RescuePatientCell: Primary fibroblasts from a SLC6A8-deficient patient.

      GeneAlteration: c.1540C>T (p.Arg514X) (previously described by Salomons et al, 2001, Am J Hum Genet, 68: 1497-1500)

      RescuePhenotype: Ability to transport creatine into the cell.

      RescueMethod: The wild type SLC6A8 open reading frame was cloned into an expression vector with EGFP. This construct was stably transfected into primary fibroblasts from patient with creatine transporter deficiency due to a nonsense variant, c.1540C>T (p.Arg514X) in SLC6A8 (previously described in PMD 11326334). Expression of the SLC6A8 fusion protein or EGFP protein (empty vector) was confirmed by the presence of green fluorescence. Expression was also confirmed by RT-PCR. Transfected cells were incubated for 24 hours with 25 umol/L creatine, 500 umol/L creatine, or 500 umol/L creatine plus 500 umol/L guanidinoproprionate (creatine transporter inhibitor). Intracellular creatine level was measured by GC-MS.

      RescueEvidence: When the wild type SLC6A8 open reading frame was expressed in primary fibroblasts from patient with creatine tarnsporter deficiency, due to a nonsense variant, c.1540C>T (p.Arg514X) in SLC6A8 (previously described in PMID 11326334), creatine uptake was restored to a level comparable with controls.

      RescueVariants: ClinVarID: 11696

    1. 31

      Case31: 2 mo (at biopsy), Indian

      Case 31 (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.257C>T (p.Pro86Leu)

      ClinVar: 553773

      CAID: CA3847150

      gnomAD: 0.00009799 (South Asian)


      CaseAddInfo: mut- type, homozygous mutations. documented consanguinity.

    2. 30

      Case30: 6 wks (at biopsy), Pakistani

      Case 30 (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.55dupG (p.Val19Glyfs)

      ClinVar: 222906

      CAID: CA10575888

      gnomAD: n/a


      CaseAddInfo: mut0 type, homozygous mutations. novel variant.

    3. 28

      Case28: 1 y 1 mo (at biopsy), European

      Case 28 (Level 2)


      CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1181dupT (p.Leu394Phefs)

      ClinVar: 222930

      CAID: CA10575868

      gnomAD: n/a


      Variant2: NM_000255.3:c.1975C>T (p.Gln659Ter)

      ClinVar: 222939

      CAID: CA10575859

      gnomAD: n/a


      CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations, unknown cis or trans.

    4. 27

      Case27: no age or ethnicity recorded

      Case 27 (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1061delCinsGGA (p.Ser354TrpfsTer20)

      ClinVar: n/a

      CAID: CA913187308

      gnomAD: n/a


      Variant2: NM_000255.3:c.1065_1068dupATGG (p.Ser357MetfsTer5)

      ClinVar: 280817

      CAID: CA10602989

      gnomAD: n/a


      CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations. Examination of NGS reads determined mutations are in trans

    5. 26

      Case26: 7 y (at biopsy), Hispanic

      Case 26 (Level 2)


      CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 7.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.970G>A (p.Ala324Thr)

      ClinVar: 550893

      CAID: CA364400785

      gnomAD: 0.0001632 (Other)


      Variant2: NM_000255.3:c.1846C>T (p.Arg616Cys)

      ClinVar: 551499

      CAID: CA3846722

      gnomAD: 0.00008688 (Latino)


      CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans. Protein change in paper (p.P649L) is different than protein change indicated by clin var and CAID (p.Arg616Cys).

    6. 29

      Case29: 3 mo (at biopsy), Chinese

      Case 29 (Level 2)


      CasePreviousTesting: same as group. found 0.3 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.Gly427Asp)

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      Variant2: Exon 13 deletion

      ClinVar: n/a

      CAID: n/a

      gnomAD: n/a


      CaseAddInfo: Variant 2 is novel. Heterozygous mutations in MUT, unknown cis or trans. Additional variant found in TCN2 gene (NM_000355.3:c.509G>A, ClinVar: 341197, CAID: CA10184685, gnomAD: 0.007469 (East Asian)). heterozygous Exon 13 deletion confirmed by microarray-based comparative genomic hybridization.

    7. 25

      Case25: 25 y (at biopsy), White

      Case 25 (Level 2)


      CasePreviousTesting: same as group. found 1.3 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.935G>T (p.Gly312Val)

      ClinVar: 218988

      CAID: CA347874

      gnomAD: n/a


      Variant2: NM_000255.3:c.1909G>A (p.Gly637Arg)

      ClinVar: n/a

      CAID: CA3846712

      gnomAD: [0.000008798] (http://insert-your-link-here.com)(European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    8. 24

      Case24: no age or ethnicity recorded

      Case 24 (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.795_796insT or NM_000255.3:c.795dupT (p.Met266TyrfsTer7)

      ClinVar: n/a

      CAID: CA913187322

      gnomAD: n/a


      Variant2: NM_000255.3:c.1207C>T (p.Arg403Ter)

      ClinVar: 167310

      CAID: CA234287

      gnomAD: 0.0001602 (African)


      CaseAddInfo: Variant 1 is novel. Mut0 type, heterozygous mutations, unknown cis or trans.

    9. 23

      Case23: 3 mo (at biopsy), French Canadian

      Case 23 (Level 2)


      CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.753+3A>G

      ClinVar: n/a

      CAID: CA3847056

      gnomAD: 0.000008890 (European non-Finnish)


      Variant2: NM_000255.3:c.1332+1delG

      ClinVar: 554656

      CAID: CA3846920

      gnomAD: 0.000008828 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans. Variant 1 is novel.

    10. 22

      Case22: 28 mo (at biopsy), Korean

      Case 22 (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1481T>A (p.Leu494Ter)

      ClinVar: 551275

      CAID: CA3846864

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

    11. 21

      Case21: 2 mo (at biopsy), White

      Case 21 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1287C>G (p.Tyr429Ter)

      ClinVar: 554278

      CAID: CA364398724

      gnomAD: 0.00006483 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    12. 20

      Case20: 5 days (at biopsy), White

      Case 20 (Level 2)


      CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    13. 19

      Case19: 1 mo (at biopsy), White

      Case 19 (Level 2)


      CasePreviousTesting: same as group. found 1.2 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.655A>T (p.Asn219Tyr)

      ClinVar: 1886

      CAID: CA249731

      gnomAD: 0.0001318 (European non-Finnish)


      Variant2: NM_000255.3:c.1332+1delG

      ClinVar: 554656

      CAID: CA3846920

      gnomAD: 0.000008828 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

    14. 18

      Case18: 2 mo (at biopsy), French Canadian

      Case 18 (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.655A>T (p.Asn219Tyr)

      ClinVar: 1886

      CAID: CA249731

      gnomAD: 0.0001318 (European non-Finnish)

      __

      Variant2: NM_000255.3:c.1240delG (p.Glu414LysfsTer17)

      ClinVar: n/a

      CAID: CA3846936

      gnomAD: 0.000008796 (European Non-Finnish)


      CaseAddInfo: mut0 type. Variant 2 is novel. heterozygous mutations, unknown cis or trans.

    15. 17

      Case17: 6 y (at biopsy), Black

      Case 17 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.631_633delGAG (p.Glu211del)

      ClinVar: n/a

      CAID: CA913187321

      gnomAD: n/a


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutations. Variant 1 is novel. MUT mutations are in trans- demonstrated by RT-PCR of mRNA. Additional variant found in MCEE gene (NM_032601.3:c.428G>A, ClinVar: 336936, CAID: CA1702575, gnomAD: 0.08102 (Latino)) MCEE variant is unlikely to be associated with patient's MMA.

    16. 16

      Case16: 5 days (at biopsy), Lao/Thai/Mexican/Portugese

      Case 16 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.581C>T (p.Pro194Leu)

      ClinVar: n/a

      CAID: CA364404418

      gnomAD: n/a


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    17. 15

      Case15: 3 wks (at biopsy), white

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.754-2A>G

      ClinVar: 552691

      CAID: CA364402853

      gnomAD: n/a


      CaseAddInfo: variant 2 is a novel, splice site mutation. Heterozygous mutations, unknown cis or trans.

    18. 13

      Case13: 21 y (at biopsy), English/Irish

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    19. 12

      Case12: 6y (at biopsy), no ethnicity recorded

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.556A>G (p.Met186Val)

      ClinVar: 551460

      CAID: CA3847093

      gnomAD: 0.00001760 (European Non-Finnish)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans

    20. 11

      Case11: 6y (at biopsy), White/Hispanic

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.6 nmol/mg protein/18 h propionate incorporation, 7.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.566A>T (p.Asn189Ille)

      ClinVar: 222915

      CAID: CA3847091

      gnomAD: 0.000008804 (European Non-Finnish)


      Variant2: NM_000255.3:c.655A>T (p.Asn219Tyr)

      ClinVar: 1886

      CAID: CA249731

      gnomAD: 0.0001318 (European non-Finnish)


      CaseAddInfo: Variant 1 is novel, unknown cis or trans. mut- type.

    21. 14

      Case14: 3 mo (at biopsy), White/Australian

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

      ClinVar: 203854

      CAID: CA312777

      gnomAD: 0.00006976 (European non-FInnish)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

    22. 10

      Case10: 6 days (at biopsy), Northern European/Filipino

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    23. 9

      Case9: 46 days (at biopsy), Hispanic

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.654A>C (p.Gln218His)

      ClinVar: 551243

      CAID: CA364404273

      gnomAD: 0.000008809 (European non-Finnish)


      CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

    24. 8

      Case8: 12 days (at biopsy), White/Mexican

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

      ClinVar: 1887

      CAID: CA249732

      gnomAD: 0.0008393 (Latino)


      Variant2: NM_000255.3:c.654A>C (p.Gln218His)

      ClinVar: 551243

      CAID: CA364404273

      gnomAD: 0.000008809 (European non-Finnish)


      CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

    25. 7

      Case7: 10 days (at biopsy), White

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.146_147ins279

      ClinVar: n/a

      CAID: n/a- could not register

      gnomAD: n/a


      Variant2: NM_000255.3:c.372_374dupGA (p.Lys124_Asp125insGlu)

      ClinVar: 203861

      CAID: CA312788

      gnomAD: 0.000008799


      CaseAddInfo: mut0 class. heterozygous mutations. identified to be in trans through cDNA analysis. variant 1 is novel and consists of a 279 base pair insertion.

    26. 6

      Case6 2 mo (at biopsy), White

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 3.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.129G>A (p.Trp43Ter)

      ClinVar: 222908

      CAID: CA10575886

      gnomAD: n/a


      Variant2: NM_000255.3:c.299A>G (p.Tyr100Cys)

      ClinVar: 218991

      CAID: CA347866

      gnomAD: 0.000008793 (European non-Finnish)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. variant 1 is novel.

    27. 5

      Case5: 1y 9 mo (at biopsy), Korean

      Case (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

      ClinVar: 92688

      CAID: CA249743

      gnomAD: 0.00008013 (African)


      Variant2: NM_000255.3:c.349G>T (p.Glu117Ter)

      ClinVar: 1882

      CAID: CA115264

      gnomAD: n/a


      CaseAddInfo: mut0 class. heterozygous mutations. unknown cis or trans.

    28. 4

      Case4: 2 y (at biopsy), Black

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 3.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

      ClinVar: 92688

      CAID: CA249743

      gnomAD: 0.00008013 (African)


      Variant2: NM_000255.3:c.323G>A (p.Arg108His)

      ClinVar: 100707

      CAID: CA235522

      gnomAD: 0.00006152 (African)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. Third variant in TCN2 gene (NM_000355.3:c.89T>G p.Leu30Arg, CAID: CA10184491, ClinVar: 529781, gnomAD: 0.01329 (African))

    29. 3

      Case3: 19y (at biopsy), Irish/Scottish/Polish

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.2 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.29dupT (p.Leu10PhefsTer39)

      ClinVar: 553287

      CAID: CA567155988

      gnomAD: 0.00003269 (South Asian)


      Variant2: NM_000255.3:c.1658delT (p.Val553GlyfsTer17)

      ClinVar: n/a

      CAID: CA450397348

      gnomAD: 0.000008808 (European non-Finnish)


      CaseAddInfo: mut0 class. heterozygous mutations. variant 1 is novel. unknown cis or trans.

    30. 2

      Case2: 1 mo (at biopsy), Palestinian

      Case (Level 2)


      CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2T>C (p.Met1Thr)

      ClinVar: 222903

      CAID: CA10575890

      gnomAD: n/a


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: mut0 class. heterozygous mutations- unknown cis or trans. 3rd mutation in CD320 gene (NM_016579.3:c.658G>A p.Gly220Arg, ClinVar: 136684, CAID: CA289989, gnomAD: 0.3086 (African) )

    31. 1

      Case1: 13 mo (at biopsy), no recorded ethnicity

      Case (Level 2)


      CasePreviousTesting: same as group. found 2.4 nmol/mg protein/18 h propionate incorporation, 4.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1A>G (p.M1?)

      ClinVar: n/a

      CAID: CA364406084

      gnomAD: n/a


      Variant2: NM_000255.3:c.2150G>T (p.Gly717Val)

      ClinVar: 1881

      CAID: CA249729

      gnomAD: 0.0006810 (African)


      CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans

    1. 2

      Patient2: Female, 5.5yo

      CasePresentingHPOs: HP:0002572, HP:0001259, HP:0003648, HP:0002919 (episodic vomiting, coma, lacticaciduria, ketonuria)

      HPOsFreeText: chronic intermittent IVA, treated with a vegetarian diet and L-carnitine supplements, abnormal excretion of isovalerate metabolites, elevation of isovaleryl glycine in urine, C5-carnitine = 16 µmol/l, birth weight = 2kg, hospitalized at 2yo for vomiting and acidosis. At physical exam at 5.5yo, weight = 18kg, height = 103cm, IQ = 92, and unremarkable systemic examination

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 4mo at onset, 13mo at diagnosis via clinical presentation, consanguineous family, full-term delivery via Caesarean section due to failure of propagation

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3:c.1207T>A

      CAID: CA391724509, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391724509

      gnomAD: n/a

      Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

      CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

      ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

      gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

    2. The variant p.Y403N is located in the turn region adjacent to the alpha helix where hydrogen bond formations are more favourable (Fig. 4). The absence of this variant in 200 normal chromosomes, the clinically severe phenotypes in the two patients, the abnormal biochemical and organic acid profiles (Table 1), and the computational prediction (Figs 3 and 4 and Table 3) suggest a potential genotype–phenotype correlation for this variant.

      Variant 1: NM_002225.3:c.1207T>A

      Variant 2: NM_002225.4(IVD):c.863C>T

      VariantEvidence: This variant is located in the turn region next to the alpha helix where hydrogen bonding is favorable, this location along with the presentation of severe phenotypes and biochemical profiles in the patients harboring these variants suggests a genotype-phenotype correlation (fig. 4)

    3. 6

      Patient6: Male, 8yo

      CasePresentingHPOs: HP:0002572 (episodic vomiting)

      HPOsFreeText: chronic intermittent IVA, 3 monthly attacks of cyclic vomiting, treated with IVA special formula, elevated isovalerylglycine, C5-carnitine = 9.06 µmol/l

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: symptom onset at 6mo, diagnosis at 72mo via clinical presentation, consanguineous family

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3(IVD):c.465+2T>C

      ClinVar: 94055, https://www.ncbi.nlm.nih.gov/clinvar/variation/94055/

      gnomAD: 0.00001991, https://gnomad.broadinstitute.org/variant/15-40702998-T-C

      Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

      CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

      ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

      gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

    1. 3

      Patient3: Female, 22yo

      CasePresentingHPOs: HP:0001249 (intellectual disability)

      HPOsFreeText: Blood C5-carnitine (μM) = 14.27, under a protein restricted diet with carnitine and glycine supplementation

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: diagnosed at 3yo after improper treatment

      CasePMIDs:

      CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

      GroupMethod1: PCR (primers in table 2)

      GroupMethod2: Direct sequencing

      CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

      Variant1: NM_002225.4:c.1007G>A (p.Cys309Tyr) listed in paper as (p.Cys307Tyr)

      CAID: CA391722967, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391722967

      gnomAD: n/a

      Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

      ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

      gnomAD: n/a

    2. 5-2

      Patient5-2 Female, 1yo, sibling to patient 5-1

      CasePresentingHPOs:

      HPOsFreeText: Blood C5-carnitine (μM) = 13.47, under a protein restricted diet with carnitine and glycine supplementation, normal development

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 2mo and asymptomatic at diagnosis

      CasePMIDs:

      CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

      GroupMethod1: PCR (primers in table 2)

      GroupMethod2: Direct sequencing

      CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

      Variant1: NM_002225.4:c.347C>T (p.Ser89Phe) listed in paper as (p.Ser87Phe)

      CAID: CA391716394, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716394

      gnomAD: n/a

      Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

      ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

      gnomAD: n/a

    1. C

      Case6 14yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001256, HP:0000098

      (Mild intellectual disability, Tall stature)

      HPOsFreeText Diagnosis was based on tall height and mild intellectual disability. Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

      CaseNotHPOs HP:0001083

      (Lens dislocation)

      NotHPOsFreeText no other seqeulae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS8+1G>A, compound heterozygous

      ClinVar 1. 120, 2. n/a

      CAID 2. need more info

      gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 28

      FamilyLabel Family 28

      Family28PresentingHPOs n/a

      HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.

      FamilyNotHPOs n/a

      NotHPOsFreeText no further sequelae

      CountryOrigin n/a

      Ethnicity Lebanese

      Race n/a

      Family28PreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      ProbandLabel Case 34

      Variant NM_000071.2(CBS):c.19dupC (p.Gln7Profs), homozygous

      ClinVar 371345

      gnomAD MAF=0.00005473, no homozygotes

      FamilyAddInfo n/a

      FamilyPMIDs n/a

    3. 1622ins

      the Asn541 from allele registry and mutalyzer confused me.

      However, there cannot be an Asn542 as there is no Asn542 in the refseq. Asn542 is created when you insert TGAA, that is true, but the HGVS tracks the most immediate change on the refeq which is actually the Asn541.

      It was also weird that mutalyzer and allele registry didn't take insTGAA, but only used insA. I wrote out the refseq, the refseq with TGAA inserted and the refseq with just A inserted. Sure enough, Asn541 is the most immediate change and the frameshift is the same "...LRGRP...stop" whether you insert TGAA or just A. Not too surprising since you are still in-frame after adding 3 bases, but cool to check.

      interesting!

