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.

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

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).

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.

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.

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.

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.

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

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.

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.

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

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

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

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

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

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

Case#: DBT-5

CasePresentingHPOs: Classic form of MSUD

Variant: NM_001918.3:c.1195T>C

CAID: CA341330334

gnomAD: Not in gnomAD

VariantEvidence: No functional evidence

CaseAddInfo:

CasePMIDs:

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.

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

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

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

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

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

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

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)

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

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

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

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

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

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

Patient14: Group 3

CasePresentingHPOs: same as group 3

CasePreviousTesting: same as group 3

CaseGenotypingMethod: same as group 3

Variant1: NM_002225.3:c.125T>C

CAID: CA391743774, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391743774

gnomAD: n/a

Variant2: IVS2-1G>C no ClinVar or CAID

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

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

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.

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.

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.

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

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

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

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

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).

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

Case#: PD, 44 years, female

CasePresentingHPOsFreeText: apo-B plasma levels <5% of normal; total cholesterol 2.57 (normal range 4-6.5 mmol/l), triglyceride 0.59 (normal range 0.3-1.8 mmol/l), apoB 17 (normal range 60-140 mg/dl).

CasePreviousTesting: On Western blot a truncated species of apo-B was found in the VLDL/chylomicron fraction (fig. 3), predicted based on size to be at the 5’ end of exon 26. The protein was absent from the HDL or infranate fractions.

CaseGenotypingMethod: Genomic DNA was digested with a panel of restriction enzymes and Southern blotted. Based on truncated apoB size (detected on Western blot), the variant was predicted to be at the end of exon 26. Approximately 1.7 kb of genomic DNA including exon 26 was amplified by the polymerase chain reaction (PCR), cloned into M13, and sequenced.

Variant: NM_000384.3(APOB):c.5463del (p.His1822fs), heterozygous

ClinVar: 17882

gnomAD: 0.000008797 (European non-Finnish)

Individual

Case#: 13940

Caseprevioustesting: SSCP Scan

Casemethod1: SSCP Scan

Casemethod2: PCR, Sanger Sequencing

Variant: NC_000022.11:g.29673267A>T (splice site acceptor, predicted/proven null)

CAID: CA16040592

gnomAD: not found

Individual

Case#: 16221

Caseprevioustesting: SSCP Scan

Casemethod1: PCR, Sanger

Variant: NM_000268.3:c.544G>T (nonsense)

CAID: CA021432

Caseaddinfo: de novo

gnomad: not found

Case#: 16773

Caseprevioustesting: SSCP Scan

Casemethod1: PCR, Sanger

Variant: NM_000268.3:c.1579G>T (nonsense)

CAID: CA021349

Caseaddinfo:

gnomad: no data

Case#: Consequence 29 Table 1 in Data Supplement (1 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.2782G>A (p.Asp928Asn)

ClinVar: 164313 https://www.ncbi.nlm.nih.gov/clinvar/variation/164313/

CAID: n/a

gnomAD: absent

Case#: Consequence 14 Table 1 in Data Supplement (1 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.1208G>A (p.Arg403Gln)

ClinVar: 14087 https://www.ncbi.nlm.nih.gov/clinvar/variation/14087/

CAID: n/a

gnomAD: absent

Patient: P100

Variant: c.120_121delAG p.Gly41Argfs*16

CAID: CA2580612030

Functional effect: Decreased expression of full-length mutant allele compared to wt allele. Observed in blood.

Case: Family G Proband GII-3, male, 13yo at report

CasePresentingHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0000054, HP:0002240, HP:0001642, HP:0000365, HP:0001822, HP:0100490, HP:0002619

CasePresentingHPOsFreeText: subcutaneous masses in genital area, dilated lateral scleral vasculature

CaseNOTHPOs: HP:0034373, HP:0007380, HP:0001256, HP:0000520

CaseNOTHPOSFreeText:

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G437R homozygous

ClinVarID: or CAID: 565/CA114352

gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: Female cousin, GII-10, is also affected but lacks the classical cutaneous findings

PreviouslyPublished: n/a

VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

Case: Family A Proband AII-8, male, Arabic, Israeli, 13yo at report

CasePresentingHPOs: HP:0000953, HP:0000998, HP:0000054, HP:0001433, HP:0011025, HP:0000365, HP:0000520, HP:0012385, HP:0001684, HP:0000823, HP:0030053, HP:0100324, HP:0100727

CasePresentingHPOsFreeText: Scrotal masses, Dilated scleral vessels

CaseNOTHPOs: HP:0008064, HP:0002619, HP:0007380

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: microarray, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G427S; G437R

ClinVarID: or CAID: 563/CA114349; 565/CA114352

gnomAD: The missense variant G427S is present in gnomAD v4.0.0 with a MAF=0.00005339 (4/74926 alleles) in the African/African American population and 0 homozygotes. The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: consanguineous parents; mother was het for G427S, but father's genotype was not provided

PreviouslyPublished: PMID: 18410979

VariantEvidence: Functional studies in Xenopus oocytes demonstrated that G427S results in a total loss of transport activity (Kang et al. 2010; PMID: 20595384).