    4. 5

      FamilyLabel Family 5

      Family5PresentingHPOs n/a

      HPOsFreeText plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

      FamilyNotHPOs HP:0001249

      (Intellectual disability)

      NotHPOsFreeText n/a

      CountryOrigin n/a

      Ethnicity Anglo-Celtic

      Race n/a

      Family5PreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      ProbandLabel Case 7

      Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS1+insC, compound heterozygous

      ClinVar 1. 120, 2. n/a

      CAID 2. need more info

      gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a

      FamilyAddInfo n/a

      FamilyPMIDs n/a

    5. c G

      Case17 4yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001083

      (Lens dislocation)

      HPOsFreeText Diagnosis was based on dislocated lenses. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient was not responsive to the treatment, plasma homocysteine levels went unchanged. This patient was given additional oral betaine(3g twice per day) with a low protein diet.

      CaseNotHPOs HP:0001249

      (Intellectual disability)

      NotHPOsFreeText no other sequelae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant NM_000071.2(CBS):c.919G>A (p.Gly307Ser), homozygous

      ClinVar 117

      gnomAD MAF= 0.00041539(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    1. OS-127 II-1

      CaseOS-127_II-1: Male, Birth onset, Germany

      CasePresentingHPOs: HP:0001992, HP:0410145 (Organic aciduria, Decreased biotinidase activity)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001263 (Global developmental delay)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous and healthy; Proband is confirmed homozygous via parental testing

      CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; Biotinidase deficiency treated via 5 mg biotin/d

      CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

      Variant: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

      ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

      gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

    1. K1

      CaseK1 Female, 12yr report, Bosnian

      CasePresentingHPOs HP:0001557, HP:0025116, HP:0001941, HP:0002098, HP:0003270, HP:0002013, HP:0001290, HP:0000750, HP:0011344, HP:0002069, HP:0002305, HP:0001290, HP:0002059, HP:0004881

      (Abnormal intrauterine movements, Fetal distress, Acidosis, Respiratory distress, Abdominal distension, Vomiting, Hypotonia, Speech delay, Severe GDD, Grand mal seizures, Athetosis, Hypotonia, Cerebral atrophy, Episodic hypoventilation)

      HPOsFreeText born at 42wk gestation. (neonatal, pre-treatment:) apgar score at 1min:7, 5min:8, 10min:8, acidosis, respiratory distress, abdominal distension, vomiting, onset of fits at 2d, resistant to ACD's. (18mo:) introduced to pyridoxine therapy, trial dose/route of 60mg oral, complete cessation of seizures, no apnoea or hypotonia/sleepiness, initial maintenance dose of 800mg. (infancy/childhood:) recurrence of seizures with febrile illness, hypotonia, speech delay/difficulties, severe IQ delay. 1wk after withdrawal from pyridoxine trial at 7y, grand mal seizures recurred(definite PDE).

      CaseNotHPOs HP:0000486

      (Squint)

      NotHPOsFreeText (infancy/childhood:) squint

      CasePreviousTesting Administration of pyridoxine relieved patient's seizures. plasma pipecolic acid: 12(nv<2.5μM), plasma AASA: 1.5(nv<0.2μM), urine AASA: 7.5(nv<1 mmol/mol creatinine). Blood lactate: 5.4mM and CSF lactate: 4.4mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 6.7(nv 0.7-2.6mmol/liter), AASA in plasma 0.9(nv<0.2mmol/liter), urine AASA 19(nv<1mmol/molcreatinine).

      Variant NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), homozygous

      ClinVar 17995

      gnomAD MAF=0.0001385(Other), no homozygotes

      CaseAddInfo parental consanguinity

      CasePMIDs 10894227 (Patient 3...), 17068770 (Patient 8)

    2. family S

      FamilyLabel Family S

      FamilySPresentingHPOs HP:0002098, HP:0010818, HP:0002280

      (Respiratory distress, Generalized tonic seizures, Mega cisterna magna)

      HPOsFreeText (neonatal, pre-treatment:) respiratory distress, generalised tonic seizures. (infancy/childhood:) mega cisterna magna

      FamilyNotHPOs n/a

      CountryOrigin n/a

      Ethnicity Arabic

      Race n/a

      FamilySPreviousTesting Cessation of seizures during pyridoxine therapy

      ProbandLabel S1, Female, 15yr report

      Variant NM_001182.4(ALDH7A1):c.312+2T>A, homozygous

      ClinVar 17997

      gnomAD not in gnomAD

      FamilyAddInfo parental consanguinity

      FamilyPMIDs n/a

    1. 3

      Case# Pat3, F, Chinese, 12day onset

      CasePresentingHPOs HP:0008344, HP:0002013, HP:0011968, HP:0001250, HP:0001263

      CaseNotHPOs HP:0001276, HP:0001279,

      CasePreviousTesting tested for serum BCAAs

      CaseMethod1 PCR

      CaseMethod2 Direct

      CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

      Variant NM_000709.3:c.178G>T, NM_000709.3:c.1214_1219dup

      CAID CA406004676(c.178), CA658820662(c.1214)

      CaseAddInfo mutations confirmed in parents by Sanger sequencing, Her elder brother was healthy. She exhibited feeding difficulties and vomiting at 12 days of age. Severe psychomotor retardation was found at the age of 3 months. Cerebral MRI showed bilateral damage to the globus pallidus, basal ganglia, capsula interna and capsula externa. After treatment, clinical improvement was observed. Currently, she is 4 years old and has moderate psychomotor retardation.

    2. 1

      Case# Pat1, M, Chinese, 3day onset

      CasePresentingHPOs HP:0008344, HP:0008872, HP:0001250, HP:0001276, HP:0001279, HP:0001263

      CaseNotHPOs HP:0002013

      CaseMethod1 PCR

      CaseMethod2 Direct

      CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

      Variant NM_000709.3:c.853+1delG ?

    1. The splice-site deletion of exon 3, found in one Indian patient, probably results in the skipping of exon 3, leading to a frame shift p.(Gly114Alafs*53)

      Case# P2, 5mon onset, Indian

      CasePresentingHPOs HP:0002151, HP:0001946, HP:0001942, HP:0001987

      CasePreviousTesting Of the negative samples, we include here only those negative for NAGS and CPS1 genes. NAGS testing was done by single-exon amplification and DNA sequencing.24 CPS1 testing was done by RNA sequencing, in most cases using stimulated lymphocytes

      CaseGenotypingMethod sequence analysis of coding exons, including flanking intronic regions of CA5A and CA5B, was performed.

      Variant NM_001739.1:c.458_459+22del (p.Gly114Alafs*53)

      CAID CA658820625

      CaseAddInfo consanguineous

    1. Patient 6

      Case6: Male, White

      CasePresentingHPOs: HP:0012072, HP:0002194, HP:0002788, HP:0001256, HP:0000722, HP:0000750, HP:0002360, HP:0005487, HP:0002057, HP:0000664, HP:0000286, HP:0000494, HP:0000368, HP:0000322, HP:0009778, HP:0004209 (Aciduria, Delayed gross motor development, Recurrent upper respiratory tract infections, Mild intellectual disability, Obsessive-compulsive behavior, Delayed speech and language development, Sleep disturbance, Prominent metopic ridge, Prominent glabella, Synophrys, Epicanthus, Downslanted palpebral fissures, Low-set posteriorly rotated ears, Short philtrum, Short thumb, Clinodactyly of the 5th finger)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous

      CasePreviousTesting: Extensive metabolic screening revealed elevated urine AAA (618 mmol/mol creatinine; ref <49) and KAA (348 mmol/mol creatinine; ref not detected) as well as plasma AAA (53 umol/L; ref <12)

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant1: NM_018706.6:c.2185G>A (p.Arg455Gln)

      CAID: CA5407838 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407838

      gnomAD: 0.0002538, https://gnomad.broadinstitute.org/variant/10-12139688-G-A

      Variant2: NM_018706.6:c.1159+5G>A

      CAID: CA5407761 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407761

      gnomAD: 0.0001170, https://gnomad.broadinstitute.org/variant/10-12133688-G-A

    2. Patient 10

      Case10: Male, Mixed, 6 yrs died

      CasePresentingHPOs: HP:0002240, HP:0006579, HP:0003560, HP:0001263, HP:0002376 (Hepatomegaly, Prolonged neonatal jaundice, Muscular dystrophy, Global developmental delay, Developmental regression)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is homozygous

      CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Niemann-Pick type C disease was diagnosed via bone marrow investigations; Metabolic screening suggested a defect in lysine metabolism with urine values of AAA and KAA increasing following a lysine challenge (200 mg/kg p.o.)

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant: NM_018706.6:c.700_701delinsGG (p.Leu234Gly)

      CAID: CA915940679 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA915940679

      gnomAD: Not in gnomAD

    3. Patient 5

      Case5: Male, 16 yrs report

      CasePresentingHPOs: HP:0012072, HP:0010864, HP:0000734 (Aciduria, Severe intellectual disability, Disinhibition)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo:

      CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Metabolic work-up at 17 years of age revealed strongly elevated AAA (549 mmol/mol creatinine; ref <14) and KAA

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant1: NM_018706.6:c.2185G>A (p.Arg455Gln)

      CAID: CA5407838 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407838

      gnomAD: 0.0002538, https://gnomad.broadinstitute.org/variant/10-12139688-G-A

      Variant2: NM_018706.6:c.2329T>C (p.Ser777Pro)

      CAID: CA376014875 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA376014875

      gnomAD: 0.000008948, https://gnomad.broadinstitute.org/variant/10-12159681-T-C

  2. www.nature.com www.nature.com
    1. Patient KM03

      Case#: KM03, F, neonatal (onset), Japanese

      CasePresentingHPOs: HP:0001254, HP:0002179, HP:0001276, HP:0001263 (Lethargy, Opisthotonus, Hypertonia, Global developmental delay)

      HPOsFreeText: Diagnosed at the time of newborn screening. Originally presented as classical form, but later determined to be the intermittent form.

      CaseNotHPOs:

      CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity: 0.12 nmol/h per mg of protein (~9% of control). The authors previously showed by immunoblot analysis that the level of E2 protein was significantly reduced (PMID 3417306).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Total RNA and genomic DNA prepared from lymphoblastoid cells or peripheral leukocytes. RT-PCR was performed with primers in exons 8 and 9 identified an insertion. Gnomic DNA was isolated and sequenced. Confirmed by restriction enzyme digestion.

      Variant: NM_001918.3:c.1018-550A>G (homozygous)

      ClinVar: 11946

      gnomAD: Not in gnomAD

      VariantEvidence: The predicted mRNA encoded a truncated protein with 282 amino acids, including 4 novel amino acids at the carboxyl terminus. 265bp fragment that included the 126 bp intronic region was subcloned into an exon trapping vector and transfected into COS-1 cells to confirm the splicing defect.

      CaseAddInfo: Consanguineous, parents were heterozygous.

      CasePMIDs: 3417306

    1. Case Report

      CaseAD: Male, 5 yrs onset

      CasePresentingHPOs: HP:0000750, HP:0002572, HP:0012537, HP:0001944, HP:0001649, HP:0002789, HP:0001252, HP:0001942, HP:0001987, HP:0002919, HP:0012120 (Delayed speech and language development, Episodic vomiting, Food intolerance, Dehydration, Tachycardia, Tachypnea, Muscular hypotonia, Metabolic acidosis, Hyperammonemia, Ketonuria, Methylmalonic aciduria)

      HPOsFreeText: Frequent catabolism episodes with vomiting were noticed without decompensation

      CaseNotHPOs: HP:0001270, HP:0001919, HP:0011015 (Motor delay, Acute kidney injury, Abnormal blood glucose concentration)

      NotHPOsFreeText: Propionyl-CoA carboxylase activity was within normal ranges in fibroblasts

      CaseAddInfo: Parents are non-consanguineous with no family history, Dietary restriction and supplementation showed amelioration of symptoms

      CasePreviousTesting: Normal ECG and MRI results; Metabolic acidosis (pH = 7.08, bicarbonates = 7.3 mmol/L, normal lactic acid, PCO2 = 25 mmHg) and hyperammmoniemia (100 µmol/L) present; Large increase in plasmatic propionylcarnitine (17.5 µmol/L; N < 0.75), undetectable methylmalonylcarnitine, and high urinary excretion of 3-hydroxypropionate and methylcitrate

      CaseGenotypingMethod: Next-generation sequencing in the proband revealed a homozygous nonsense founder variant in the MCEE gene.

      Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

      ClinVar: 2343, http://www.ncbi.nlm.nih.gov/clinvar/variation/2343

      gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A

    1. c.1A > T

      Case# PB1, Saudi Arabia

      CasePresentingHPOs HP:0000707, HP:0003011, HP:0025031, HP:0001939, HP:0002715

      CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

      CaseMethod1 PCR

      CaseGenotypingMethod PCR of coding exons of BCKDHA (9 exons), BCKDHB (11 exons) DBT (11 exons) and DLD (14 exons).

      Variant NM_000056.3:c.1A>T

      CAID CA364657845

      gnomAD 0.00003656 (European (Non-Finnish)), 0.00001346 (Overall)

      VariantEvidence none

      CaseAddInfo consanguineous family

    1. Patient 3

      Case3: Newborn, Hmong (China)

      CasePresentingHPOs:

      HPOFreeText: Born after normal pregnancy, postnatal course normal except for moderately elevated C5-acylcarnitine found during NBS. Treatment with L-carnitine supplementation.

      CaseNotHPOs:

      CasePreviousTesting: Urine 2-MBG 55.7 ug/mg creatinine (ref 0.3-7.5); urine IVG 1.2 ug/mg creatinine (ref 0.3-14.3).

      CaseGenotypingMethod: PCR and sequencing of entire gene.

      Variant: NM_001609.3:c.1165A>G (p.Met389Val) (homozygous)

      CAID: CA5730948

      gnomAD: East Asian 0.0005513

      VariantEvidence: PCR of cDNA using primers in exon 9 and exon 11 showed that exon 10 was missing. Analysis of intron exon junctions flanking exon 10 did not reveal any changes.

      CaseAddInfo: Diagnosis confirmed by Western blot of fibroblasts which showed no SBCAD protein.

      CasePMIDs:

    2. Patient 1

      Case1: Newborn, male, Hmong (China)

      CasePresentingHPOs:

      HPOFreeText: Delivered at 33 weeks of gestation as a result of preterm labor. Postnatally required care for respiratory distress and pneumonia. NBS revealed elevated C5 acylcarnitine. Treated with L-carnitine supplementation and discharged at 4 weeks. Normal development at 12 months.

      CaseNotHPOs:

      CasePreviousTesting: Plasma C5-acylcarnitine 0.7, 3.4 umol/L (ref <0.6); urine 2-MBG 1.8, 10.2, 13.4, 28.7 ug/mg creatinine (ref 0.3-7.5); urine IVG 0.1, 0.3, 0.4, 1.1 ug/mg creatinine (ref 0.3-14.3).

      CaseGenotypingMethod: PCR and sequencing of entire gene.

      Variant: NM_001609.3:c.1165A>G (p.Met389Val) (homozygous)

      CAID: CA5730948

      gnomAD: East Asian 0.0005513

      VariantEvidence: PCR of cDNA using primers in exon 9 and exon 11 showed that exon 10 was missing. Analysis of intron exon junctions flanking exon 10 did not reveal any changes.

      CaseAddInfo: Diagnosis confirmed by Western blot of fibroblasts which showed no SBCAD protein. Treatment discontinued without consequence.

      CasePMIDs:

    3. Patient 2

      Case2: Newborn, Hmong (China)

      CasePresentingHPOs:

      HPOFreeText: Born after normal pregnancy, postnatal course normal except for moderately elevated C5-acylcarnitine found during NBS. Treatment with L-carnitine supplementation. Treatment was discontinued without consequence.

      CaseNotHPOs:

      CasePreviousTesting: Plasma C5-acylcarnitine 3.0, 3.2 umol/L (ref <0.6); urine 2-MBG 2.9, 15.5 ug/mg creatinine (ref 0.3-7.5); urine IVG 0.1, 0.6 ug/mg creatinine (ref 0.3-14.3).

      CaseGenotypingMethod: PCR and sequencing of entire gene.

      Variant: NM_001609.3:c.1165A>G (p.Met389Val) (homozygous)

      CAID: CA5730948

      gnomAD: East Asian 0.0005513

      VariantEvidence: PCR of cDNA using primers in exon 9 and exon 11 showed that exon 10 was missing. Analysis of intron exon junctions flanking exon 10 did not reveal any changes.

      CaseAddInfo: Diagnosis confirmed by Western blot of fibroblasts which showed no SBCAD protein.

      CasePMIDs:

    1. Results

      NonPatientCell: E-Coli (DH5α)

      GeneFunction: GO:0006559

      GeneAlteration: PAH cDNA was cloned into a pMAL-c2E expression vector encoding an N-terminal MBP tag and an enterokinase cleavage site. PAH mutants were constructed using site-directed mutagenesis and confirmed using DNA sequencing. Both the wild-type and the 10 mutant vectors were transformed into E. coli DH5α via overexpresion of fusion proteins at midexponential phase. The proteins were purified and concentration was determined.

      FunctionalEvidence: Expression of the 10 mutant proteins compared to the wild-type demonstrated that several of these mutants induce protein destabilization and subsequent loss of function. Upon deconvolution analysis, five variants showed significanly distrubed oligomerization and a preponderance to misfold and form high-molecular-weight protein aggregates. Enzyme kinetic parameter analysis demonstrated moderate reduction in PAH activity and severely affected allostery in all but one mutation, indicating the strong possibility of global confirmational changes. Protein confirmation was tested by limited proteolysis with proteinase K with six out of eight tested mutants decreasing the half-life of the protein by >50% and decreased stability in five out of eight. Thermal protein denaturation was analyzed by fluorescence and demonstrated that all of the mutations led to substantial distortion of the protein's confirmation and/or loss of structural integrity compared to the wild-type, especially those in the regulatory domain. Finally, amino acid replacements were shown to disrupt local networks of amino acid interactions and alter the normal oligomeric state and therfore the function of the protein.