Kang et al. (2010) performed functional characterization of the G437R mutation in Xenopus oocytes and observed transport activity that was approximately half that of wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to wildtype, suggesting decreased stability.

Case: Family J Proband JII-1, male, 12yo at report

CasePresentingHPOs: HP:0000953, HP:0030053, HP:0000998, HP:0000054, HP:0002240, HP:0031664, HP:0000365, HP:0012385, HP:0034373, HP:0001084, HP:0000771

CasePresentingHPOsFreeText: subcutaneous masses in genital area, dilated lateral scleral vasculature

CaseNOTHPOs: HP:0001822, HP:0000520, HP:0002619, HP:0007380, HP:0001256

CaseNOTHPOSFreeText:

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3

Variant: c.1045delC homozygous

ClinVarID: or CAID: 566/CA351488

gnomAD: The frameshift variant p.Leu349fs, located in exon 6/6, is present in gnomAD v4.0.0 with a MAF=0.000001799 (2/1112010 alleles) in the European Non-Finnish population and 0 homozygotes.

AddCaseInfo: Consanguineous, unaffected parents. 6 unaffected siblings

PreviouslyPublished: n/a

VariantEvidence: Kang et al. (2010; PMID: 20595384) performed functional characterization of the 1045delC mutation in Xenopus oocytes and observed near-total loss of transport activity compared to wildtype SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated mistrafficking of the mutant protein to the endoplasmic reticulum or Gogli apparatus

Case: Family H Proband HII-2, female, 50yo at report

CasePresentingHPOs: HP:0000823, HP:0002240, HP:0001822, HP:0034373, HP:0100490, HP:0002619, HP:0000520, HP:0001838, HP:0007380, HP:0001084, HP:0001871, HP:0004322, HP:0000135, HP:0000141, HP:0012410, HP:0011974

CasePresentingHPOsFreeText: stasis ulcers

CaseNOTHPOs: HP:0000953, HP:0000998, HP:0030053, HP:0001256

CaseNOTHPOSFreeText: dilated lateral scleral vasculature

CasePreviousTesting: Direct sequencing of AIFM2, ADAMTS14, EIF4EBP2, C10ORF54, PPA1, H2AFY2, LRRC20, NODAL, PRF1, TYSND1, SAR1A, PSAP, NPFFR1, and C10ORF27

CaseGenotypingMethod: Microarray, homozygosity mapping, haplotype analysis, direct sequencing of exons of SLC29A3, restriction digestion

Variant: G437R homozygous

ClinVarID: or CAID: 565/CA114352

gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

AddCaseInfo: Consanguineous parents, not genotyped. 3 unaffected, not genotyped siblings

PreviouslyPublished: n/a

VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

CaseFSIP2_3 male, 45yo report, Tunisian

CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

(male infertility, asthenospermia, sperm tail anomaly)

HPOsFreeText Sperm volume: 3.4mL, sperm concentration: 0.66 million/mL, total motility: 0h, vitality: 30%, normal spermatozoa: 0%, absent flagella: 6%, short flagella: 78%, coiled flagella: 6%, flagella of irregular caliber: 6%

CaseNotHPOs n/a

CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

Variant NM_173651.3(FSIP2):c.1607_1616delAAAGATTGCAinsTGT (p.Lys536Metfs)

ClinVar 586970

gnomAD not in gnomAD

CaseAddInfo Consanguineous parents

CasePMIDs 29449551

CaseFSIP2_2 male, 52yo report, Tunisian

CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

(male infertility, asthenospermia, sperm tail anomaly)

HPOsFreeText Sperm volume: 4.7mL, sperm concentration: 1.25 million/mL, total motility: 0h, vitality: 7%, normal spermatozoa: 0%, absent flagella: 16%, short flagella: 50%, coiled flagella: 18%, flagella of irregular caliber: 36%

CaseNotHPOs n/a

CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

Variant NM_173651.3(FSIP2):c.2282dup (p.Asn761Lysfs)

ClinVar 586973

gnomAD not in gnomAD

CaseAddInfo Consanguineous parents

CasePMIDs 29449551

CaseFSIP2_1 male, 44yo report, Tunisian

CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

(male infertility, asthenospermia, sperm tail anomaly)

HPOsFreeText Sperm volume: 2.5mL, sperm concentration: 6.7 million/mL, total motility: 1h, vitality: 47%, normal spermatozoa: 0%, absent flagella: 2%, short flagella: 32%, coiled flagella: 26%, flagella of irregular caliber: 57%

CaseNotHPOs n/a

CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

Variant NM_173651.3(FSIP2):c.910del (p.Gln304Lysfs)

ClinVar 586972

gnomAD not in gnomAD

CaseAddInfo Consanguineous parents

CasePMIDs 29449551

Case1: Male, United States, Birth onset

CasePresentingHPOs: HP:0001558, HP:0003552, HP:0002804, HP:0001762, HP:0001188, HP:0000023, HP:0001385, HP:0006380, HP:0004482, HP:0004322, HP:0003782, HP:0011220, HP:0000160, HP:0000470, HP:0000301, HP:0002751, HP:0003306, HP:0001270, HP:0003808, HP:0003044, HP:0012453, HP:0001193, HP:0012785, HP:0003273, HP:0012894, HP:0002174, HP:0004370, HP:0002362, HP:0002942, HP:0012418, HP:0002789, HP:0002205, HP:0002870, HP:0003458, HP:0040129, HP:0003236, HP:0003388, HP:0002015, HP:0003557, HP:0003803, HP:0003715, HP:0012240, HP:0100295 (Decreased fetal movement, Muscle stiffness, Arthrogryposis multiplex congenita, Talipes equinovarus, Hand clenching, Inguinal hernia, Hip dysplasia, Knee flexion contracture, Relative macrocephaly, Short stature, Eunuchoid habitus, Prominent forehead, Small mouth, Short neck, Abnormality of facial musculature, Kyphoscoliosis, Spinal rigidity, Motor delay, Abnormal muscle tone, Shoulder flexion contracture, Bilateral wrist flexion contracture, Ulnar deviation of the hand or of fingers of the hand, Flexion contracture of finger, Hip contracture, Paraspinal muscle hypertrophy, Postural tremor, Abnormality of temperature regulation, Shuffling gait, Thoracic kyphosis, Hypoxemia, Tachypnea, Recurrent respiratory infections, Obstructive sleep apnea, EMG: myopathic abnormalities, Abnormal nerve conduction velocity, Elevated serum creatine phosphokinase, Easy fatigability, Dysphagia, Increased variability in muscle fiber diameter, Type 1 muscle fiber predominance, Myofibrillar changes, Increased intramyocellular lipid droplets, Muscle fiber atrophy)

HPOsFreeText: Jaw contracture, Heel contracture, Strong bilateral grasp, Occasional grunting, Supplemental oxygen required, Ultrastructural evidence of accumulation of mitochondria, Focal Z-line streaming and broadening

CaseNotHPOs: HP:0100543, HP:0001315, HP:0001324, HP:0002486, HP:0100288, HP:0002353, HP:0002363, HP:0003116, HP:0003798 (Cognitive impairment, Reduced/absent deep tendon reflexes, Muscle weakness, Myotonia, EMG: myokymic discharges, EEG abnormality, Abnormality of brainstem morphology, Abnormal echocardiogram, Nemaline bodies)

NotHPOsFreeText: N/A

CaseAddInfo: Case is de novo and confirmed via parental testing

CasePreviousTesting: Negative Results from WES: ACTA1, MYH3, TPM2, HSPG2, TNNT3, TNNI2, FKRP, CRYAB, and microarray.

CaseGenotypingMethod: DNA was obtained from blood and WES was performed on the samples using Illumina technology. Mutations were analyzed and filtered.

Variant: NM_152263.4(TPM3):c.670_672GAA[1] (p.Glu225del)

ClinVar: 235143 https://www.ncbi.nlm.nih.gov/clinvar/variation/235143/

gnomAD: Not in gnomAD

Case# NonNew, male, 40yr

CasePresentingHPOs HP:0002119, HP:0002375 , HP:0031317

CaseNotHPOs Annotate with the HPOs that were noted not to manifest within the proband of interest.

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseMethod2 as mentioned

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.1073C>T (p.Ser358Leu)

ClinVar 734

VariantEvidence ?????Surely the presenting relevant phenotypes is not enough, neither are the in silico programs they are running forpathogenicity prediction. There seems to be nothing else provided????

CaseAddInfo De Novo, Maternity/Paternity confirmed

Case# Baskin RW, Female, 31

CasePresentingHPOs HP:0004756, HP:0011841, HP:0002013

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.934C>T (p.Arg312Trp)

ClinVar 36873

gnomAD 0.03553 link

Case: Individual 13, male, AOR= 8 years 4 months

CasePresentingHPOs: HP:0000252, HP:0000750, HP:0001263, HP:0001290, HP:0000527, HP:0006332, HP:0001212, HP:0004279, HP:0000202, HP:0010289, HP:0000540

CasePresentingHPOText: Began walking 18 Noted as limited vocabulary and saccadic speech. Noted to have short fingers.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0002360, HP:0000708, HP:0000924, HP:0002719

CaseNOTtextHPO: no ID per the WISC-V. CT scan normal

CasePreviousTesting: Karyotyping, Fragile X Syndrome (FMR1), and Array-CGH (Agilent 180K) were all normal

CaseGenotypingMethod: Trio WES (exome capture Agilent CRE and HiSeq 4000).