      FAVariant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      FAVariant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

      ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

      FAVariant3: NM_000277.3(PAH):c.165T>G (p.Phe55Leu)

      ClinVar: 92734 https://www.ncbi.nlm.nih.gov/clinvar/variation/92734/

      FAVariant4: NM_000277.3(PAH):c.1249T>C (p.Tyr417His)

      ClinVar: 102579 https://www.ncbi.nlm.nih.gov/clinvar/variation/102579/

      FAVariant5: NM_000277.3(PAH):c.940C>T (p.Pro314Ser)

      ClinVar: 102905 https://www.ncbi.nlm.nih.gov/clinvar/variation/102905/

    1. 12

      Case12(Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: PCR

      CaseGenotypingMethod: same as group __

      Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

      ClinVar: 30800

      CAID: CA259906

      gnomAD: 0.0005562 (East Asian)


      Variant2: NM_015506.2(MMACHC):c.481C > T (p.Arg161Ter)

      ClinVar: 95703

      CAID: CA223189

      gnomAD: 0.0001241 (African)


      CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) not a carrier

    2. 7

      Case 7 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: PCR

      CaseGenotypingMethod: same as group


      Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

      ClinVar: 30800

      CAID: CA259906

      gnomAD: 0.0005562 (East Asian)


      Variant2: NM_015506.2(MMACHC):c.445_446delTG (p.Cys149Hisfs*32)

      ClinVar: 203834

      CAID: CA312741

      gnomAD: 0.00008509 (Latino)


      CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for both variants

    3. 3

      Case 3 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: PCR

      CaseGenotypingMethod: same as group


      Variant1: NM_015506.2(MMACHC):c.463_465delGGG

      ClinVar: n/a

      CAID: n/a

      gnomAD: n/a


      Variant2: NM_015506.2(MMACHC):c.609G>A

      ClinVar: 30800

      CAID: CA259906

      gnomAD: 0.0005562 (East Asian)


      CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) not a carrier

    4. 11

      Case 11(Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: PCR

      CaseGenotypingMethod: same as group __

      Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

      ClinVar: 30800

      CAID: CA259906

      gnomAD: 0.0005562 (East Asian)


      CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) carrier for p.W203X variant

    5. 1

      Case 1 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: PCR

      CaseGenotypingMethod: same as group


      Variant1: NM_015506.2(MMACHC):c.80A>G (p.Gln27Arg)

      ClinVar: 552467

      CAID: CA827620

      gnomAD: not in gnomAD


      Variant2: NM_015506.2(MMACHC):c.482G>A

      ClinVar: 1425

      CAID: CA223191

      gnomAD: 0.001132 (latino)


      CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) carrier of p.Gln27Arg maternal mutation

    1. 2.1. Subjects

      FamilyGL: N/A

      FamilyPresentingHPOs: HP:0012237 (Urocanic aciduria)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0001507, HP:0100543, HP:0010904 (Growth abnormality, Cognitive impairment, Abnormal circulating histidine concentration)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Genomic DNA was obtained via peripheral blood from the siblings and both parents. PCR and direct sequencing in both forward and reverse directions was used to amplify and sequence the 21 coding exons of UROC1.

      FamilyPreviousTesting: Plasma samples from both subjects demonstrated significant elevations in cis-urocanate, trans-urocanate and imidazole propionate; Z-scores for compounds in alternative histidine degradation pathways were found to be within normal limits, including 1-methylhisitidine, imidazole lactate, and 1-methylhistamine; Table 1 shows detailed metabolite levels; Family history was negative for metabolic disorders or any other familial diseases

      FamilyAddInfo: Family appears to be asymptomatic, Siblings are confirmed compound heterozygous via parental sequencing (father het for Variant 2, mother het for Variant 1)

      Variant1: NM_144639.3:c.356C>G (p.Pro119Arg)

      CAID: CA2591587, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2591587

      gnomAD: 0.0001596, https://gnomad.broadinstitute.org/variant/3-126227314-G-C

      Variant2: NM_144639.3:c.907G>C (p.Ala303Pro)

      CAID: CA2591263, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2591263

      gnomAD: 0.00009300, https://gnomad.broadinstitute.org/variant/3-126220119-C-G

      Affected: 2

      Unaffected: 3

      AddSegregationInfo: Not enough affected

    1. 43

      Case40 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 84(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 312(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R161Q variant destroys an AciI restriction site. Thus, while the patient's DNA fragments would not be cleaved, control fragments would be cleaved. The 848del variant creates a MspI site. This would lead to cleaved patient fragments and uncleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.482G>A (p.Arg161Gln), 2. NM_000159.3(GCDH):c.848delT (p.Leu283Argfs), compound heterozygous

      ClinVar 1. 188789, 2. 370672

      gnomAD 1. MAF=0.0001384(Other), no homozygotes, 2. MAF= 0.0003331(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 6, 7

      Case6 unknown sex, Spain

      CasePresentingHPOs HP:0000707

      (Neurological abnormality)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 500(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 461(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling (Case 7) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 3200mmol/mol creatinine and 3-OH-glutarate was 843mmol/mol creatinine.

      CasePMIDs n/a

    3. 4, 5

      Case4 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 4135(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 752(nv 2–14 mm/mol creatinine).In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling(Case 5) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2166mmol/mol creatinine and 3-OH-glutarate was 420mmol/mol creatinine.

      CasePMIDs see note on previous studies

    4. 20

      Case20 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 3571(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 232(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R132Q variant destroys an AciI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.395G>A (p.Arg132Gln), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

      ClinVar 1. 377917, 2. 370106

      gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    5. 32

      Case32 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 69(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 429(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 3.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

      ClinVar 1. 2088, 2. 2085

      gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    6. 39, 40

      Case39 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 16(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 77(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.764C>T (p.Ser255Leu), compound heterozygous

      ClinVar 1. 2083, 2. 374435

      gnomAD 1. MAF= 0.0004013(African), no homozygotes, 2. MAF= 0.00005437(East Asian), no homozygotes

      CaseAddInfo Sibling (Case 40) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 10mmol/mol creatinine and 3-OH-glutarate was 31mmol/mol creatinine.

      CasePMIDs see notes on previous studies

    7. 30

      Case30 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 25(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 571(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 1. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

      ClinVar 1. 2088, 2. 2085

      gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    8. 22

      Case22 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 1028(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 291(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing.

      Variant NM_000159.3:c.541G>A(p.Glu181Lys), homozygous

      ClinVar n/a

      CAID CA404318015

      gnomAD not in gnomAD

      CaseAddInfo n/a

      CasePMIDs see note on previous studies

    1. 5

      Case5 Female, 24yo report, USA, Lumbee

      CasePresentingHPOs HP:0001344, HP:0002540, HP:0003150

      (Nonverbal, Non-ambulatory, Glutaricaciduria)

      HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 2yo and feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting n/a

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    2. 4

      Case4 Female, 9yo report, USA, Lumbee

      CasePresentingHPOs HP:0003150, HP:0011471, HP:0002540, HP:0001344, HP:0100309, HP:0012751, HP:0200147, HP:0100952

      (Glutaricaciduria, Gastronomy tube feeding in infancy, Non-ambulatory, Nonverbal, Subdural haematoma, Abnormal basal ganglia MRI signal intensity, Neuronal loss in basal ganglia, Enlarged sylvian fissure)

      HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 6mo. After decompensation, brain MRI found subdural hematomas, atrophied temporal lobes with widened Sylvian fissures, and elevated signal intensity in basal ganglia. Follow-up report studies noted volume loss in basal ganglia. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting n/a

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    3. 3

      Case3 Male, 5yo report, USA, Lumbee

      CasePresentingHPOs HP:0003150

      (Glutaricaciduria)

      HPOsFreeText Patient had elevated glutaric acid and small 3-hydroxyglutaric acid in urine. Patient feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs HP:0002540, HP:0001344, HP:0011471

      (Non-ambulatory, Nonverbal)

      NotHPOsFreeText Patient did not present with acute metabolic decompensation.

      CasePreviousTesting Patient's NBS detected glutarylcarnitine of 1.07μM(cutoff at >0.38). GCD enzyme activity was 0%.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    1. Case#: Patient 5, Japanese, 8 years old (report) CaseHPOs: Hyperornithinemia

      CaseHPOsFreeText: (From Hayasaka et al. 1981; PMID 7260021, Patient 2). First noted visual problems at age 5 years, glasses prescribed for myopia. Evaluation for night blindness at age 8. Best corrected visual acuity was RE 04 with correction of myopia (-8 D), LE 04 with correction of myopia (-10 D). Typical chorioretinal atrophy with scallop margins at the peripheral fundus and an abnormal reflex in the macular area. Concentric constriction of visual fields. Dark adaptation curve was monophasic. ERG was subnormal, and the electro-oculogram was flat. The ciliary processes were normal by cycloscopy. Not responsive to Vitamin B6.

      CaseNotHPOsFreeText: Normal lens

      CasePreviousTesting: Serum ornithine 12.95 mg/dl (normal 0-36-1-56). OAT activity was not detectable in cell extracts from skin fibroblasts. CaseAddInfo: No consanguinity reported CaseMethod1: PCR

      CaseMethod2: Sequence analysis

      CaseGenotypingMethod: DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele. Variant: NM_000274.3(OAT):c.1276C>T (p.Arg426Ter)

      ClinVar: 177

      gnomAD: Maximum population minor allele frequency = 0.00002893 (Latino); no homozygotes in any population.

    2. Case#: Patient 2; English/Dutch/German/French

      CaseHPOs: Clinical details in Weleber et al, 1982, “Gyrate atrophy of the choroid and retina… Birth defects: Original Article Series 18 (6) 219-230. Article has been requested.

      CaseHPOsFreeText: Not responsive to Vitamin B6.

      CaseNotHPOs:

      CasePreviousTesting: OAT activity was nondetectable in the patient’s fibroblasts. Northern analysis detected no OAT mRNA. Western blot analysis of OAT protein in the patient's fibroblasts demonstrated an essentially negligible amount of OAT.

      CaseMethod1: PCR

      CaseMethod2: Sequence analysis

      CaseGenotypingMethod: Truncated 5.0-kbp EcoRI OAT gene fragment in addition to the normal 5.8-kbp fragment on Southern blot analysis (Inana et al., 1988), suggesting heterozygosity for a deletion. Cloning and sequencing of the truncated fragment revealed a deletion of 1,072 base pairs. DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele.

      Variant: Variant 1: A 1,072-bp deletion starting in intron 5, 172 bp upstream of exon 6, and ending in intron 6, 772 bp downstream of exon 6 Variant 2: NM_000274.3(OAT):c.627T>A (p.Tyr209Ter)

      ClinVar: Variant 1: 174; Variant 2: 175

      gnomAD: Variant 1: Not listed (but large deletion may not be picked up) Variant 2: Maximum population minor allele frequency = 0.00004645 (European non-Finnish); no homozygotes in any population.

    1. ee

      CaseKLC2: Male, 32 yrs death, Japan, Asian

      CasePresentingHPOs: HP:0001249, HP:0002078, HP:0000651, HP:0008353, HP:0000992 (Intellectual disability, Truncal ataxia, Diplopia, Neutral hyperaminoaciduria, Cutaneous photosensitivity)

      HPOsFreeText: Monoamino-monocarboxylic aciduria

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are first-cousin consanguineous, Max LOD score is 2.1 for family

      CasePreviousTesting: Defects in the intestinal absorption of monoamino-monocarboxylic acids determined by oral loading; Urine analyses confirmed the absence of hyperaminoaciduria in the mother (III-4), father (III-5) and the younger brother (IV-3), Brother of proband

      CaseGenotypingMethod: DNA was isolated from peripheral blood samples and from liver samples collected at autopsy. A genome-wide screen with 343 different markers was carried out and linkage analysis performed using homozygosity mapping. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous frameshift mutation that perfectly segregated with the phenotype.

      CasePMIDs: 2582682, 11394870

      Variant: NM_001003841.3(SLC6A19):c.882_883TG1

      ClinVar: 2018 https://ww.ncbi.nlm.nih.gov/clinvar/variation/2018/

      gnomAD: 0.000008900, https://gnomad.broadinstitute.org/variant/5-1214174-CTG-C?dataset=gnomad_r2_1

    1. Patient 4

      Case4 sex unknown, Netherlands, Dutch

      CasePresentingHPOs HP:0001250, HP:0002194

      (Seizures, Delayed motor skills)

      HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 8do, first administered pyridoxine(and age at trial) 2mo, initial dose:100mg, maintenance dose:100mg/day, mildly affected motor skills. (PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"

      CaseNotHPOs n/a

      NotHPOsFreeText intrauterine seizures

      CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 4.0(nv <1mmol/mol cr), α‐AASA plasma 1.1(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 7.0(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)

      Variant NM_001182.4(ALDH7A1):c.834G>A (p.Val278=)

      ClinVar 18002

      gnomAD not in gnomAD(C and not G at that position?)

      CaseAddInfo Metabolic testing of sibling(Patient 6, heterozygous for the p.Val278= variant): α‐AASA urine 0.2(nv <1mmol/mol cr), α‐AASA plasma <0.2(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 2.2(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk), but was not metabolically confirmed for PDS, development was also normal

      CasePMIDs 17088338 , 16159904

    1. Proband

      CaseF7P: 1 yr report, India

      CasePresentingHPOs: HP:0001010, HP:0000750, HP:0001249, HP:0006801, HP:0004923 (Hypopigmentation of the skin, Delayed speech and language development, Intellectual disability, Brisk deep tendon reflexes, Hyperphenylalaninemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguinous, Father was confirmed heterozygous, Proband is heterozygous for this mutation with no second pathogenic mutation located

      CasePreviousTesting: Blood phenylalanine before treatment was 1105 μmol/l, Blood tyrosine before treatment was 87 μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

      CaseGenotypingMethod: Genomic DNA was isolated from blood samples of proband and family members. PCR amplification and sequencing was used to screen for mutations. Each mutation was confirmed by bi-directional DNA sequencing.

      Variant: NM_000277.3:c.*144A>G

      CAID: CA16020999 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA16020999

      gnomAD: 0.001284, http://gnomad.broadinstitute.org/variant/12-103232809-T-C

    2. Proband

      CaseF3P: 4 yrs report, India

      CasePresentingHPOs: HP:0001010, HP:0000750, HP:0001249, HP:0006801, HP:0004923 (Hypopigmentation of the skin, Delayed speech and language development, Intellectual disability, Brisk deep tendon reflexes, Hyperphenylalaninemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguinous, Parents were confirmed heterozygous, Variant may not undergo NMD however would be missing essential domains (but PAH level supports some residual function)

      CasePreviousTesting: Blood phenylalanine before treatment was 439 μmol/l, Blood tyrosine before treatment was 121 μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

      CaseGenotypingMethod: Genomic DNA was isolated from blood samples of proband and family members. PCR amplification and sequencing was used to screen for mutations. Each mutation was confirmed by bi-directional DNA sequencing.

      Variant: NM_000277.3:c.976del (p.Trp326Glyfs*15)

      CAID: CA16020912 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA16020912

      gnomAD: Not in gnomAD

    1. 5

      Case5: Female, 10m, Chinese, part of Family 1

      HPOsFreeText: (at 20 days) 1.38 C4 umol/L, 0.19 C4/C2, 1.79 C4/C3, 2.58 (mmol/mol creatinine) urine isobutyrylglycine

      Case5 (Level 2):


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.286G>A (p.Gly96Ser)

      ClinVar: n/a

      CAID: CA6372895

      gnomAD: 0.001453 (East Asian)

      Variant2: NM_014384.2:c.1092+1G>A

      ClinVar: n/a

      CAID: CA6373205

      gnomAD: 0.00005790 (Latino)


      CaseAddInfo: younger sister of patient 6, trans heterozygous, inherited one allele from each parent

    2. 4

      Case4: Male, 1y 2m, Chinese

      HPOsFreeText: (at 21 days) 0.77 C4 umol/L, 0.07 C4/C2, 0.86 C4/C3

      NotHPOsFreeText: normal urine isobutyrylglycine

      Case4 (Level 2):


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.286G>A (p.Gly96Ser)

      ClinVar: n/a

      CAID: CA6372895

      gnomAD: 0.001453 (East Asian)

      Variant2: NM_014384.2:c.444G>T (p.Pro148=)

      ClinVar: n/a

      CAID: CA6372946

      gnomAD: 0.0002772 (Other)


      CaseAddInfo: trans heterozygous, inherited one allele from each parent

    1. Table 2

      Case11a: Male, Sweden

      CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Arthrogryposis)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001627 (Cardiac abnormality)

      NotHPOsFreeText: N/A

      CaseAddInfo: Severe congenital myopathy, Deceased in 5 months

      CasePreviousTesting: N/A

      CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

      Variant: NM_198271.4:c.1069G>T (p.Glu357Ter)

      ClinVar: 162219 https://www.ncbi.nlm.nih.gov/clinvar/variation/162219/

      gnomAD: Not in gnomAD

    1. 18

      Case18 Female, 9.9yo report, Ethnicity: Austrian

      CasePresentingHPOs HP:0003571, HP:0008872, HP:0001531, HP:0001254, HP:0002789, HP:0002045

      (propionicacidemia, feeding difficulties in infancy, failure to thrive in infancy, lethargy, tachypnea, hypothermia)

      HPOsFreeText feeding difficulties, failure to thrive, lethargy, tachypnea, hypothermia, exanthema (5do). Scored 55 on Snijders-Omen Test for IQ

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosed by selective metabolic screening. PCC activity in patient lymphoblasts was 0.4% of control.

      Variant NM_000532.4:c.1199-2A>G (Gly400fs), homozygous

      ClinVar n/a

      CAID CA354648962

      gnomAD not in gnomAD

      CaseAddInfo parents not consanguineous

      CasePMIDs n/a

    2. 54

      Case54 Male, 7.3yo report, Ethnicity: Turkish

      CasePresentingHPOs HP:0003571, HP:0008872, HP:0002013, HP:0008947, HP:0002789, HP:0002045

      (propionicacidemia, feeding difficulties in infancy, vomiting, infantile hypotonia, tachypnea, hypothermia)

      HPOsFreeText feeding difficulties, vomiting, hypotonia, tachypnea, hypothermia(3do). 55 IQ on Culture Free Test

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosis by selective metabolic screen. Patient fibroblasts had 1.5% PCC activity of control

      Variant NM_000532.4(PCCB):c.990dupT (p.Glu331Terfs), homozygous

      ClinVar 167423

      gnomAD MAF= 0.001001(African), no homozygotes

      CaseAddInfo parental consanguinity

      CasePMIDs n/a

    1. P17

      FamilyPY: White, United Kingdom

      FamilyPresentingHPOs: HP:0002131, HP:0001260, HP:0008003, HP:0030453 (Episodic ataxia, Dysarthria, Jerky ocular pursuit movements, Abnormal visual electrophysiology)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0000640, HP:0000648, HP:0003390, HP:0011402, HP:0001272, HP:0002283 (Gaze-evoked nystagmus, Optic atrophy, Sensory axonal neuropathy, Demyelinating sensory neuropathy, Cerebellar atrophy, Global brain atrophy)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Blood genomic DNA was enriched and whole exome sequenced. Alightment to hg19 and variant filtering was performed with putative pathogenic variants being confirmed via Sanger sequencing.