Variant: hg19:chr2: g.4804618 6_4804619 0del, c.1825_1829del, p.(Glu609) OR* NM_001190274.1:c.1825_1829del

CA ID: CA658820930

de novo

gnomAD: n/a

AddCaseInfo:

VariantEvidence: The Gln609Ter mutation occurs in exon 15 which encodes the second CASH domain. The nonsense mutation most likely disrupts the second and third CASH domains and the zinc-finger ubiquitin binding region. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 15, male, AOR= 11 years 5 months

CasePresentingHPOs: HP:0002167, HP:0002342, HP:0001250, HP:0002376, HP:0002360, HP:0000717, HP:0007018, HP:0000718, HP:0000735, HP:0002553, HP:0000154, HP:0000289, HP:0000179, HP:0000293, HP:0009909, HP:0004209, HP:0000403, HP:0009921, HP:0002020

CasePresentingHPOText: Began walking at 14 months old. Noted as having limited vocabulary, short sentences and single words. Noted as having one single seizure at 5 years old. Developmental regression noted at 1 year old. Has food seeking behavior.

CaseNOTHPOs: HP:0000202, HP:0000924,

CaseNOTtextHPO:

CasePreviousTesting: ArrayCGH, Prader will and Anglican syndrome methylation studies, and RAI1 analysis (by DHPLC) were all normal

CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

Variant: hg19:chr2: g.4804051 5_4804052 2dup, c.2084- 6_2085dup, p.(Gly697) OR* NM_001190274.1:c.2084-6_2085dup

CA ID: CA658765223

de novo

gnomAD: n/a

AddCaseInfo:

VariantEvidence: The c.2084−6_2085dup id suggested to lead to a stop codon at Gly697, which is located in exon 18. Exon 18 is upstream of the third CASH domain, which regulates substrate recognition. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 3, male, 7.5 yo

CasePresentingHPOs: HP:0000750, HP:0001263, HP:0001290, HP:0002360, HP:0007018, HP:0000736, HP:0004673, HP:0000735, HP:0000629, HP:0000316, HP:0004209, HP:0001212, HP:0001382,

CasePResentingHPOText: Subject began walking at 18 months. Testing for autism gave the following results: WPPSI-III-NL: TIQ 98, VIQ 106, PIQ 96.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0000202, HP:0000504,

CasePreviousTesting: Metabolic screening, SNP-array, and Fragile X (FMR1) testing were normal

CaseGenotypingMethod: Trio-WES. Individual is noted as being mosaic (60%) for the FBXO11 mutation. Testing also identified a VUS in TP73 (NM_0054 27.3):chr1: g.3644250 G>A, c.901G>A; p.(Asp301Asn). Not noted as de novo, so assume inherited and parents were not noted as having behavioral abnormalities or intellectual disability.

Variant: hg19:chr2: g.4806611 8=/T>C, c.467=/A> G p.(Gln156Arg) or NM_001190274.1:c.467A>G

CA ID: CA346813225

de novo Trio-WES performed so maternity and paternity could be investigated with this method.

gnomAD: n/a

AddCaseInfo:

VariantEvidence: Individual is noted as being mosaic (60%) for the FBXO11 mutation. Gln156 is located just N-terminal to the F-box region of FBXO11, and is conserved across species. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the Q156R mutation on FBXO11 function.

FamilyName: Families A,B,C Founder, Pakistani

FamilyPresentingHPOs: HP:0002033,

FamilyNotHPOs:

CountryOrigin: Pakistani

Ethnicity:

Race: Asian

FamilyPreviousTesting: n/a

FamilyMethod1: same as group

FamilyMethod2: same as group

FamilyGenotypingMethod: Identified region of homozygosity on Chromosome 9, that also encoded for the genes CER1, FREM1, IFN4A, IFNA10, TEK, and IFNK. Potentially deleterious mutations were found in FREM1 and IFNA10 were noted in supplement, but when the refseq was cross referenced to gnomAD, the variants were present in a substantial number homozygotes. For a lethal conditions, this would indicate benign variation.

Affected: 7

Unaffected:

Segregations:

PublishedLOD: 4.52

eLOD: n/a

AddSegregationInfo: All families from Pakistani origin. Family A and C were Pakistani. Family B was from Kashmir, on the Pakistani border.

ProbandLabel: Family A-IV:6/ CaseA IV:6, male, Pakistani, died as 12 days old

Homozygous

Variant: NM_001031689.2(PLAA):c.68G>T (p.Gly23Val)

ClinVar or CAID: 427941

gnomAD: n/a

FamilyAddInfo:

FamilyPMIDs:

CasePresentingHPOs: HP:0025116, HP:0001561, HP:0008872, HP:0008936, HP:0002509, HP:0002033, HP:0002015, HP:0001007, HP:0003196, HP:0000343, HP:0000218, HP:0000369, HP:0007598, HP:0100259, HP:0010576, HP:0007633, HP:0031605, HP:0000851, HP:0011968, HP:0100022, HP:0002871, HP:0001522

CaseNOTHPOs:HP:0001507

AddCaseInfo:

VariantEvidence: PLAA G23V homozygous mice were generated by Crispr/Cas9 genome editing. Examination of PLAA protein levels in the cerebellum of the homozygous G23V mutant mice vs the wildtype littermates (Figure 3A) revealed significantly reduced protein expression, indicating the G23V variation effects protein stability, and indicates a loss of function mechanism for the variant.

Score: Default for homozygous missense.

Note: Will score the phenotypes associated with the G23V mouse as experimental evidence seperately.

Case# Zhong 2:4, Male, China

CasePresentingHPOs HP:0007675, HP:0000580, HP:0007994, HP:0100019

CasePreviousTesting Yes, genome wide scan, exons 1-22

CaseMethod1 WES

CaseMethod2 Sanger

Variant NM_004698.2:c.1345C>G

CAID CA342279767

CasePMIDs 21281067

Case# B16, female, 30

CasePresentingHPOs HP:0003124 Hypercholesterolemia

CasePreviousTesting The APOB domains, including amino acids 2955–3092 and amino acids 3303–3492, were analysed in the 600 molecularly undefined ADH cases by direct Sanger sequencing

CaseMethod1 as mentioned

CaseMethod2 as mentioned

CaseGenotypingMethod Exome sequencing

Variant NM_000384.2(APOB):c.10182G>T (p.Lys3394Asn)

ClinVar 438310

gnomAD n/a

VariantEvidence Deficient LDL uptake (fig. 2).

Case# F2:II.2, F, 5mo onset, Turkey

CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0100543, HP:0001250, HP:0002061, HP:0012444, HP:0001943, HP:0002151, HP:0002919, HP:0045045, HP:0040145, HP:0001270, HP:0001259, HP:0003236, HP:0000648

HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Cognitive impairment, Seizures, Lower limb spasticity, Brain atrophy, Hypoglycemia, Elevated lactate, Ketonuria, Elevated acylcarnitine, Dicarboxylic acidemia, Motor delay, Coma, Elevated CK, Optic atrophy

HPOFreeText: "starting from the age of five months, psychomotor development appeared delayed. At the age of one year, spasticity predominantly involving the legs was noted. Nevertheless, the child was relatively active and was able to sit and crawl. However, after an episode of infection, she lost already acquired skills. Laboratory investigations during this episode showed transiently elevated CK activity (up to 2,970 U/l; NR < 269 U/l). At the age of 15 months, the girl suffered from a febrile upper airway infection during which she suddenly became comatose."

CasePreviousTesting "Sequence analysis of the mitochondrial DNA and CPT2 did not show clinically relevant variants. Laboratory investigations revealed hypoglycemia (31 mg/dl; NR >50 mg/dl) and severe lactic acidosis (lactate up to 16.6 mmol/L; NR < 2.1 mmol/L). Biochemical analysis of fresh muscle tissue showed moderately reduced ATP production rate and a mildly reduced activity of mitochondrial complex I. Brain MRI demonstrated mild global brain atrophy without focal abnormalities. Eye examination showed bilateral optic atrophy. Acylcarnitine profiling showed normal free carnitine concentrations in dried blood while C14:1 acylcarnitine was mildly elevated (0.31 μmol/L; NR 0-0.25 μmol/L). Analysis of organic acids in urine revealed increased concentrations of dicarboxylic acids and ketone bodies as well as massive excretion of lactate." Then at 12 years, elevated TSH concentration (7.17 μIU/ml; NR 0.28-4.31 μIU/ml).

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

Variant NM_001283106.2(TANGO2):c.418C>T (p.Arg140Ter)

ClinVar 224774

CAID CA358667

gnomAD 1.501e-05(European (Non-Finnish)), 8.254e-06(Total)

VariantEvidence (Figure 3) In assessment of Palmitate-Dependent Mitochondrial Respiration, oxygen consumpition rates were decreased in patient fibroblasts by ~20% compared to control.

CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." consanguineous parents, healthy older sibling

CasePMIDs n/a

Case# F1:II.2, F, 2yo onset, European

CasePresentingHPOs HP:0001263, HP:0006846, HP:0003201, HP:0011675, HP:0002925, HP:0001250, HP:0012444, HP:0001943, HP:0002151, HP:0045045, HP:0040145, HP:0001259, HP:0002133, HP:0002913, HP:0003128, HP:0002061, HP:0001664, HP:0008936, HP:0001344, HP:0000252, HP:0003236, HP:0001946, HP:0100543

HPOcont: Global developmental delay, Acute encephalopathy, Rhabdomyolysis, Arrhythmia, Elevated TSH, Seizures, Brain atrophy, Hypoglycemia, Elevated lactate, Elevated acylcarnitine, Dicarboxylic acidemia, Coma, Status epilepticus, Myoglobinuria, Lactic acidosis, Lower limb spasticity, Torsade de pointes, Trunk hypotonia, Absent Speech, Microcephaly, Elevated CK, Ketosis, Cognitive Impariment