      FamilyPreviousTesting: Underwent brain MRI and CSF examination with oligoclonal band analysis; Negative genetic testing for SCA1, 2, 3, 6, 7, 17 (now known as ATXN1, ATXN2, CACNA1A, ATXN7, and TBP, respectively), DRPLA (now known as ATN1), FA (now known as FXN) and FMR1

      FamilyAddInfo: N/A

      Variant: NM_004172.5(SLC1A3):c.1496G>A (p.Arg499Gln)

      ClinVar: 242994, https://www.ncbi.nlm.nih.gov/clinvar/variation/242994/

      gnomAD: 0.0001471, https://gnomad.broadinstitute.org/variant/5-36686238-G-A

      Affected: 3

      Segregations: 2

      AddSegregationInfo: Pedigree in Sup Data, Not enough info provided

    1. Case 4

      Case# Case 4, F, Chinese, 5day onset

      CasePresentingHPOs HP:0008344, HP:0011968, HP:0001954, HP:0002373

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.4(BCKDHB):c.93_103dupGGCGCGGGGCT (p.Phe35Trpfs), NM_000056.3:c.550del

      ClinVar 189101 (dup)

      CAID CA658820648 (del)

      gnomAD low quality site (dup)

    2. Case 3

      Case# Case 3, M, Chinese, 3day onset

      CasePresentingHPOs HP:0008344, HP:0001954, HP:0005972, HP:0011968, HP:0008947

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.3:c.659del(p.D229fs)

      CAID CA658820635

      CaseAddInfo Mother was not tested but WES was used in the patient and father

    1. Patient 11

      Case11: Male, 3 wk at initiation of follow up, African American ancestry

      HPOsFreeText: NBS C4-acylcarnitine 1.4 umol/L, lasma C4 acylcarnitine 1.87 umol/L, in vitro probe isoC4-acylcarnitine 0.053 umol/ g protein

      NotHPOsFreeText: normal in vitro probe C4-aclycarnitine, normal urine isobutyrylglycine, normal urine C4-acylcarnitine, normal urine C4/C3 ratio

      CaseAddInfo: mild biochemical phenotype observed. Suggested to be at minimum a carrier of IBD deficiency- however presence of promoter mutation, large deletion, or splice-site alteration undetectable by direct gene sequencing cannot be ruled out.

      Case11 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: heterozygous for mutation

    2. Table 1:

      Case6: Female, 16 days at initiation of follow up, European ancestry

      HPOsFreeText: NBS C4-acylcarnitine 2.0 umol/L, Plasma C4-acylcarnitine 1.36 umol/L, in vitro probe isoC4-acylcarnitine 0.160 umol/g protein, in vitro probe C4-acylcarnitine 0.150 umol/g protein, urine c4 acylcarnitine 19.13 mmol/mol creatinine, urine C4/C3 ratio 101

      CaseNotHPOs: normal urine isobutyryglycine

      CaseAddInfo: no data for clinical condition or SCAD gene variants

      Case6 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2(ACAD8):c.958G>A (p.Ala320Thr)

      ClinVar: 372297

      CAID: CA6373180

      gnomAD: 0.001725 (European Finnish)


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: compound heterozygote, specified allele 1 and 2 but not maternal and paternal. no potential splice site alteration

    3. younger brother

      Case7a: Male, 7 days at initiation of follow up, Hispanic ancestry

      HPOsFreeText: NBS C4-acylcarnitine 2.2 umol/L, plasma C4-acylcarnitine 2.09 umol/L, in vitro probe isoC4-acylcarnitine 0.070 umol/g protein, urine C4-acylcarnitine 3.58 mmol/mol creatinine, Urine C4/C3 ratio 130.

      CaseNotHPOs: normal in vitro probe C4-acylcarnitine, normal urine isobutyrylglycine,

      CaseAddInfo: younger brother of patient 7b, part of Family2, unremarkable clinical condition

      Case7a (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_014384.2:c.687T>G (p.Phe229Leu)

      ClinVar: n/a

      CAID: CA6373030

      gnomAD: 0.00008673 (Latino)


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: no potential splice site alteration, no data for SCAD gene variants

    1. Subject C

      CaseGuC: Male, 5 days onset

      CasePresentingHPOs: HP:0200134, HP:0011153, HP:0010850, HP:0011199, HP:0001252, HP:0003487, HP:0003423, HP:0010864, HP:0011344, HP:0002188, HP:0002059 (Epileptic encephalopathy, Focal motor seizure, EEG with spike-wave complexes, EEG with generalized sharp slow waves, Muscular hypotonia, Babinski sign, Thoracolumbar kyphoscoliosis, Severe intellectual disability, Severe global developmental delay, Delayed CNS myelination, Cerebral atrophy)

      HPOsFreeText: Multiple seizure types, Bilateral T2 prolongation in caudate heads and putamina

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant is confirmed heterozygous de novo

      CasePreviousTesting: Investigations include electroencephalography (EEG), head MRI, neurometabolic testing, and chromosome microarray; Individuals with self-limiting benign electroclinical syndromes, such as childhood absence epilepsy (onset > 4 years), were excluded; Head circumference was 44 cm at 4 months (91st percentile); Partial response to ketogenic diet and phenytoin, no response to other antiseizure medications;

      CaseGenotypingMethod: Variants within co-expressed candidate genes in Table S1 were extracted from exome sequencing data. Variants were annotated and were verified with Sanger sequencing of the proband and parents.

      Variant: NM_004171.4(SLC1A2):c.866C>G (p.Pro289Arg)

      ClinVar: 438737, https://www.ncbi.nlm.nih.gov/clinvar/variation/438737/

      gnomAD: Not in gnomAD

    1. III4/F

      Case# FIII.4, F, 19 day old diagnosis, Cyprus (Greek Cypriot)

      CasePresentingHPOs HP:0010910, HP:0010911, HP:0010913, HP:0001254, HP:0011968, HP:0001290, HP:0001276, HP:0002789, HP:0002353,

      HPOcont: Hypervalinemia, Hyperleucinemia, Hyperisoleucinemia, Lethargy, Poor feeding, Hypotonia, Hypertonia, Tachypnea, Abnormal EEG

      HPOfreetext: Reduced alloisoleucine and grunting

      CasePreviousTesting Tested blood BCAA (AIleu: 0, Ileu: 220 (NR: 26–100), Leu: 3270 (NR: 65–220), Val: 459 (NR: 90–300), urine organic acids (Increased:lactate, 2-keto-glutarate, 2-keto-isocaproic, 2-OH-isovaleric, 2-keto-isovaleric, 2-keto-3-methylvaleric, 4-OH-phenylacetate, 4-OH-phenylpyruvate and BCKD activity (0.03(NR: 0.4–3.4) (Fibroblasts))

      CaseMethod1 PCR

      CaseMethod2 Direct Sequencing

      CaseGenotypingMethod Direct sequencing repeated on proband and father for deletion varaint

      Variant (1) NM_000709.3(BCKDHA):c.632C>T (p.Thr211Met) (2) NM_000709.3:c.718delG

      ClinVar (1) 93365

      CAID (2) register link if I put that in correctly

      gnomAD (1) 0.0001163(East Asian), 0.00002043 (Overall)

      CaseAddInfo nonconsanguineous

    1. Individual 1

      Case1: Female

      CasePresentingHPOs: HP:0011343, HP:0012072, HP:0007018 (Moderate global developmental delay, Aciduria, Attention deficit hyperactivity disorder)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous, Unremarkable family history, Variants are parentally confirmed with c.2185 G>A apparently de novo

      CasePreviousTesting: At 2 yrs had elevated 2-oxoadipate (range = 10–120 mmol/mol creatinine) and 2-hydroxyadipate (range = 5–40 mmol/mol creatinine) in urine (Reference 0 mmol/mol creatinine); Elevated 2-aminoadipate (120 μmol/l); Moderate protein restriction did not influence disease course and was discontinued, Serial cranial magnetic-resonance-imaging studies showed no morphological abnormalities; Neuropsychological testing at 8 years revealed an IQ of 117; Symptoms improved after implementation of methylphenidate and at 14 is clinically normal; No mutation detected in ODC

      CaseGenotypingMethod: Whole exome sequencing was performed to identify mutations responsible for the biochemical abnormality. Exonic sequences were enriched and sequenced with data analysis being used to filter according to inheritance and low allele frequencies in controls. This narrowed down to eight different genes (ADAMTS10, AIRE, C8orf38, DHTKD1, OVOS2, CAMTA2, LPPR3, and RADIL) of which three had been associated with unrelated phenotypes and only one other had predicted pathogenic variants, DHTKD1.

      Variant1: NM_018706.7(DHTKD1):c.1A>G (p.Met1Val)

      ClinVar: 39563 https://www.ncbi.nlm.nih.gov/clinvar/variation/39563/

      gnomAD: Not in gnomAD

      Variant2: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

      ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/

      gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A

    2. Individual 2

      Case2: Female

      CasePresentingHPOs: HP:0000252, HP:0001270, HP:0000750, HP:0001252 (Microcephaly, Motor delay, Delayed speech and language development, Muscular hypotonia)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0000407 (Sensorineural hearing impairment)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous, Compound heterozyosity was confirmed in trans via parental testing

      CasePreviousTesting: At 2 yrs levels were at 2-oxoadipate, 520–970 mmol/mol creatinine; 2-hydroxyadipate, 100–150 mmol/mol creatinine; 2-aminoadipate, elevated; Moderate protein restriction did not influence disease course; IQ of 87

      CaseGenotypingMethod: After confirmation of the DHTKD1 mutations in Individual 1, Sanger sequencing confirmed compound heterozygous mutations in the same gene here.

      Variant1: NM_018706.7(DHTKD1):c.1228C>T (p.Arg410Ter)

      ClinVar: 39565 https://www.ncbi.nlm.nih.gov/clinvar/variation/39565/

      gnomAD: 0.00005437, https://gnomad.broadinstitute.org/variant/10-12136140-C-T

      Variant2: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

      ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/

      gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A

    1. 3.1.1. Patient 1

      CaseFI1: Female, Tunisia, 18 months report

      CasePresentingHPOs: HP:0001511, HP:0001508, HP:0001263, HP:0001249, HP:0001337, HP:0000325, HP:0000272, HP:0000303, HP:0000411, HP:0007495, HP:0000518, HP:0000963, HP:0000973, HP:0100678, HP:0012785, HP:0004220, HP:0009162, HP:0010107, HP:0002827, HP:0002808, HP:0001252, HP:0008619, HP:0001629, HP:0001684, HP:0001643, HP:0005301, HP:0003572, HP:0005961, HP:0025082, HP:0030774 (Intrauterine growth retardation, Failure to thrive, Global developmental delay, Intellectual disability, Tremor, Triangular face, Malar flattening, Mandibular prognathia, Protruding ear, Prematurely aged appearance, Cataract, Thin skin, Cutis laxa, Premature skin wrinkling, Flexion contracture of finger, Short middle phalanx of the 5th finger, Absent middle phalanx of 5th finger, Short proximal phalanx of hallux, Hip dislocation, Kyphosis, Muscular hypotonia, Bilateral sensorineural hearing impairment, Ventricular septal defect, Secundum atrial septal defect, Patent ductus arteriosus, Persistent left superior vena cava, Low plasma citrulline, Hypoargininemia, Abnormal cutaneous elastic fiber morphology, Mitochondrial swelling)

      HPOsFreeText: Weight: 1770 g (< 3rd percentile); length: 39 cm (< 3rd percentile); OFC: 31 cm (< 3rd percentile); Hand and foot malformations; First metacarpal was bowed bilaterally; Serum Ornithine at 23 μmol/l (ref 21–77), Serum Citrulline at 3 μmol/l (ref 27–43), Serum Arginine at 39 μmol/l (ref 49-129), Serum Proline at 105 μmol/l (ref 71-303), Serum Glutamate at 61 μmol/l (ref 8-64), Serum Aspartate at 8 μmol/l (ref <14)

      CaseNotHPOs: HP:0002305, HP:0012443, HP:0009832 (Athetosis, Abnormality of brain morphology, Abnormal distal phalanx morphology of finger)

      NotHPOsFreeText: Urinary organic acids, oligosaccharides, purines and pyrimidines were normal

      CaseAddInfo: Parents are first-degree cousins, Deletion leads to a frameshift and a premature termination codon

      CasePreviousTesting: A skin biopsy was taken and amino acid profiles were analyzed from plasma according to standard procedures

      CaseGenotypingMethod: Familial DNA was extracted from peripheral blood samples. Direct sequencing of PYCR1 and exons 2-18 of ALDH18A1 was performed in the affected individual with no result for Exon 15. To confirm if a deletion was responsible, copy number analysis by qPRC was performed with Exon 15 showing a dramatic decrease in signal compared to the others in the affected individual suggesting a homozygous deletion. The parents showed a 50% reduction suggesting a heterozygous phase for the deletion. Different primer combinations allowed for confirmation of the breakpoints with a microdeletion of exon 15 and flanking intronic sequence (1522 bp) with a guanosine insertion.

      Variant: NM_002860.4(ALDH18A1):c.1802-2_1924-901del

      ClinVar: 156547 https://www.ncbi.nlm.nih.gov/clinvar/variation/156547/

      gnomAD: Not in gnomAD

    1. 11

      Patient11: Group 2

      CasePresentingHPOs: same as group 2

      CasePreviousTesting: same as group 2

      CaseGenotypingMethod: same as group 2

      Variant1: NM_002225.3(IVD):c.941C>T (p.Ala314Val) listed in paper as c.932C>T (p.Ala282Val)

      ClinVar: 100060, https://www.ncbi.nlm.nih.gov/clinvar/variation/100060/

      gnomAD: 0.0006507, http://gnomad.broadinstitute.org/variant/15-40707653-C-T

      Variant2: NM_001354598.2:c.868G>A

      CAID: CA391720951, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391720951

      gnomAD: n/a

    1. ID no. 817

      Case817: Female, 7 years report, Spain

      CasePresentingHPOs: HP:0003153, HP:0002345, HP:0002174 (Cystathioninuria, Action tremor, Postural tremor)

      HPOsFreeText: Elevated urine cystathionine (1916 umol/g creatine; reference <46), Normal plasma tHcys (3.5 umol/l; reference <7.5), Post treatment normal urine cystathionine (24 umol/g creatine)

      CaseNotHPOs: HP:0003345, HP:0001249 (Glutathione synthetase deficiency, Mental retardation)

      NotHPOsFreeText: N/A

      CaseAddInfo: Patient is homozygous for this variant

      CasePreviousTesting: Karyotype, magnetic resonance imaging, specific genetic tests for neurogenetic diseases and screening for inborn errors of metabolism (lactate, pyruvate, ammonium, uric acid, amino acids, organic acids, glycosaminoglycanes, creatine and guanidinoacetate, purines and pyrimidines, and isoelectric focusing pattern of transferrin), as well as folate, pyridoxine and cobalamine deficiencies, neural tumors and genetically determined homocystinurias, were all ruled out.

      CaseGenotypingMethod: All twelve exons of the CTH gene and the intronic flanking sequences of the subjects and their parents was PCR amplified and directly sequenced.

      Variant: NM_001902.5:c.200C>T (p.Thr67Ile)

      ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

      gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

    1. F-22

      CaseF-22 male, 5do onset, Ethinicity: North Indian, Muslim

      CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0001250, HP:0001987, HP:0001946, HP:0045045, HP:0003571

      (Acute encephalopathy, Lethargy, Poor feeding, Seizures, Hyperammonemia, Ketosis, Elevated acylcarnitines, Propionicacidemia)

      HPOsFreeText Serum ammonia 700micromolar

      CaseNotHPOs n/a

      CasePreviousTesting Also screened for variants in PCCA

      Variant NM_000532.4(PCCB):c.183+5G>A

      ClinVar 217896

      gnomAD MAF= 0.00003328(South Asian), no homozygotes

      CaseAddInfo consanguineous, no abnormality in family history noted

      CasePMIDs n/a

    2. Bidirectional sequencing on 3500 Genetic Analyzer (Applied Biosystems) was done, and mutations in both the genes were analyzed by blasting them against the reference genomic sequences of PCCA (NM_000282.3) and PCCB (NM_000532.4).

      Method 1: Sanger

      GenotypingMethod: Coding regions as well as exon–intron boundaries PCCA and PCCB amplified by PCR then analyzed with bidirectional sequencing. Variants were blasted against references genomes PCCA (NM_000282.3) and PCCB (NM_000532.4).

    3. F-15

      CaseF-15 female, 1yo onset, Ethnicity: North Indian, Hindu

      CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0002098, HP:0002013, HP:0001942, HP:0001943, HP:0003571

      (Acute encephalopathy, Lethargy, Poor feeding, Respiratory distress, Vomiting, Metabolic acidosis, Hypoglycemia, Propionicacidemia)

      HPOsFreeText Ketones present, acycarnitines 6.2(normal <3.6nmol/mL), died after acute crisis(1yo)

      CaseNotHPOs n/a

      CasePreviousTesting Also screened for variants in PCCA

      Variant NM_000532.4(PCCB):c.493C>T (p.Arg165Trp)

      ClinVar 217894

      gnomAD MAF= 0.00001456(European(non-Finnish), no homozygotes

      CaseAddInfo nonconsanguineous, no abnormality in family history noted

      CasePMIDs n/a

    1. The retrieved soluble fraction of mutated GNMT lacked measurable enzymatic activity

      VariantEvidence: Expression of recombinant GMT was performed in E. coli. Firstly, the wild-type protein showed high solubility compared to the mutant of which only a minor fraction was soluble. Furthermore, enzyme activity was measured and the mutant GMNT lacked any activity while the wild-type exibits activity of >200 pmol/min/ug.

      Variant: NM_018960.4:c.296G>A (p.Arg99His)

    1. P43

      Case43: Male, Chinese, 2.3y (end of study)

      HPOsFreeText: 2y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case43 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2107G>A (p.Gly703Arg)

      ClinVar: n/a

      CAID: CA364394252

      gnomAD: 0.00006152 (African)


      CaseAddInfo: one variant, not homozygous.