HPOFreeText: "At the age of 2 7/12 years, she suffered from an infection and suddenly became comatose with status epilepticus. Her renal function was transiently impaired due to massive rhabdomyolysis with myoglobinuria. The girl’s condition subsequently improved but she was unable to sit due to truncal hypotonia. She developed progressive spasticity in the legs, and communicated only non-verbally. Two months later a second episode occurred, which was again triggered by an infection and presented with similar clinical and laboratory findings. A third metabolic decompensation with lactic acidosis, hypoglycemia and rhabdomyolysis occurred six weeks later. This time, additional cardiac involvement with long QT syndrome and torsade de pointes tachyarrhythmia required intensive care treatment and implantation of a cardioverter-defibrillator (ICD) device. Seizures occurred which were responsive to antiepileptic medication. The girl remained with severely impaired psychomotor capabilities, marked truncal muscular hypotonia, moderate spasticity in the lower limbs, dystonic movements in the upper limbs, absent speech, and impaired social interaction. Secondary microcephaly became evident (head circumference < P3)."

CasePreviousTesting "marked hypoglycemia (18 mg/dl; normal range (NR) > 50 mg/dl). Initial laboratory testing documented massively elevated plasma creatine kinase (CK) activity (maximum 300,000 U/l, NR < 227 U/l) as well as elevated plasma lactate concentrations up to 3.8 mmol/l (NR < 1.6 mmol/l). Urine organic acid analyses during crises showed a massive excretion of ketone bodies (around 2,000 mmol/mol creatinine), lactate (2,000 mmol/mol creatinine; NR < 285 mmol/mol creatinine), and dicarboxylic acids (values given in mmol/mol creatine: adipic (1,513; NR < 34), glutaric (24; NR = not detectable), sebacic (712; NR < 1.4), suberic (494; NR < 10), decenedioic (581; NR = not detectable), and of note malonic (145; NR = not detectable) acid). Acylcarnitine profiling in dried blot spots collected during the crisis showed free carnitine concentrations within normal ranges while several acylcarnitines were elevated 2-5-fold above the respective normal range (i.e. C5DC, C6DC, C10:1, C12, C12:1, C14:1, C14:2). In addition, an elevated TSH concentration (16.6 mU/l; NR 0.5-4.5 mU/l) was detected and treatment with L-thyroxine was initiated. Targeted sequencing of CPT2, ETFA, ETFB, ETFDH, and GCDH did not reveal clinically relevant variants."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES, confirmed with Sanger in patient and parents

Variant (1) NM_001283106.2(TANGO2):c.4delT (p.Cys2Alafs) (2) NM_152906.5:c.(56+1_57-1)(*1?)del

ClinVar (1) 224773

CAID (1) CA358861

gnomAD n/a

CaseAddInfo "measurement of pyruvate-dependent oxygen consumption rates in fibroblast cell lines from individuals F1:II.2 and F2:II.2 was unremarkable." Healthy twin brother.

CasePMIDs n/a

CasePt15 Male, 2mo report, Italian

CasePresentingHPOs HP:0002789, HP:0001950, HP:0001987, HP:0003572, HP:0003217 (Tachpnea, Respiratory alkalosis, Hyperammonemia, Low plasma citrulline, High plasma glutamine)

HPOsFreeText Tachypnoeic, respiratory alkalosis(36h), coma(48h), hyperammonemia, low citrulline, elevated glutamine

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(6[normal 16-40μmol/l]), glutamine(1824[normal 530–913μmol/l]) and ammonia(1300[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.1145C>T (p.Pro382Leu), 2. NM_001875.4:c.2891G>A (p.Gly964Asp) compound heterozygous

ClinVar n/a

CAID 1. CA2086267, CA64723299

gnomAD 1. 0.00007189(European (Non-Finnish)), 0.00003664(Total), 2. n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs 21120950

CasePt12 Female, 2do death, Italian

CasePresentingHPOs HP:0001290, HP:0002098, HP:0001987, HP:0003572, HP:0003217 (Hypotonia, Respiratory distress, Hyperammonemia, Low plasma citrulline, High plasma glutamine

HPOsFreeText Hypotonia and respiratory stress at birth, hyperammonemia, low citrulline, elevated glutamine

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(0[normal 16-40μmol/l]), glutamine(2300[normal 530–913μmol/l]) and ammonia(1831[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant NM_001875.4:c.1981G>C (p.Gly661Arg) homozygous

ClinVar n/a

CAID CA350438282

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs n/a

CasePt11 male, 3yo report, Italian

CasePresentingHPOs HP:0001987 (Hyperammonemia)

HPOsFreeText severe hyperammonemia at 48h of life

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(<2[normal 16-40μmol/l]), glutamine(1600[normal 530–913μmol/l]) and ammonia(3400[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.2440C>T (p.Arg814Trp), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

ClinVar n/a

CAID 1. CA2086638, 2. CA350439297

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs 21120950

CasePt9 male, 5do death, Italian

CasePresentingHPOs HP:0001987 (Hyperammonemia)

HPOsFreeText Hyperammonemia

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing: ammonia(2750[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.2429A>G (p.Gln810Arg), 2. NM_001875.4:c.3953T>A (p.Leu1318Ter) compound heterozygous