    2. P42

      Case42: Female, Chinese, 2.3y (end of study)

      HPOsFreeText: 10 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case42 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2080C>T (p.Arg694Trp)

      ClinVar: 218996

      CAID: CA347907

      gnomAD: 0.00006534 (South Asian)


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: heterozygous mutations in trans.

    3. P41

      Case41: Male, Chinese, 10.3y (end of study)

      HPOsFreeText: 8.8y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case41 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1790T>G (p.Ille597Arg)

      ClinVar: 551764

      CAID: CA364395663

      gnomAD: n/a


      Variant2: NM_000255.3:c.2106delA (p.VAl704Ter)

      ClinVar: 555523

      CAID: CA658821513

      gnomAD: n/a


      CaseAddInfo: both variants novel. heterozygous mutations in trans.

    4. P39

      Case39: Female, Chinese, 3.4y (end of study)

      HPOsFreeText: 1y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case39 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: one variant, not homozygous.

    5. P40

      Case40: Female, Chinese, 2.1y (end of study)

      HPOsFreeText: 8 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case40 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1777G>T (p.Glu593Ter)

      ClinVar: 558328

      CAID: CA364395728

      gnomAD: n/a


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: variant 1 is novel. heterozygous mutations in trans

    6. P38

      Case38: Male, Chinese, 1.5y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case38 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: one variant, not homozygous.

    7. twin sisters P35 and P36

      FamilyLabel: Family 1

      Family1PresentingHPOs: HP:0001987, HP:0001942, HP:0003128, HP:0002912 (hyperammonemia, metabolic acidosis, lactic acidosis, methylmalonic acidemia)

      NotHPOsFreeText: normal plasma total homocysteine

      CountryOrigin: China

      Ethnicity: Chinese

      ProbandLabel: Case35, Case36

      Family1 (Level 2)


      FamilyPreviousTesting: tandem mass spectrometry for blood levels, gas chromatography-mass spectrometry for urine, NBS

      FamilyMethod1: PCR

      FamilyGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes from patients and their parents. Exonic ad flanking intronic regions of the MUT gene were amplified through PCR. PCR products were sequenced directly using forward and reverse primers on ABI 3700 sequencer. Mutation analysis using MUT reference NM_000255.3. Nucleotide numbering reflects cDNA numbering (initiation codon= codon1). All detected mutations were confirmed in the patients' parents. Novel variants were screened in 100 alleles from 50 control children. Novel variants were considered pathogenic when predicted to be deleterious by two algorithms.

      FamilyAddInfo: counted in group annotation also. identical twins. mut- and mut0 mutation together may explain relatively good clinical condition.

    8. P37

      Case37: Female, Chinese, 5.8y (end of study)

      HPOsFreeText: 3y onset

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case37 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1677-1G>A (p.=)

      ClinVar: 550012

      CAID: CA3846767

      gnomAD: 0.0003511 (East Asian)


      CaseAddInfo: one variant, not homozygous

    9. P36

      Case36: Female, Chinese, 9.3(end of study)

      NotHPOsFreeText: asymptomatic, no onset

      Case36 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1943G>A (p.Gly648Asp)

      ClinVar: n/a

      CAID: CA3846709

      gnomAD: 0.0001087 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, but no symptoms. identical twin to Case35/P35.

    10. P35

      Case35: Female, Chinese, 9.3y (end of study)

      NotHPOsFreeText: asymptomatic, no onset

      Case35 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1943G>A (p.Gly648Asp)

      ClinVar: n/a

      CAID: CA3846709

      gnomAD: 0.0001087 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, but no symptoms. identical twin to Case36/P36.

    11. P34

      Case34: Male, Chinese, 5.5y (end of study)

      HPOsFreeText: 2 mo onset, poor neurologic outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case34 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      Variant2: NM_000255.3:c.1880A>G (p.His627Arg)

      ClinVar: 551830

      CAID: CA3846719

      gnomAD: 0.00002639 (European non-Finnish)

      CaseAddInfo: heterozygous mutations in trans

    12. P33

      Case33: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: Neonatal development

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case33 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      CaseAddInfo: one variant, not homozygous

    13. P31

      Case31: Male, Chinese, 3.7y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case31 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: one variant, not homozygous.

    14. P30

      Case30: Male, Chinese, 1 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case30 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.925T>G (p.Trp309Gly)

      ClinVar: n/a

      CAID: CA364401026

      gnomAD: n/a


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: heterozygous mutations in trans, died at 1 mo

    15. P32

      Case32: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case32 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      Variant2: NM_000255.3:c.1677-1G>A (p.=)

      ClinVar: 550012

      CAID: CA3846767

      gnomAD: 0.0003511 (East Asian)


      CaseAddInfo: heterozygous mutations in trans

    16. P29

      Case29: Male, Chinese, 3.2 y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case29 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.755dupA (p.His252GlinfsTer6)

      ClinVar: n/a

      CAID: CA3847037

      gnomAD: 0.0001090 (East Asian)


      Variant2: NM_000255.3:c.1741C>T (p.Arg581Ter)

      ClinVar: 554675

      CAID: CA364395893

      gnomAD: n/a


      CaseAddInfo: heterozygous mutations in trans

    17. P28

      Case28: Male, Chinese, 6.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case28 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.754-1G>A (p.=)

      ClinVar: n/a

      CAID: CA364402849

      gnomAD: n/a


      Variant2: NM_000255.3:c.1061C>T (p.Ser354Phe)

      ClinVar: n/a

      CAID: CA364400211

      gnomAD: n/a


      CaseAddInfo: heterozygous mutations in trans.

    18. P27

      Case27: Male, Chinese, 1.8y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case27 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: one variant, not homozygous.

    19. P26

      Case26: Female, Chinese, 6.6y (end of study)

      HPOsFreeText: responsive to vitamin B12

      NotHPOSFreeText: asymptomatic, no onset

      Case26 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: one variant, not homozygous. asymptomatic.

    20. P25

      Case25: Male, Chinese, 3 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case25 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

      ClinVar: 203860

      CAID: CA312786

      gnomAD: 0.0001088 (East Asian)

      CaseAddInfo: heterozygous mutations in trans. died at 3 mo.

    21. P24

      Case24: Male, Chinese, 6.5y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case24 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1540C>A (p.Gln514Lys)

      ClinVar: n/a

      CAID: CA364397122

      gnomAD: n/a

      CaseAddInfo: heterozygous mutations in trans. Variant 2 is novel

    22. P23

      Case23: Female, Chinese, 3y (end of study)

      HPOsFreeText: 1.8y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case23 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1295A>C (p.Glu432Ala)

      ClinVar: n/a

      CAID: CA364398703

      gnomAD: n/a

      CaseAddInfo: heterozygous mutations in trans

    23. P22

      Case22: Female, Chinese, 1.3y (end of study)

      HPOsFreeText: 11 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case22 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: heterozygous mutations in trans

    24. P21

      Case21: Male, Chinese, 9 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case21 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)

      CaseAddInfo: heterozygous mutations in trans, died at 9 mo

    25. P20

      Case20: Female, Chinese, 1 y (end of study)

      HPOsFreeText: neonatal onset, poor neruological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case20 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      Variant2: NM_000255.3:c.1105C>T (p.Arg369Cys)

      ClinVar: 218989

      CAID: CA347895

      gnomAD: 0.00006536 (South Asian)


      CaseAddInfo: heterozygous mutations in trans

    26. P19

      Case19: Female, Chinese, 2.4 y (end of study)

      HPOsFreeText: 1.8 y onset

      NotHPOsFreeText: normal cognitive and motor development without further episodes of metabolic decompensation, not responsive to vitamin B12

      Case19 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.655A>G (p.Asn219Asp)

      ClinVar: n/a

      CAID: CA364404270

      gnomAD: n/a


      Variant2: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)

      ClinVar: 552079

      CAID: CA3847064

      gnomAD: 0.0002008 (East Asian)


      CaseAddInfo: heterozygous mutations in trans

    27. P17

      Case17: Male, Chinese, 6.5y (end of study)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12, normal cognitive and motor development without further episodes of metabolic decompensation

      Case17 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.554C>T (p.Ser185Phe)

      ClinVar: n/a

      CAID: CA364404475

      gnomAD: n/a


      Variant2: NM_000255.3:c.2062G>T (p.Glu688Ter)

      ClinVar: n/a

      CAID: CA3846672

      gnomAD: 0.00006152 (African)


      CaseAddInfo: heterozygous mutations in trans.

    28. P16

      Case16: Male, Chinese, 2.4 y (end of study)

      HPOsFreeText: neonatal onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case16 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.454C>T (p.Arg152Ter)

      ClinVar: 426467

      CAID: CA3847107

      gnomAD: 0.00009813 (South Asian)


      Variant2: NM_000255.3:c.1280G>A (p.Gly427Asp)

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      CaseAddInfo: heterozygous mutations in trans.

    29. P18

      Case18: Male, Chinese, 5 mo (age at death)

      HPOsFreeText: neonatal onset

      NotHPOsFreeText: not responsive to vitamin B12

      Case18 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.626dupC

      ClinVar: n/a

      CAID: CA825482501

      gnomAD: n/a


      Variant2: NM_000255.3:c.1531C>T (p.Arg511Ter)

      ClinVar: 556124

      CAID: CA3846855

      gnomAD: 0.00003270 (South Asian)


      CaseAddInfo: variant 1 is novel. Heterozygous mutations in trans.

    1. Patients 2–4

      Family2to4: Maltese

      FamilyPresentingHPOs: N/A

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0001270, HP:0007018, HP:0001252, HP:0000750, HP:0000252 (Motor delay, Attention deficit hyperactivity disorder, Muscular hypotonia, Delayed speech and language development, Microcephaly)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Whole exome sequencing was performed as a trio with both parents. Identified DHTKD1 mutations were evaluated for possible effects and filtered for frequencies and predicted pathogenicity. No other candidate genes were found during the WES analysis for either patient sequenced. Sanger sequencing confirmed the proband's siblings are homozygous for the variant and that each parent is a carrier.

      FamilyPreviousTesting: Amino acid and organic acid testing showed elevated urinary 2-aminoadipic, 2-ketoadipic, and glutaric acids in the proband as well as in two elder brothers, ages 5 and 7.

      FamilyAddInfo: Parents are consanguineous, All three affected siblings are clinically normal

      Variant: NM_018706.6:c.915G>C (p.Gln305His)

      CAID: CA5407680 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5407680

      gnomAD: Other 0.0001630, https://gnomad.broadinstitute.org/variant/10-12131182-G-C

      Affected: 3

      Unaffected: 2

      AddSegregationInfo: Candidate gene sequencing

    1. Proband II.1

      CaseII-2: Female, Turkey

      CasePresentingHPOs: HP:0001558, HP:0000337, HP:0045075, HP:0000463, HP:0000343, HP:0000278, HP:0000470, HP:0000767, HP:0002375, HP:0002033, HP:0006829 (Decreased fetal movement, Wide forehead, Sparse eyebrow, Anteverted nares, Long philtrum, Retrognathia, Short neck, Pectus excavatum, Decreased spontaneous movement, Poor suck, Severe muscular hypotonia)

      HPOsFreeText: Birth weight was 2050 g and length was 43 cm, Absent Moro reflex, Required ventilator support from birth

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Born with fractures of the right humerus and left femur

      CasePreviousTesting: N/A

      CaseGenotypingMethod: Whole blood smaples were obtained from the parents and the probands and DNA was extracted. WES was performed on II-2, with the results being sequenced and filtered for pathogenicity. Once the LMOD3 variant was detected, PCR amplification and Sanger sequencing was used to amplify exon 1 and confirm the results.

      Variant: NM_198271.4:c.138dup (p.Ser47Glnfs*13)

      ClinVar: 162215 https://www.ncbi.nlm.nih.gov/clinvar/variation/162215/

      gnomAD: European (Non-Finnish) 8.879e-6, Overall 8.049e-6 https://gnomad.broadinstitute.org/variant/3-69171399-T-TG

    1. Biallelic

      Case#: Patient 2, male, 5 years (report), Turkish

      CaseHPOs: HP:0003235, HP:0002240 (hypermethioninemia, hepatomegaly)

      CaseHPOsFreeText: Identified by newborn screening.

      CaseNotHPOsFreeText: No signs of hepatic failure, no clinical symptoms.

      CasePreviousTesting: On day of life 3, elevated methionine concentration in blood of 390 µmol/L (normal 20–40). Total homocysteine in plasma was 59 µmol/L (normal 5–15). At later age (not specified), plasma methionine ranged from 1000 to 2070 µmol/L, while total homocysteine in plasma ranged from 30 to 55 µmol/L.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.125T>C (p.Leu42Pro) (homozygous)

      ClinVar: N/A

      CAID: CA377363776

      gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population.

      VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to ~10 and ~20% of wild type respectively (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

      Points: 0.5

    2. Biallelic

      Case#: Patient 1, female, 25 years (report), German

      CaseHPOs: HP:0003235 (hypermethioninemia)

      CaseHPOsFreeText: Identified by newborn screening.

      CaseNotHPOsFreeText: Hepatic, vascular or neurological symptoms have never been noted, and cranial MRI was normal at the age of 20 years

      CasePreviousTesting: Over a period of 25 years, methionine concentrations ranged from 850 to 1100 µmol/L (normal 20–40), and fasting total plasma homocysteine was 30–45 µmol/L (normal 5–15).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.65C>T (p.Ser22Leu) (homozygous)

      ClinVar: N/A

      CAID: CA377364910

      gnomAD: The highest population minor allele frequency in gnomAD is 0.00002891 (Latino)

      VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to <50% of wild type (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

      CaseAddInfo: Parents are reported to be unrelated

      Points: 0.5

    1. six

      CaseSA6P: Male, 7 months onset, European

      CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001250, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Seizures, Hyperammonemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Has father with confirmed variant and similar phenotypes

      CasePreviousTesting: Leucine load test showed leucine sensitivity; Protein/leucine restriction and dioxazide was effective at reducing symptoms

      CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

      Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

      ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

      gnomAD: Not in gnomAD

    1. Lo

      Case# Lo, M, 10mo diagnosis---originally 1985

      CasePresentingHPOs HP:0011968, HP:0001531, HP:0000737, HP:0007281, HP:0002013, HP:0001259, HP:0005979, HP:0001943

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod

      Variant NM_000709.3:c.1265A>G(p.Lys422Arg), NM_000709.3:c.137dup(p.Ser47IlefsTer4)

      CAID CA406015486(miss), CA658820686(dup)

      VariantEvidence 3978850: in patient fibroblasts-rate of decarboxylation of alpha-ketoacids: alpha ketoisovalerate[0<0.31], Pyruvate[0.40>.34], alpha-ketoglutarate[0.14>0.10] (Table 1), BCKDH activity[0.0003<0.107] (Table 2), E1 subunit activity[0.6<5.9] (Table 3)--[ProbandvsNormal]

      CaseAddInfo 3978850( a positive dinitrophenylhydrazine test and elevated urinary a-ketoisocaproate, a-methyl-P-OH-valerate and a-OH-isoval- erate,

      CasePMIDs 3978850, 2914958

    1. Patient1

      Case1: female, 2.3y (initial referral), Italian, Family 1

      CasePresentingHPOs: HP:0001508, (failure to thrive)

      HPOsFreeText: birthweight 3060 g, SGOT 11 mo 150 U/L, SGPT 11 mo 160 U/L, 1.8y elevated plasma lactic acid 2.9 mmol/L. 3.9 y alkaline phosphatase 928 U/L, 4.7 y serum tricglycerides 184 mg/dl, fasting plasma methionine 644 umol/L. increased urinary methionine excretion 40 umol/mmol. increased lactic acid excretiom 107 umol/mmol. mild centrilobular fibrosis in liver. some eosinophils present in liver.

      CaseNotHPOs: HP:0001404, HP:0001397, HP:0012465, HP:0001396, (hepatocellular necrosis, hepatic steatosis, elevated hepatic iron concentration, cholestasis)

      NotHPOsFreeText: hepatic dysfunction. normal tHcy.

      CaseAddInfo: proband, second child, low methionine diet (300 mg/day) at 2.4 y decreased plasma methionine to normal.

      Case (Level 2)


      Variant1: NM_018960.5(GNMT):c.149T>C (p.Leu50Pro)

      ClinVar: 4169

      CAID: CA248600

      gnomAD: 0.0002319 (East Asian)


      Variant2: NM_018960.5(GNMT):c.529C>A (p.His177Asn)

      ClinVar: 4170

      CAID: CA248601

      gnomAD: 0.0006993 (European non-Finnish)


      CaseAddInfo: compound heterozygote, Leu50Pro maternal mutation, His177Asn paternal mutation. The amino acid shifts are one # different than those predicted in the paper (Leu49Pro and His176Asn).

    2. Patient 2

      Case2: male, 9.6 y (evaluation), Italian, Family 1

      CasePresentingHPOs:

      HPOsFreeText: birth weight 3850 g, 5y slightly elevated serum transaminases SGOT 60 U/L, SGPT 52 U/L. elevated alkaline phosphatase 1042 U/L). elevated triglycerides (342 mg/dl). fasting plasma methionine elevated to 426 umol/L. elevated tHcy 13 umol/L, elevated urinary methionine 34 umol/mmol. increased pyruvate excretion.

      CaseNotHPOs:

      NotHPOsFreeText: normal neurological examination and normal somatic growth. normal serum amylase and lipase. hepatic dysfunction.

      CaseAddInfo: proband, first child

      Case (Level 2)


      Variant1: NM_018960.5(GNMT):c.149T>C (p.Leu50Pro)

      ClinVar: 4169

      CAID: CA248600

      gnomAD: 0.0002319 (East Asian)


      Variant2: NM_018960.5(GNMT):c.529C>A (p.His177Asn)

      ClinVar: 4170

      CAID: CA248601

      gnomAD: 0.0006993 (European non-Finnish)


      CaseAddInfo: compound heterozygote, Leu50Pro maternal mutation, His177Asn paternal mutation. The amino acid shifts are one # different than those predicted in the paper (Leu49Pro and His176Asn).

    1. d

      CaseST-11: Male, 1 day onset, Turkey

      CasePresentingHPOs: HP:0001319, HP:0000316, HP:0008070, HP:0001410, HP:0001987, HP:0004322, HP:0004482 (Neonatal hypotonia, Hypertelorism, Sparse hair, Liver dysfunction, Hyperammonemia, Short stature, Relative macrocephaly)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguineous, Proband is homozygous for this variant

      CasePreviousTesting: See Group

      CaseGenotypingMethod: See Group

      Variant: NM_001123.3:c.905T>C (p.Phe302Ser)

      CAID: CA377399030, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399030

      gnomAD: Not in gnomAD

    2. l

      FamilyST-VII: Iran

      FamilyPresentingHPOs: HP:0002197, HP:0000316, HP:0001889 (Generalized-onset seizure, Hypertelorism, Megaloblastic anemia)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0002904, HP:0001410, HP:0001943, HP:0001257, HP:0001347, HP:0001251, HP:0001276 (Hyperbilirubinemia, Decreased liver function, Hypoglycemia, Spasticity, Hyperreflexia, Ataxia, Hypertonia)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: See Group

      FamilyPreviousTesting: See Supp Info for methionine/transaminase values; Normal height, weight and head circumference at birth

      FamilyAddInfo: Family is consanguineous, Family is homozygous for this variant

      Variant: NM_006721.4(ADK):c.1022A>G (p.His341Arg)

      ClinVar: 265772, https://www.ncbi.nlm.nih.gov/clinvar/variation/265772/

      gnomAD: Not in gnomAD

      Affected: 2

      Unaffected: 0

      Segregations: 1

      AddSegregationInfo: Not enough info

    3. G

      FamilyST-I: Turkey

      FamilyPresentingHPOs: HP:0000961, HP:0000825, HP:0001643, HP:0002240, HP:0001395 (Cyanosis, Hyperinsulinemic hypoglycemia, Patent ductus arteriosus, Hepatomegaly, Hepatic fibrosis)

      HPOsFreeText: N/A

      FamilyNotHPOs: N/A

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: See Group

      FamilyPreviousTesting: See Supp Info for methionine/transaminase values

      FamilyAddInfo: Family is homozygous for this variant

      Variant: NM_001123.3:c.905T>C (p.Phe302Ser)

      CAID: CA377399030, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399030

      gnomAD: Not in gnomAD

      Affected: 2

      Unaffected: 0

      Segregations: 1

      AddSegregationInfo: Not enough info

    1. 1874

      Case1874(T.C.) Female, 5yo diagnosis, Irish

      CasePresentingHPOs HP:0010864, HP:0000939, HP:0002942, HP:0000766, HP:0000276, HP:0000275, HP:0000218, HP:0000689, HP:0002857, HP:0001166, HP:0001634, HP:0001263, HP:0000750, HP:0002240, HP:0002353

      (Severe intellectual disability, Osteoporosis, Thoracic kyphosis, Sternal anomaly, Long face, Thin face, High palate, Malocclusion, Genu valgum, Arachnodactyly, Lens dislocation, Mitral valve prolapse, Delayed milestones, Speech delay, Enlarged liver, EEG abnormality)

      HPOsFreeText Patient had severe intellectual disability. Her spine was normal, but long bones were osteoporotic. Upon exam at 5yo, she had mild kyphosis of upper thoracic spine, mild sternal depression, marked genu valgum, and arachnodactyly. Patient was also myopic with bilateral lens dislocation. She had prominent recurrent malar flush, long and thin face, high-arched palate, malocclusion and mitral valve prolapse.

      (PMID: 20329304): Patient was born at term after normal pregnancy weighing 3.4kg. Normal neonatal course, but with delayed milestones. Speech at 5yo was monosyllabic , but verbal comprehension was good. No convulsions at this time. She had a palpable liver, 2cm below margin, but had normal consistence. She had an abnormal EEG with non-specific diffuse changes and excess slow-wave activity. Patient's IQ was 36.

      CaseNotHPOs HP:0001250, HP:0002086, HP:0000707

      (Seizures, Respiratory abnormality, Neurologic abnormality)

      NotHPOsFreeText n/a

      CasePreviousTesting Plasma homocysteine was 70μM pretreatment. Pyroxidine treatment reduced those levels to trace amounts. In patient fibroblasts, no CBS protein was detect on Western blot and CBS assay detected no activity. (PMID: 20329304): "Full hemogram, routine urine analysis, liver function tests, serum ion and iron-binding capacity, plasma magnesium, serum calcium, inorganic phosphate, fasting blood sugars, blood urea nitrogen, and bone marrow examination were all normal". Heavy homocysteine spot shown on chromatogram of urinary amino acids.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod Created a bacteria expression system in E.coli by substituting one of three fragments of (PCR amplified)patient cDNA into WT CBS sequence already subcloned in expression plasmids. Bacteria were screened based on which ones did not have CBS activity. Those that did not have activity were thought to have LOF variants in CBS. Plasmids containing the inactivating fragments, ones cut with NcoI/XmaI, were sequenced.

      Variant 1. NM_000071.2:c.233C>G (p.Pro78Arg);2. NM_000071.2:c.306G>C (p.Lys102Asn) - 1&2 in cis

      ClinVar 1. 188988;2. 188989

      gnomAD 1. MAF=0.0001631(Other), no homozygotes, 2. MAF=0.0001630(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs 20329304

    2. 75) w

      Case1875(M.C.) Female, 22yo died, Irish

      CasePresentingHPOs HP:0001263, HP:0001249, HP:0001250, HP:0002650, HP:0002625, HP:0005625, HP:0002857, HP:0000545, HP:0000276, HP:0000275, HP:0000218, HP:0000678, HP:0002878, HP:0001695, HP:0002240

      (Developmental delay, Intellectual disability, Seizures, Scoliosis, Deep vein thrombosis, Osteoporosis of vertebrae, Genu valgum, Myopia, Long face, Narrow face, High palate, Crowded teeth, Respiratory failure, Cardiac arrest, Enlarged liver)

      HPOsFreeText Diagnosed with homocystinuria after exam for developmental delay at 13mo. Patient had severe intellectual disability and seizures. At 14yo she had surgery for scoliosis, postsurgery she had a popliteal vein thrombosis. In addition to osteoporosis of the spine, she had genu valgum and myopia. The patient also had a long and narrow face, high-arched palate and crowded teeth. Respiratory failure and cardiac arrest at 22yo likely due to overuse of antiasthmatic medication.

      (PMID:20329304): She was delivered normally at term, weighed 3kg, made uncomplicated neonatal progress, no history of convulsions,reached early milestones at expected times but did not sit up until 13mo. On report she was well fed and well developed, but with persistent shadow in right upper load on roentgenogram, enlarged liver of normal consistence, spleen was not palpable, negative neurological exam, mental age was 9mo. Aortogram was negative for vascular abnormalities in upper left chest. Skull and long bones were normal but osteoporosis of the spine was detected by roentgenogram.

      CaseNotHPOs HP:0001083

      (Lens dislocation)

      NotHPOsFreeText no malar flush, lens displacement, or skeletal deformity on exam at 13mo.

      CasePreviousTesting Plasma homocysteine was 45μM pretreatment. Pyroxidine treatment reduced those levels to trace amounts. In patient fibroblasts, no CBS protein was detect on Western blot and CBS assay detected no activity. (PMID: 20329304): "Full hemogram, routine urine analysis, liver function tests, serum ion and iron-binding capacity, plasma magnesium, serum calcium, inorganic phosphate, fasting blood sugars, blood urea nitrogen, and bone marrow examination were all normal". Strong positive on cyanide nitroprusside, heavy homocysteine spot on chromatogram of urinary amino acids.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod Created a bacteria expression system in E.coli by substituting one of three fragments of (PCR amplified)patient cDNA into WT CBS sequence already subcloned in expression plasmids. Bacteria were screened based on which ones did not have CBS activity. Those that did not have activity were thought to have LOF variants in CBS. Plasmids containing the inactivating fragments, one cut with NcoI/XmaI and another cut with Bpu1102/BstX, were sequenced.

      Variant 1. NM_000071.2:c.715G>A (p.Glu239Lys),

      1. NM_000071.2:c.233C>G (p.Pro78Arg);3. NM_000071.2:c.306G>C (p.Lys102Asn) - 2&3 in cis, compound heterozygous

      ClinVar 1. n/a, 2. 188988;3. 188989

      CAID 1. CA410600501

      gnomAD 1. not in gnomAD, 2. MAF=0.0001631(Other), no homozygotes, 3. MAF=0.0001630(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs 20329304

    3. These patients

      FamilyLabel Family 1

      Family1PresentingHPOs HP:0000924, HP:0000939

      (Skeletal anomalies, Osteoporosis)

      HPOsFreeText Patients diagnosed with homocystinuria after finding abnormally high homocysteine on urine sample exam.

      FamilyNotHPOs n/a

      NotHPOsFreeText n/a

      CountryOrigin Ireland

      Ethnicity n/a

      Race n/a

      Family1PreviousTesting Tested pretreatment plasma homocysteine in each patient. Pyroxidine treatment dramatically reduced plasma homocysteine in all patients. In patient fibroblasts, no CBS protein was detect on Western blot and CBS assay detected no activity. (PMID: 20329304): "Full hemogram, routine urine analysis, liver function tests, serum ion and iron-binding capacity, plasma magnesium, serum calcium, inorganic phosphate, fasting blood sugars, blood urea nitrogen, and bone marrow examination were all normal". Heavy homocysteine spot was detected on chromatogram of urinary amino acids.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod Created a bacteria expression system in E.coli by substituting one of three fragments of (PCR amplified)patient cDNA into WT CBS sequence already subcloned in expression plasmids. Bacteria were screened based on which ones did not have CBS activity. Those that did not have activity were thought to have LOF variants in CBS. Plasmids containing the inactivating fragments were sequenced.

      ProbandLabel 1875

      Variant 1. NM_000071.2:c.715G>A (p.Glu239Lys),

      1. NM_000071.2:c.233C>G (p.Pro78Arg);3. NM_000071.2:c.306G>C (p.Lys102Asn) - 2&3 in cis, compound heterozygous

      ClinVar 1. n/a, 2. 188988;3. 188989

      CAID 1. CA410600501

      gnomAD 1. not in gnomAD, 2. MAF=0.0001631(Other), no homozygotes, 3. MAF=0.0001630(Other), no homozygotes

      FamilyAddInfo Father unavailable for study. Mother was clinically/biochemically healthy with an unexplained macrocytosis. Mother had absent CBS activity, but no homocystinuria symptoms and was heterozygous for the Glu239Lys variant. The variant was found in inactive bacteria carrying the BB segment. Presence of the variant was reinforced by amplifying, subcloning, then sequencing her genomic DNA of the region corresponding to BB.

      FamilyPMIDs 20329304

    1. The patient

      Case1 (Level 1)

      Case1: male, 5y (at time of study, born 1998), Greece, Gypsy (Roma)

      CasePresentingHPOs: HP:0002587, HP:0008872, HP:0001662, HP:0003235 (projectile vomiting (at birth), feeding difficulties in infancy, bradycardia (infancy), hypermethioninemia)

      HPOsFreeText: 3350 g birthweight, elevated serum aminmotransferases, mildly elevated ALT and AST at 2y, mild ferritin elevation 173 ng/ml, serum triglycerides 155 mg/dl, total cholesterol 248 mg/dl, aspartate transaminase 31 to 154 U/L, alanine transaminase 34-180 U/L, urine methionine 508-627 umol/L, methionine excretion 60 umol/mmol, plasma methionine 1005-1049 umol/L, plasma AdoMet 1643-2222 nmol/L, plasma cystathionine 740-900 nmol/L, plasma phosphatidylcholine 2622-2641 umol/L, plasma betaine 218-382 umol/L, plasma dimethylglycine 11.7-12.1 umol/L

      CaseNotHPOs: HP:0002240 (hepatomegaly)

      NotHPOsFreeText: normal apgar score, normal blood ammonia, normal lactate, normal tyrosine, , normal plasma N-methylglycine 1.4-1.6 umol/L, normal plasma AdoHcy 32-43 nmol/L, normal plasma tHcy 11.1-12.1 umol/L, normal plasma tCys 206-217 umol/L, normal plasma choline 10.2-14.0 umol/L

      CaseAddInfo: Adopted at 9 mo, no family info,

      CasePMIDs: n/a

      Case1 (Level 2)


      CasePreviousTesting: metabolite assays: tHcy- fluorescent polarization method; urinary organic acids- gas chromatography mass spectrometry; plasma methionine, tHcy, cystathionine, tCys, dimethylglycine, sarcosine- capillary gas chromatography

      CaseMethod1: PCR

      CaseGenotypingMethod: genomic DNA isolated from blood samples (affected patient and 10 healthy American controls). 1.9 kb 5'-fragment of GNMT gene prepared using PCR primers and 1.8 kb 3' fragment prepared using other primers. PCR fragments were purified. Sequencing done by dideoxy sequencing method. Plasmid pGE3 containing wild-type GNMT cDNA was used to prepare mutated human GNMT cDNA. Fragments of all exons and most introns and 300 nucelotides at 5' and 3' flanking ends were sequence using the GNMT sequence specified by GI 8671581 which found a single nucleotide substitution in AAC codon of exon 3:3415A>G.


      Variant: NM_018960.5(GNMT):c.422A>G (p.Asn141Ser)

      ClinVar: 218931

      CAID: CA347847

      gnomAD: not in gnomAD


      CaseAddInfo: No additional point mutation was found in the coding regions of patients GNMT gene, so the paper concludes that either he is homozygous or he has a deletion on the other allele that overlaps 3415A>G change and prevented PCR amplification in region of question.

    1. Biallelic

      Case#: Hazelwood case, 43 yrs (report), male

      CaseHPOs: HP:0003235, HP:0012185 (hypermethioninemia, carpal tunnel)

      CaseHPOsFreeText: Elevated urine methionine; Halitosis due to elevated breath dimethylsulphide; mild aortic insufficiency “attributable to rheumatic fever”, Gilbert disease (based on transient hyperbilirubinemia)

      CaseNotHPOsFreeText: Normal brain MRI with no evidence of demyelination (age 43 years). Developmentally, physically, and mentally normal. Liver histology was normal (age 31 years). Normal neurologic exam. Normal electrolytes and blood chemistry, normal cholesterol, normal AST, ALT, and LDH, normal testosterone.

      CasePreviousTesting: 25–30-fold elevation of plasma methionine (716-941 uM; controls 15-40, mean 26). Normal plasma tyrosine, normal homocysteine. Urine methionine 352-578 umol/day (controls 39-225, mean 99). Urine transamination metabolites 174-254 mmol/mol creatinine (controls ~1.8); breath dimethylsulfide 2.52-5.86 nmol/L (controls 0.13-0.65, mean 0.34); 7% normal activity of hepatic methionine adenosyltransferase in liver; hepatic activities of cystathionine-beta-synthase, gamma-cystathionase, and betaine homocysteine methyltransferase were normal.

      CaseMethod1: SSCP

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.539insTG (homozygous)

      ClinVar: NA

      CAID: CA210326818

      gnomAD: The highest population minor allele frequency = 0.00001759 (non-Finnish); no homozygotes in any population.

      CaseAddInfo: Both parents are heterozygous for the variant. Possible consanguinity - the patient’s father’s maternal grandfather and his mother’s paternal grandmother shared the same name and had lived their entire lives in an isolated West Virginia community.

      CasePMIDs: 3812486, 3339126

      Points: 1.5 points. This individual is homozygous for a frameshift variant in MAT1A. The highest population minor allele frequency = 0.00001759 (non-Finnish); no homozygotes in any population. The score is reduced because only some, but not all, causes of hypermethioninemia have been ruled out.

    1. HCU-102-3

      Case# HCU-102-3, 8yo report, Iran, Sistani

      CasePresentingHPOs HP:0001083, HP:0003235, HP:0000924

      (Ectopia lentis, Increased methionine in blood, Skeletal abnormality)

      HPOsFreeText skeletal abnormality/elongated long bone, increased urinary cysteine, elevated plasma methionine

      CaseNotHPOs HP:0001249, HP:0002970, HP:0001010, HP:0000501

      (Intellectual disability, Genu varum, Hypopigmentation, Glaucoma)

      NotHPOsFreeText n/a

      CasePreviousTesting plasma methionine 108μm/l(normal range 6-40μm/l)

      CaseMethod1 Sanger

      CaseMethod2 n/a

      CaseGenotypingMethod Sanger sequenced exon 3 of the CBS gene

      Variant NM_000071.2(CBS):c.346G>A (p.Gly116Arg), homozygous

      ClinVar 188787

      gnomAD MAF=0.00002892(Latino), no homozygotes

      CaseAddInfo from the province of Sistan and Baluchestan. no known consanguinity although the patient is homozygous for a founder variant

      CasePMIDs n/a

    2. families

      FamilyLabel HCU-103

      Family#PresentingHPOs HP:0001249

      (Intellectual disability)

      HPOsFreeText elevated plasma homocysteine, elevated urinary cysteine

      FamilyNotHPOs HP:0001083, HP:0002970, HP:0001010, HP:0000501, HP:0000924

      (Ectopia lentis, Genu varum, Hypopigmentation, Glaucoma, Skeletal abnormalities)

      NotHPOsFreeText skeletal abnormality/elongated long bones

      CountryOrigin Iran

      Ethnicity Sistani

      Race n/a

      Family#PreviousTesting tested for homocysteine in plasma and for cysteine in urine

      FamilyMethod1 Sanger

      FamilyMethod2 n/a

      FamilyGenotypingMethod Sanger sequenced exon 3 of the CBS gene

      ProbandLabel HCU-103-4

      Variant NM_000071.2(CBS):c.346G>A (p.Gly116Arg), homozygous

      ClinVar 188787

      gnomAD MAF=0.00002892(Latino), no homozygotes

      FamilyAddInfo from the province of Sistan and Baluchestan. no known consanguinity although the affected individuals are homozygous for a founder variant

      FamilyPMIDs n/a

    1. Case presentation

      Case#: 64 year old (report), female

      CaseHPOsFreeText: At age 52 years, sudden difficulty with swallowing and speech, ophthalmoparesis with a vertical and horizontal eye movement disorder, dysesthesia of the hands with a quality of “pins and needles” and a glove-like distribution, as well as generalized areflexia. Diagnosed with Miller Fisher syndrome. Treatment with intravenous immunoglobulins led to remission of symptoms. Abdominal pain since childhood. At 63 years of age, she had generalized epileptic seizures with prolonged postictal confusion, persisting diarrhea, abdominal pain, renal failure, repeat episodes of lactic acidosis. Ventilated for >8 weeks due to massive metabolic acidosis and respiratory failure during seizure; tracheotomy, PEG. VitB6 supplement. Rehabilitation, and recovered after several months.

      CaseNotHPOsFreeText: Muscle strength was normal. Abdominal computer tomography (CT), magnetic resonance imaging (MRI) and gastroscopy were normal. No signs of infection in CSF. CT and MRI of the brain as well as abdominal- and thorax-CT were normal initially then fat embolies in brain, pulmonary embolism, vertebral fractures. EMG was normal. No signs of malnutrition or liver disease (which can cause hyperprolinemia).