ClinVar n/a

CAID 1. CA350440293, 2. CA350439297

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs 12955727

CasePt5 male, 15mo death, Italian

CasePresentingHPOs HP:0001987, HP:0001254, HP:0001252, HP:0003572, HP:0003217 (Hyperammonemia, Lethargy, Hypotonia, Low plasma citrulline, High plasma glutamine)

HPOsFreeText neonatal severe hyperammonemia, mildly hypotonic, lethargy, low plasma citrulline, elevated glutamine

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(6[normal 16-40μmol/l]), glutamine(1500[normal 530–913μmol/l]) and ammonia(1214[normal< 75 μg/dl])

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4:c.1440_1441del (p.Thr481CysfsTer?), 2. NM_001122634.3:c.3004C>T (p.Arg1002Trp) compound heterozygous

ClinVar n/a

CAID 1. CA2086366, 2. CA64748170

gnomAD 1. 0.00001802(European (Non-Finnish), 0.000008153(Total), 2. n/a

VariantEvidence n/a

CaseAddInfo Older brother who died with post-mortem suspicion of CPSD or NAGS deficiency.

CasePMIDs 21120950

Family#PresentingHPOs HP:0001987 (Hyperammonemia)

HPOFreeText: Severe hyperammonemia

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity Italian

Race n/a

Family#PreviousTesting Elevated plasma ammonia in both siblings (3454 in Pt7 and 1858 in Pt8[normal<75 μg/dl]).

Family#Method1 PCR

Family#Method2 n/a

Family#GenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Affected 2

Unaffected n/a

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo n/a

ProbandLabel Pt7, Female, 5mo death

CasePresentingHPOs HP:0002283, HP:0100806, HP:0003572, HP:0003217 (Diffuse brain atrophy, Sepsis, Low plasma citrulline, High plasma glutamine)

CaseHPOsFreeText Severe hyperammonemia(2do), Severe diffuse brain atrophy on MRI(1mo), sepsis(5mo)

CasePreviousTesting Low plasma citruline(0[normal 16-40μmol/l]) and elevated glutamine(2488[normal 530–913 μmol/l])

Variant 1. NM_001875.4:c.1263+5G>C, 2. NM_001875.4:c.2429A>G (p.Gln810Arg)

ClinVar n/a

CAID 1. To register, 2. CA350440293

gnomAD n/a

VariantEvidence c.1263+5G>C causes a splice defect (Table 2)

FamilyAddInfo Brother, Pt8, died with similar clinical features and was diagnosed with CPS1D post-mortem.

FamilyPMIDs 12955727, 12655559

CasePt1 female, 3yo diagnosis, Italian

CasePresentingHPOs HP:0001508, HP:0002014, HP:0000505, HP:0002167, HP:0002013, HP:0001252, HP:0002321, HP:0001987, HP:0003217, HP:0002910, HP:0012747, HP:0100543, HP:0001256 (Failure to thrive, Diarrhea, Visual impairment, Speech impairment, Vomiting, Hypotonia, Vertigo, Hyperammonemia, Hyperglutaminemia, Elevated transaminases, Abnormal brain MRI signal intensity, Cognitive impairment, Mild ID)

HPOsFreeText normal psychomotor dev, failure to thrive and diarrhea(first years), visual/speech impairment, vomiting, hypotonia, vertigo(referred at 3y,2mo), , hyperammonemia, high glutamine, elevated transaminases, normal orotic levels, hyperintense signal in cortical-subcortical frontal region on brain MRI, cognitive impairment:IQ 53(3yo) mild ID(21yo)

CaseNotHPOs n/a

CasePreviousTesting Metabolic testing plasma citrulline(17.3[normal 16-40μmol/l]), glutamine(1244[normal 530–913μmol/l]) and ammonia(300[normal< 75 μg/dl]), elevated transaminases 350 UI/L, normal orotic levels, CPS1 residual enzyme activity "low" in liver biopsy.

CaseMethod1 PCR

CaseMethod2 n/a

CaseGenotypingMethod PCR using primers 80 nucleotides from the splice sites flanking the 38 exons of CPS1. Tested both patients and parents. (found in 12955727, Funghini et al. (2003))

Variant 1. NM_001875.4(CPS1):c.3047A>G (p.Asn1016Ser), 2. NM_001875.4:c.3500C>G (p.Thr1167Arg) compound het

ClinVar 1. 551211

CAID 2. CA350437190

gnomAD 1. 0.00006534(African), 0.000008123(Total) 2. n/a

VariantEvidence enzyme assay showing low CPS1 activity mentioned

CaseAddInfo n/a

CasePMIDs 21120950

Case# RQMR10_V-2

Demographics: Female, 20 yrs at report,

CasePresentingHPOs HP:0000729, HP:0001763, HP:0001761, HP:0001956, HP:0000577

CaseNotHPOs

CasePreviousTesting

CaseMethod1

CaseMethod2

CaseGenotypingMethod

Variant NM_017890.4:c.6879delT(p.Phe2293Leufs*24)

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

VariantEvidence The proband is homozygous for the variant. This variant introduces a frameshift, resulting in premature protein truncation. The variant was found to cosegregate with disease in the family and was not found in 293 healthy ethnicity-matched controls. It is reported in a heterozygous state at a frequency of 0.00003250 in South Asians in gnomAD.