      CasePreviousTesting: No evidence of porphyria on “laboratory tests”, or diseases of copper metabolism, lead poisoning, or adrenoleukodystrophy. Muscle biopsy showed nonspecific atrophy, but no evidence of mitochondrial disease. Serum proline 3085 μmol/l (reference 90-342 μmol/l), urine proline 46,531 μmol/g Crea (reference < 100 μmol/g Crea), CSF proline 104 mg/dl (reference < 6 mg/dl), urine Hydroxyproline 1395 μmol/g Crea (reference <100). Vitamin-B6 was decreased at 3.3 μg/l (reference > 4.9 μg/l). “targeted genetic analyses by Sanger sequencing revealed no pathogenic variant within the PRODH-gene (hyperprolinemia type I)”

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: “targeted genetic analyses by Sanger sequencing” for ALDH4A1 (no further details).

      Variant: Compound heterozygous, confirmed in trans (the patient’s son only has one of the variants) 1) NM_003748.3:c.62+1G>A, 2) NM_003748.3:c.349G>C (p.Asp117His)

      ClinVar: 1) N/A; 2) N/A

      CAID: 1) CA338769667; 2) CA338760898

      gnomAD: 1) Not in gnomAD; 2) Not in gnomAD

      VariantEvidence: No functional evidence for the missense change. Score: This patient is an adult with hyperprolinemia who is compound heterozygous for two variants in ALDH4A1, c.62+1G>A and c.349G>C (p.Asp117His). Neither variant is in gnomAD. Variants in PRODH have been ruled out.

    1. Results Mutant G

      NonPatientCell: EFO:0002529 (INS-1), EFO:0000856 (islet of Langerhans), CL:0000182 (Hepatocyte)

      GeneFunction: GO:0004353 (glutamate dehydrogenase [NAD(P)+] activity)

      GeneAlteration: Recombinant adenoviruses encoding WT human GLUD1 and the S498L variant were generated via an expression system, with the human GLUD1 gene being amplified and sub-cloned into a plasmid with a promoter. Digestion using EcoRV was used to discriminate between the wild-type and the mutant with sequencing verifying each step of the cloning. This adenovirus was amplified in HEK-293 cells and INS-1E β-cells were transduced with it. Mouse and human hepatocytes were isolated and seeded before being transduced with the same adenoviruses. The transfection efficency was confirmed via immunoblotting.

      FunctionalEvidence: The enzymatic activity was evaluated in both wild-type and mutant mice, with both showing very low activity without glutamate concentrations and the mutant showing higher activity when glutamate was increased. The reductive direction using α-ketoglutarate as substrate was also tested with similar increased results for the mutant. Sensitivity of both lines to the reaction activator (ADP) and inhibitor (GTP) levels were tested, showing that the mutant was more sensitive to the ADP activator and slightly reduced for the GTP inhibitor (particularly in the presence of ADP). Mitochondiral function in wid-type and mutant cells was assessed, demonstrating that glucose response from mutant and WT cells was preserved but that glutamine stimulation abnormally generates ATP in mutant cells.Calcium stimulation was also activated by both glutamine and glucose in mutant cells while only being affected by glucose in WT. Studies in mutant and WT-transfected mouse and human islets showed increased insulin and ammonia production in mutants from stimulation through this responsive glutamine sensitivity. All of this supports GLUD1's pathogenic mechanism, specifically causing a hyperctive mutant protein that responds to glutamine levels rather than simply glucose.

      FAVariants: NM_005271.5(GLUD1):c.1493C>T (p.Ser498Leu)

      ClinVar: 16122, https://www.ncbi.nlm.nih.gov/clinvar/variation/16122/

    1. II. 1

      CaseBII-1: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 890 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband for Family B

      Variant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      gnomAD: 0.001766, https://gnomad.broadinstitute.org/variant/12-102840493-G-A?dataset=gnomad_r3

      Variant2: NM_000277.3(PAH):c.1241A>G (p.Tyr414Cys)

      ClinVar: 593 https://www.ncbi.nlm.nih.gov/clinvar/variation/593/

      gnomAD: 0.0005264, https://gnomad.broadinstitute.org/variant/12-102840474-T-C?dataset=gnomad_r3

    2. II.2

      CaseEII-2: N/A

      CasePresentingHPOs: N/A

      HPOsFreeText: Pretreatment phenylalanine level at 320 umol/L

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: N/A

      Variant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      gnomAD: 0.001766, https://gnomad.broadinstitute.org/variant/12-102840493-G-A?dataset=gnomad_r3

      Variant2: NM_000277.3(PAH):c.533A>G (p.Glu178Gly)

      ClinVar: 92746 https://www.ncbi.nlm.nih.gov/clinvar/variation/92746/

      gnomAD: 0.0001473, https://gnomad.broadinstitute.org/variant/12-103249087-T-C

    1. 12258M19866 years726<0.5Intermediate?S97fs

      Case# Patient 12, Male, Turkish, 6yo diagnosis

      CasePresentingHPOs HP:0004923

      CasePreviousTesting screened for BH4 deficiency using dried blood and urine spots, Final di-agnosis was made by measurements of neurotransmitter and pterinmetabolites in cerebrospinal fluid (CSF) and urine, in addition toDHPR enzyme activity, which was assessed in whole red bloodcells

      CaseMethod1 PCR

      CaseMethod2 DGGE

      Variant NM_000320.2:c.371delC(p.S97fs)

      CAID CA658795310

      VariantEvidence frameshift

    1. Family 8

      CaseFZ8: Male, United States, 3 yrs report

      CasePresentingHPOs: HP:0001511, HP:0008897, HP:0001999, HP:0000973, HP:0100678, HP:0000963, HP:0010648, HP:0001388, HP:0001374, HP:0001181, HP:0000938, HP:0000270, HP:0025356, HP:0001252, HP:0000518, HP:0000325, HP:0011220, HP:0000337, HP:0000411, HP:0000369, HP:0100790, HP:0005116, HP:0000717, HP:0008872, HP:0000486, HP:0500163, HP:0003572, HP:0500139 (Intrauterine growth retardation, Postnatal growth retardation, Abnormal facial shape, Cutis laxa, Premature skin wrinkling, Thin skin, Dermal translucency, Joint laxity, Congenital hip dislocation, Adducted thumb, Osteopenia, Delayed cranial suture closure, Psychomotor retardation, Muscular hypotonia, Cataract, Triangular face, Prominent forehead, Broad forehead, Protruding ear, Low-set ears, Hernias, Arterial tortuosity, Autism, Feeding difficulties in infancy, Strabismus, Hypoornithinemia, Low plasma citrulline, Hypoprolinemia)

      HPOsFreeText: Typical facial gestalt

      CaseNotHPOs: HP:0002645, HP:0012443, HP:0001762, HP:0002650, HP:0000252, HP:0001348 (Wormian bones, Abnormality of brain morphology, Talipes equinovarus, Scoliosis, Microcephaly, Brisk reflexes)

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant is confirmed de novo in this case with one other confirmed and one non-confirmed case with the same variant and similar presentation, No family history

      CasePreviousTesting: N/A

      CaseGenotypingMethod: ALDH18A1 and PYRC1 were investigated by Sanger sequencing, with the latter revealing no abnormalities and the former showing a heterozygous change at the Arg138 residue.Investigation revealed no further variants in the coding regions. Familial sequencing revealed the inheritance was de novo with no variants in the parents.

      Variant: NM_002860.4(ALDH18A1):c.413G>A (p.Arg138Gln)

      ClinVar: 217260 https://www.ncbi.nlm.nih.gov/clinvar/variation/217260/

      gnomAD: Not in gnomAD

    1. Patient K.A. (BIODEF 264)

      Case: K.A./ BIODEF 264, male, Caucasian, 1 day

      CasePresentingHPOs:  HP:0008297, HP:0040206, HP:0040210, HP:0001252

      HPOText: Plasma Phe level of 290umol/L at 3 days old, 853 umol/L at 6 days old, and 1997 umol/L at 13 days old. Urinary pterins indicated high neopterin/biopterin ratio and increased levels of primapterin. At 1 month old, neopterin and biopterin levels in normal range. At one month old showed mild hypotonia (extermities and trunk), but at 2.5 years Phe diet stopped and patient developed normally.

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.292C>T (p.Gln98Ter)

      ClinVar ID: 16799

      No-stars, 1 submission from OMIM.

      Homozygous, non-LOF.

      gnomAD: MAF (Euro-NF)= 2.2291E-4 (29/126606) hets only. No homozygotes recorded

      http://gnomad.broadinstitute.org/variant/10-72643730-G-A

      AddCaseInfo: The only individual in the family diagnosed with HyperPhe.

      VariantEvidence: The mutant Q97X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mQ97X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some activity in vitro. Interestingly, when more Q97X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was 2-3 times higher than wildtype (text only, no figures to compare).

      Patient part of the BIODEF database: PMID:8830181

    2. Patient I.B. (BIODEF 273)

      Case: I.B./ BIODEF 273, male, Ashkenazi Jewish, 3 days

      CasePresentingHPOs: HP:0040210, HP:0008297,

      HPOText: Plasma Phe levels were 240 umol/L at 3 days old, and 1845 umol/L at 14 days old. A low-Phe diet caused a rapid decline of Phe level to normal within 36 hours. An oral BH4–loading test (10 mg/kg body weight) resulted in a decrease of plasma Phe from 540 μmol/liter to 234 μmol/liter and then to 196 μmol/liter within 4 and 8 h, respectively. At 1 month, pterin and neurotransmitter in the CSF were normal. Starting a 2 month of age the patient was administered a low Phe diet and BH4 for 4 months. After the 4 months, the BH4 was discontinued, and Phe levels are between 120-300 umol/L at 5 years. Patient is developing normally.

      CaseNOTHPOs: n/a

      CasePreviousTesting: n/a

      CaseGenotypingMethod: Direct nucleotide-sequence determination of PCR products from blood samples was performed for the coding exons (2-4) of PCBD1.

      Variant: NM_000281.3(PCBD1):c.259G>T (p.Glu87Ter) 

      ClinVar ID: 16795

      No star, one submission for OMIM

      Homozygous

      gnomAD: MAF (Ashkenazi Jewish)= 1.183E-3 (12/10146) in heterozygous only. No homozygous reported.

      http://gnomad.broadinstitute.org/variant/10-72643763-C-A

      AddCaseInfo: The proband's older sister (J.B., 18 . months older) has the same genotype (homozygous for the T79I mutation), but was never noted as having HyperPhe, and was never treated. She has developed "normally." This family is recorded as Family B in the paper.

      VariantEvidence: The mutant E86X/E87X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mutant E86X/E87X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some enzyme activity in vitro. Interestingly, when more E86X/E87X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was similar to wildtype levels (text only, no figures to compare).

      Patient part of the BIODEF database: PMID:8830181

    1. Biallelic

      Case#: Patient 10, male, 5.9 years (report)

      CaseHPOs: HP:0003235 (hypermethioninemia)

      CaseHPOsFreeText: Identified by newborn screening

      CaseNotHPOsTest: Normal neurologic and/or muscular status, IQ 111

      CasePreviousTesting: Plasma methionine 484-742; transamination products in plasma 5.01-6.21 uM (normal 0.2-0.54) and in urine 45.2-75.6 mmol/mol creatinine (normal 1.2-4.6), urine dimethylsuphide 10 nM (normal – trace-2 nM).

      Variant: p.Arg199Cys (homozygous)

      ClinVar: N/A

      CAID: CA5576749

      gnomAD: The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

      VariantEvidence: When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal.

      CasePMIDs: 7573050

      Points: 1 point. This individual is homozygous for a missense change, p.Arg199Cys, in MAT1A. When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal. The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

    1. Clinical data

      Case#: Guo 2015 Proband, M, 18 months (onset), Chinese

      CasePresentingHPOs: HP:0002329, HP:0011968, HP:0002317, HP:0012088, HP:0001946

      Onset of symptoms upon episode of fever. Slightly reduced muscle tension. Second episode 2 months later and plasma amino acid analysis was performed: 431.67 umol/L leucine (normal 4.2-367), 167.13 umol/L isoleucine (normal 26.9-146), 47.81 umol/L valine (normal 117.6-495.7), 44.88 umol/L alloisoleucine (normal 0-7.7).

      CaseNotHPOs: HP:0002373, HP:0002013, HP:0002361

      CaseGenotyping Method: BCKDHA, BCKDHB, DBT, and DLD were screened for mutations using second generation sequencing. Direct sequencing was performed on the parents to confirm variants.

      Variant: 1. NM_000056.3:c.767A>G (p.Y256C); 2. NM_000056.3:c.768C>G (p.Y256X)

      CAID: 1. CA364659935; 2. CA142287564

      gnomAD: 1. 4.069e-6 overall

    1. 2DBT

      Case#: Patient 2, Lebanon, Arab

      CasePresentingHPOs: Intermediate form of MSUD

      CasePreviousTesting: Previously diagnosed with MSUD by GC/MS/MS.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Genomic DNA extracted, sequencing of BCKDHA, BCKDHB and DBT.

      Variant: NM_001918.3:c.224G>A (homozygous)

      CAID: CA341345382

      gnomAD: Not in gnomAD

      VariantEvidence: Mutation is present in lipoyl-binding domain, likely preventing binding of the lipoyl co-factor. Possibly results in a defect in the lipoyl-binding function (Alamut software analysis).

      CaseAddInfo: Same variant reported in patient 1 from the same geographical location, but unrelated according to the authors.

    1. Malaysian Family 2

      FamilyBJG_F2: Malaysia

      FamilyPresentingHPOs: N/A

      HPOsFreeText: N/A

      FamilyNotHPOs: N/A

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: See Group

      FamilyPreviousTesting: See Group

      FamilyAddInfo: Proband is confirmed homozygous for this variant

      Variant: NM_006721.4(ADK):c.89G>A (p.Gly30Glu)

      ClinVar: 29605, https://www.ncbi.nlm.nih.gov/clinvar/variation/29605/

      gnomAD: Not in gnomAD

      Affected: 2

      Unaffected: 0

      Segregations: 1

      AddSegregationInfo: Not enough info

    1. Italian family

      FamilyPA2: Italy

      FamilyPresentingHPOs: HP:0000519, HP:0002020, HP:0002572, HP:0002313, HP:0003693, HP:0002036, HP:0001761, HP:0003487, HP:0009830, HP:0001288, HP:0001348 (Developmental cataract, Gastroesophageal reflux, Episodic vomiting, Spastic paraparesis, Distal amyotrophy, Hiatus hernia, Pes cavus, Babinski sign, Peripheral neuropathy, Gait disturbance, Brisk reflexes)

      HPOsFreeText: N/A

      FamilyNotHPOs: N/A

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: ALDH18A1 was directly sequenced upon investigation for a causal role in SPG9, due to being within the linked region 10q23.3-q24.2, not having been discarded as a candidate gene, and mutations having been known to cause cutis laxa. Previous haplotype analysis also confirmed the linkage to this specific genomic region. This revealed one mutation in each pedigree that strictly co-segregated with the disease. Exome NGS sequencing within the interval showed only two variants were unknown in ExAC with the MYOF substitution unlikely to be disease causing due to poor conservation.

      FamilyPreviousTesting: N/A

      FamilyAddInfo: Family shows autosomal dominant segregation and haplotyping, Proband is PA2:III-21

      FamilyPMIDs: 9973297

      Variant: NM_002860.4(ALDH18A1):c.755G>A (p.Arg252Gln)

      ClinVar: 217117 https://www.ncbi.nlm.nih.gov/clinvar/variation/217117/

      gnomAD: Not in gnomAD

      Affected: 11

      Unaffected: 15

      Segregations: 17

      pLOD: 4.83

      AddSegregationInfo: Candidate gene sequencing

    1. AHN3.4

      CaseAHN3.4: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variants segregate with the disease

      CasePMIDs: 15286788

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3:c.719G>A (p.Arg240Gln)

      CAID: CA3182844, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182844

      gnomAD: 0.0001307, https://gnomad.broadinstitute.org/variant/5-1213633-G-A

      Variant2: NM_001003841.3(SLC6A19):c.1701+1G>A

      ClinVar: 623442, https://www.ncbi.nlm.nih.gov/clinvar/variation/623442/

      gnomAD: 0.00005286, https://gnomad.broadinstitute.org/variant/5-1221429-G-A

    2. AHN5.1

      CaseAHN5.1: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant 1 is in-trans with Variants 2 and 3, which are in cis; Variant segregates with the disease

      CasePMIDs: 17555458

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3:c.196G>A (p.Gly66Arg)

      CAID: CA359061114 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359061114

      gnomAD: Not in gnomAD

      Variant2: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A

      Variant3: NM_001003841.3(SLC6A19):c.718C>T (p.Arg240Ter)

      ClinVar: 2020 https://www.ncbi.nlm.nih.gov/clinvar/variation/2020/

      gnomAD: 0.0001960, https://gnomad.broadinstitute.org/variant/5-1213632-C-T

    3. AHN9.2

      CaseAHN9.2: Australia, White

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variants segregate with the disease

      CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;

      CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

      Variant1: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A

      Variant2: NM_001003841.3:c.1550A>G (p.Asp517Gly)

      CAID: CA3183226, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3183226

      gnomAD: 0.00004675, https://gnomad.broadinstitute.org/variant/5-1221277-A-G

    1. AM7162

      CaseAM7162: Female, 6 yrs report

      CasePresentingHPOs: HP:0001992, HP:0002179, HP:0010864, HP:0008936, HP:0002509, HP:0000750, HP:0011968, HP:0008872, HP:0100247, HP:0002373, HP:0001347, HP:0011449 (Organic aciduria, Opisthotonus, Severe Intellectual disability, Muscular hypotonia of the trunk, Limb hypertonia, Delayed speech and language development, Feeding difficulties, Feeding difficulties in infancy, Recurrent singultus, Febrile seizure, Hyperreflexia, Knee clonus)

      HPOsFreeText: Birth weight 2.86 kg, Cranial circumference is 49 cm (3rd percentile), weight 18.6 kg (25th percentile) and height 115 cm (50th percentile) at 6 yrs of age

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are first cousin consanguineous; Proband is confirmed homozygous for this variant via a QFM‐PCR assay for the dosage of ACY1 exons 12 and 13; Variant leads to skipping of Exon 13 and a resulting frameshift with a premature termination

      CasePreviousTesting: Urinary organic acid analysis confirmed by enzyme assay showed elevated levels of N ‐acetylated derivatives of glutamic acid, leucine, valine and isoleucine; Several genetic investigations, such as karyotyping, ring 15 chromosome analysis and mutational analysis of MECP5 and STXBP1 genes, were performed and were found to be normal; MRI showed dilatation of the left temporal horn at the age of 13 months;

      CaseGenotypingMethod: Genomic DNA was isolated and the ACY1 gene was PCR-amplified and sequenced. PCR analysis of retrotranscribed RNA was performed to analyze the effect of this variant on splicing.

      Variant: NM_000666.3(ACY1):c.1001_1001+5del

      ClinVar: 162019, https://www.ncbi.nlm.nih.gov/clinvar/variation/162019/

      gnomAD: 0.00001758, https://gnomad.broadinstitute.org/variant/3-52022618-ATGTGAG-A

    1. one male

      CaseWA: Male, 2 yrs onset, Germany

      CasePresentingHPOs: HP:0002013, HP:0012470, HP:0004372, HP:0002069, HP:0010819, HP:0007359, HP:0010845, HP:0002133, HP:0007979, HP:0000572, HP:0000577, HP:0000543, HP:0001263, HP:0001310, HP:0002075, HP:0002317, HP:0002188 (Vomiting, Setting-sun eye phenomenon, Lowered consciousness, Bilateral tonic-clonic seizure, Atonic seizure, Focal-onset seizure, EEG with generalised slow activity, Status epilepticus, Gaze-evoked horizontal nystagmus, Visual loss, Exotropia, Optic disc pallor, Global developmental delay, Dysmetria, Dysdiadochokinesis, Unsteady gait, Delayed CNS myelination)

      HPOsFreeText: Tonic flexion of the right limbs, The right hemisphere showed continuous spike and slow-spike waves with a temporo-occipital maximum

      CaseNotHPOs: HP:0010841 (Multifocal epileptiform discharges)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are nonconsanguineous, Proband is confirmed homozygous via parental testing

      CasePreviousTesting: EEG showed severe cerebral dysfunction of the right hemisphere (continuous subdelta and delta activity); Antiepileptic treatment with phenobarbital was initiated after the first seizure but was replaced by levetiracetam after the second seizure

      CaseGenotypingMethod: Exome sequencing was performed and potential variants prioritized. Identified variants were selected for Sanger sequencing in both the proband and parents.

      Variant: NM_004171.4:c.1421+1G>C

      CAID: CA380121375, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA380121375

      gnomAD: Not in gnomAD

    1. Theproband

      CaseC: Male, Childhood onset, Asian, China

      CasePresentingHPOs: HP:0004923 (Hyperphenylalaninemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are confirmed heterozyogus and proband is homozygous for this mutation

      CasePreviousTesting: "Classical Severe PKU" presence confirmed by Guthrie test and clinical criteria described in PMID:7006308, Plasma phenylalanine level in excess of 20 mg/dl, Homozygous for RFLP haplotype 4

      CaseGenotypingMethod: PCR amplification of PAH exon three plus the flanking intronic regions was performed. The genomic DNA was cloned and sequenced to confirm the presence of the mutation. Haplotype analysis confirmed linkage disequillibrium with RFLP haplotype 4.

      Variant: NM_000277.3(PAH):c.331C>T (p.Arg111Ter)

      ClinVar: 581 https://www.ncbi.nlm.nih.gov/clinvar/variation/581/

      gnomAD: 0.0001230, https://gnomad.broadinstitute.org/variant/12-103288534-G-A

    1. t

      CaseSE4: Male, Australia

      CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseGenotypingMethod: Five loci were investigated for evidence of linkage to Hartnup due to their established role in amino acid transport including SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A19. These 5 regions were studied with microsattelite markers and produced linkage only between D5S392 and D5S417, the region with SLC6A18 and 19. SLC6A18 did not increase neutral amino acid uptake in X. laevis oocytes so SLC6A19 was investigated and directly sequenced in the families each of which displayed a causal variant.

      CasePreviousTesting: SLC1A5 had no causative variants detected.

      CaseAddInfo: Asymptomatic except for hyperaminoaciduria

      Variant: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

      ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

      gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A?dataset=gnomad_r2_1

    2. M

      FamilySE1: Australia

      FamilyPresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

      HPOsFreeText: N/A

      FamilyNotHPOs: N/A

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Five loci were investigated for evidence of linkage to Hartnup due to their established role in amino acid transport including SLC3A2, SLC7A8, SLC1A5, SLC6A18, and SLC6A19. These 5 regions were studied with microsattelite markers and produced linkage only between D5S392 and D5S417, the region with SLC6A18 and 19. SLC6A18 did not increase neutral amino acid uptake in X. laevis oocytes so SLC6A19 was investigated and directly sequenced in the families each of which displayed a causal variant.

      FamilyPreviousTesting: SLC1A5 had no causative variants detected.

      FamilyAddInfo: Family is asymptomatic except for hyperaminoaciduria

      Variant1: NM_001003841.3(SLC6A19):c.1173+2T>G

      ClinVar: 449553 https://www.ncbi.nlm.nih.gov/clinvar/variation/449553/

      gnomAD: 0.00008019, https://gnomad.broadinstitute.org/variant/5-1217062-T-C?dataset=gnomad_r2_1

      Variant2: NM_001003841.3:c.725T>C (p.Leu242Pro)

      CAID: CA3182847 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182847

      gnomAD: 0.0001307, https://gnomad.broadinstitute.org/variant/5-1213639-T-C

      Affected: 3

      Unaffected: 3

      pLOD: 2.68 combined max LOD score for linkage between D5S392 and D5S417

      AddSegregationInfo: Pedigree in SuppFig1A, Candidate gene sequencing

    1. 2927 (F)

      Case2927: Female, 2 years diagnosis, Czech

      CasePresentingHPOs: HP:0001270, HP:0001263, HP:0003153, HP:0012443, HP:0000486, HP:0012795, HP:0000639, HP:0000545, HP:0000646, HP:0002280, HP:0030890, HP:0000488, HP:0001744 (Motor delay, Global developmental delay, Cystathioninuria, Abnormality of brain morphology, Strabismus, Abnormality of the optic disc, Nystagmus, Myopia, Amblyopia, Enlarged cisterna magna, White matter hyperintensity, Retinopathy, Splenomegaly)

      HPOsFreeText: Normal total homocysteine (7.1 μM/l; reference 5.1–13.9), Elevated cystathionine (6 μM/l; reference 0.04–0.34), Normal total cysteine (306 μmol/l; reference 203–369), Birth weight was 2400 g, Responsive to B6 treatment

      CaseNotHPOs: HP:0002240, HP:0001977 (Hepatomegaly, Abnormal thrombosis)

      NotHPOsFreeText: N/A

      CaseAddInfo: Patient is homozygous for this mutation

      CasePreviousTesting: Cystathionine (Cysta), total cysteine (tCys), and total homocysteine (tHcy) panels

      CaseGenotypingMethod: PCR amplification of CTH coding regions and exon-intron boundaries was performed. These fragments were sequenced and aligned with a reference to find mutations. Those found were confirmed by restriction digest of 100 controls.

      Variant: NM_001902.5:c.200C>T (p.Thr67Ile)

      ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

      gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

    1. AC013 II-1

      CaseAC013_II-1: Female, 7 yrs report, Turkey

      CasePresentingHPOs: HP:0001992, HP:0001249, HP:0004322, HP:0001513, HP:0030838 (Organic aciduria, Intellectual disability, Short stature, Obesity, Hip pain)

      HPOsFreeText: BMI 93rd percentile

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are consanguineous, Proband is asserted homozygous for this variant

      CasePreviousTesting: Identified by the assessment of urinary organic acids by gas chromatography–mass spectrometry; Accumulation of N-acetylated amino acids was much less pronounced than in previously reported patients; Metabolic studies were initiated after the patient complained of pain in her left hip

      CaseGenotypingMethod: Genomic DNA was extracted either from peripheral blood or EBV-transformed lymphocytes. PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries of ACY1 was performed.

      Variant: NM_000666.3(ACY1):c.1133G>A (p.Arg378Gln)

      ClinVar: 809490, https://www.ncbi.nlm.nih.gov/clinvar/variation/809490/

      gnomAD: 0.003104, https://gnomad.broadinstitute.org/variant/3-52022997-G-A

    1. a single base deletion (c.G222del) in exon 2 led to a frame-shift terminating the protein at position 74 of 412 amino acids

      Case 18-IV-1

      Proband? Yes

      Phenotype HPOs: HP:0001249, HP:0000708, HP:0008762, HP:0002373, HP:0002197, HP:0010892, HP:0000729

      HPOFreeText: Failure to meet developmental milestones: did not sit until one year, never crawled, began to walk at two years, said her first words at two years old and never spoke in sentences.

      NotHPOs: HP:0001507

      Demographics: Female, Turkey, 21yrs (at report - final age)

      Previous Testing? The proband tested negative for known metabolic disorders. additionally, no chromosomal abnormalities were identified and cranial MRI was normal.

      Genotyping Method:

      Variant Info:


      Variant: c.222del (p.Met74IlefsTer15)

      CAID:CA891862642 ID created for this curation

      gnomAD: Found. Highest MAF 0.00003249 (South Asia), No homozygotes (all populations)

      Variant Evidence: Authors show reduced BCKDK mRNA levels and undetectable BCKDK protein levels in patient derived fibroblasts, suggesting nonsense-mediated decay.


      Additional Case Info: Family described to be of Egyptian ancestry. Parental first-cousin consanguinity. Had one sibling who was similarly affected. Allele Registry CAID created for this curation.

      Other Reporting PMIDs:

    1. 7

      CasePU7: Female, 8 months report, White

      CasePresentingHPOs: HP:0012120, HP:0003193, HP:0004322, HP:0000964 (Methylmalonic aciduria, Allergic rhinitis, Short stature, Eczema)

      HPOsFreeText: Malonic aciduria

      CaseNotHPOs: HP:0003353 (Propionyl-CoA carboxylase deficiency)

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband cannot be confirmed in-trans due to lack of parental testing

      CasePreviousTesting: 6.3 propionate incorporation (nmol/mg protein/18 h); Plasma homocysteine and plasma amino acid levels were within the reference range; MMA levels responded partially to cobalamin treatment

      CaseGenotypingMethod: Genomic DNA was extracted from fibroblasts. Next-generation sequencing was performed with 24 genes being sequenced including all coding exons and 20 bp of their flanking intronic regions.

      CasePMIDs: PMID:30740739 as Case 5

      Variant1: NM_001243279.3:c.1239+2T>G

      CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

      gnomAD: Not in gnomAD

      Variant2: NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp)

      ClinVar: 31134, https://www.ncbi.nlm.nih.gov/clinvar/variation/31134/

      gnomAD: 0.004790, https://gnomad.broadinstitute.org/variant/16-89220556-C-T

    1. To evaluate the effect

      Case1

      Variant: NM_013391.3:c.326A>G (p.His109Arg)

      VariantEvidence: The above mutation was introduced into hDMGDH cDNA and both the wild-type and mutant sequences were expressed in E. coli, Saccharomyces cerevisiae, and other mammalian tissue culture samples. In the mutant E coli, no active enzyme could be detected. Similarly, no antigen could be detected in the other cells. The wild-type cells had detectable activity and much higher levels of mRNA than the mutants. Western blot of the cellular extracts showed that the levels of wild-type and mutant protein were similar, but the activity was undetectable.

    1. 4

      CaseGM01781: Female, 18 years report, Caucasian, Europe

      CasePresentingHPOs: HP:0003153 (Cystathioninuria)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is a compound heterozygote for these variants, Variants were confirmed in trans by parental testing

      CasePreviousTesting: N/A

      CaseGenotypingMethod: Primers were developed and the CTH exons 1-12 and exon-intron boundaries were PCR amplified and sequenced. All sequence variations were verified by restriction enzyme analysis and/or repeat sequencing.

      Variant1: NM_001902.5:c.200C>T (p.Thr67Ile)

      ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

      gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

      Variant2: NM_001902.5:c.718C>G (p.Gln240Glu)

      ClinVar: 2940 https://www.ncbi.nlm.nih.gov/clinvar/variation/2940/

      gnomAD: European (Non-Finnish) 1.759e-5, Overall 7.957e-6 https://gnomad.broadinstitute.org/variant/1-70896071-C-G

    1. A 2-year-old boy

      Case: Male, 5 days onset, Iran

      CasePresentingHPOs: HP:0002572, HP:0004923 (Episodic vomiting, Hyperphenylalaninemia)

      HPOsFreeText: Brown eyes

      CaseNotHPOs: HP:0001249, HP:0032807 (Intellectual disability, Neonatal seizure)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are consanguineous first cousins

      CasePreviousTesting: Screened for HPAs by Guthrie test and on special diet

      CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. PAH gene was screened but no mutations were found. BH4-metabolizing genes were screened via STR markers, with PCBD1 having a homozygous pattern. Direct sequencing revealed a homozygous termination codon extension.

      Variant: NM_000281.4(PCBD1):c.313T>C (p.Ter105Gln)

      ClinVar: 428616, https://www.ncbi.nlm.nih.gov/clinvar/variation/428616/

      gnomAD: 0.00003301, https://gnomad.broadinstitute.org/variant/10-72643709-A-G

    1. Homozygous c.295 C>T in exon 3 (p.Gln99X, precursor protein)

      Case1: Newborn, Indian (consanguineous)

      CasePresentingHPOs:

      HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

      CaseNotHPOs:

      CasePreviousTesting: Followup C5 carnitine 0.88 nM/ml (ref <0.8). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

      CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

      Variant: NM_001609.3(ACADSB):c.295C>T (p.Gln99Ter) (homozygous)

      ClinVar: 281177

      gnomAD: 0.00006537 South Asian

      VariantEvidence: LOF

      CaseAddInfo:

      CasePMIDs:

    1. Amale1-year-oldC

      Case: Citron-1/ BIODEF 270, male, 4 days

      CasePresentingHPOs: HP:0008297

      HyperPhe was noted, with a plasma Phe level of 700uM. Normal neopterin and biopterin levels were observed in the urine, but the presence of primapterin was found.

      CaseNOTHPOs:

      CasePreviousTesting: n/a

      CaseGenotypingMethod: PCR of exons 2-4 of PCBD1 followed by direct sequencing of the products.

      Variant 1: NM_000281.3(PCBD1):c.259G>T (p.Glu87Ter)

      ClinVar ID 1: 16795

      Variant 2: NM_000281.3(PCBD1):c.244T>C (p.Cys82Arg)

      ClinVar ID 2: 16796

      Compound heterozygous

      gnomAD 1: MAF (Ash-Jews)= 1.183E-3, all hets no homozygous.

      gnomAD 2: MAF (Euro-NF)= 2.690E-5 all hets, no homozygous noted. http://gnomad.broadinstitute.org/variant/10-72643778-A-G

      AddCaseInfo: Parents were tested and found to have normal Phe levels. The father carriers the termination variant, E87X, the mother harbors the C82R, and both parents are heterozygous for their respective PCBD1 variants.

      VariantEvidence:  For the Glu87Ter variant, Thony et al., PMID: 9585615 showed that the mutant E86X/E87X protein was expressed in E.Coli to determine the solubility of the mutant enzyme and the activity. The mutant E86X/E87X fragment was mostly found in the insoluble fraction of the supernatant. The remaining fraction obtained in the soluble fraction did retain some enzyme activity in vitro. Interestingly, when more E86X/E87X was obtained in the soluble fraction (by growing the E.coli at 20 degrees C), the Km (Michaelis constant) was similar to wildtype levels (text only, no figures to compare).

      For the C82R/C81R variant was analyzed by Ayling et al., 2000 (PMID:10924272) and was found to still be retained in the soluble fraction in bacteria expressing the recombinant protein. Furthermore, enzyme assays show that the soluble C82RPCBD1 variant retained activity, albeit at 40% of the wildtype.

    1. HIBCHD patient

      Case1: Female, Anglo-Celtic, Birth onset

      CasePresentingHPOs: HP:0001511, HP:0008872, HP:0025404, HP:0000737, HP:0010845, HP:0001263, HP:0001290, HP:0002059, HP:0012448, HP:0002079, HP:0002474, HP:0002421 (Intrauterine growth retardation, Feeding difficulties in infancy, Abnormal visual fixation, Irritability, EEG with genaralized slow activity, Developmental delay, Hypotonia, Cerebral atrophy, Delayed myelination, Thinning of the corpus callosum, Communication delay, Poor head control)

      HPOsFreeText: Birth weight was 2160 g, Inability to follow with eyes at four months, EEG showed poorly modulated background, MRI showed markedly increased signals in the brain stem, upper pons, basal ganglia and thalami, Inability to sit unsupported

      CaseNotHPOs: HP:0001250, HP:0001946 (Seizures, Ketosis)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents were not consanguineous, parental testing confirms in trans

      CasePreviousTesting: Routine metabolic investigations at 4 months (plasma and CSF amino acids, urine amino and organic acids, transferrin isoforms, very long chain fatty acids) were uninformative, Increased excretion of SCPC, Increased levels of urine metabolites derived from methacrylate such as S-(2-carboxypropyl)cysteine (18,27 μmol/mmol of creatinine; reference <5.3), N-acetyl-S-(2-carboxypropyl)cysteine (30,42 μmol/mmol of creatinine; reference <4.2), S-(2-carboxypropyl)cysteine carnitine ester (5.8,5.3 μmol/mmol of creatinine; reference <1.0), and S-(2-carboxypropyl)cysteamine (13,16 μmol/mmol of creatinine; reference <10), Increased erythro-2,3-dihydroxy-2-methylbutyrate compared to controls, The coding region of the E1α gene was sequenced and was found normal

      CaseGenotypingMethod: The HIBCH gene was sequenced after the metabolite testing. Other details were not described.

      Variant1: NM_014362.4(HIBCH):c.1033G>A (p.Gly345Ser)

      ClinVar: 208532 https://www.ncbi.nlm.nih.gov/clinvar/variation/208532/

      gnomAD: European (Non-Finnish) 8.805e-6, Overall 3.982e-6 https://gnomad.broadinstitute.org/variant/2-191073618-C-T

      Variant2: NM_014362.4(HIBCH):c.129dup (p.Gly44Argfs*20)

      ClinVar: 208531 https://www.ncbi.nlm.nih.gov/clinvar/variation/208531/

      gnomAD: South Asian 9.834e-5, Overall 1.597e-5 https://gnomad.broadinstitute.org/variant/2-191161628-C-CT