CaseAddInfo

CasePMIDs

Case#: ATM02_V-3

Demographics: Male, 18 yrs at report

CasePresentingHPOs: HP:0000752, HP:0001581

CaseNotHPOs:

CasePreviousTesting:

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod:

Variant: NM_017890.4:c.6879delT

ClinVar:

CAID: CA4824093

gnomAD:

VariantEvidence: This variant has been reported in two apparently unrelated families of common ethnicity, and therefore likely founder mutation. Hence, the score is reduced from default.

CaseAddInfo:

CasePMIDs:

CaseF3:III-2: Female, Italy

CasePresentingHPOs: N/A

CaseAddInfo: Proband for F3

CaseF9: Female, Italy, 48 years diagnosis

CasePresentingHPOs: HP:0001873 (Thrombocytopenia)

HPOsFreeText: World Health Organization bleeding score is 0 (1 members); Mean platelet count is 117 ×10^9/L; Mean platelet volume is 14.4 fL, Mean platelet diameter is 3.3 μm

CaseAddInfo: N/A

CaseF1:III-1: Female, Italy

CasePresentingHPOs: HP:0001634 (Mitral valve prolapse)

CaseAddInfo: Proband for F1

Case#: Zahari_HA91

Demographics: Malay

CasePresentingHPOs: HP:0003125 Moderate hemophilia FVIII:C:1-5%

CaseNotHPOs:

CasePreviousTesting: No

CaseMethod1: PCR

CaseMethod2: Sanger

CaseGenotypingMethod: F8 coding regions (26 exons) including the intron/exon boundaries and the promoter regions were amplified using 26 sets of primers and subsequently sequenced.

Variant: NM_000132.3:c.6429+2T>A

ClinVar:

CAID: CA414899265

gnomAD: Not found

VariantEvidence: The splice donor site variant occurs in the intron 22. However, the proband did not carry the intron 22 inversion. The variant is scored default points.

CaseAddInfo:

CasePMIDs:

another individual with this variant, but PM3 has already been met and this variant is path without this additional case

Family Name: Family 4

FamilyPresentingHPOs: HP:0000705

FamilyNotHPOs:

CountryOrigin: Turkey

Ethnicity: Turkish

Race: n/a

FamilyPreviousTesting: candidate gene sequencing, array comparative genomic hybridization, or exome sequencing

FamilyGenotypingMethod: WES, haplotype analysis

Affected: 2

Unaffected: 2

Segregations: 1

PublishedLOD: n/a

eLOD: 0.85

AddSegregationInfo: non-consanguineous family

ProbandLabel: Family 4: III:1, female, 10 yo

Variant: NM_033068.2(ACP4):c.713C>T (p.Ser238Leu)

ClinVar or CAID: 374862, https://www.ncbi.nlm.nih.gov/clinvar/variation/374862/

genomAD: 8.127e-6, http://gnomad.broadinstitute.org/variant/19-51297008-C-T

FamilyAddInfo: parents unaffectd

CasePresentingHPOs: HP:0006297, HP:0011073, HP:0006316

CasePresentingHPOTerm: hypoplasia of dental enamel, black staining of cervical teeth, large dental spacing due to thin enamel

CaseNotHPOs: HP:0010299

AddCaseInfo:

VariantEvidence:

Case#: Family 1-III:2

CaseHPOs: HP:0003563, HP:0001397 (decreased LDL cholesterol, hepatic steatosis)

CaseNotHPOs: HP:0002910, HP:0000819 (elevated liver enzymes, diabetes)

CasePreviousTesting: TC 104 mg/dl, LDL-C 7 mg/dl, HDL-C 91 mg/dl, TG 31 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

ClinVar: N/A

CAID: CA346011071

gnomAD: 0.000008796 (European non-Finnish)

Case#: Family IV-I:1, male, 84 year old man

CaseHPOs: HP:0003563, HP:0001397 (decreased LDL cholesterol, liver steatosis)

CaseNotHPOs: HP:0000819 (Diabetes)

CasePreviousTesting: TC 106 mg/dl, LDL-C 33 mg/dl, HDL-C 60 mg/dl, TG 60 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

CaseGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation and co-segregation analysis among family members.

Variant: NM_000384.2:c.11153C>G (p.Ser3718Ter), heterozygous

CAID: CA345983128

gnomAD: Absent

Variant evidence: APOB- p.Ser3718* mutations lead to the formation of expected truncated ApoB forms (ApoB-81) of 418 kDa (Fig. 1C, right panel) that can be secreted by the liver and lipidated.

Case#: Family 1-III:1, male, 17 years, son of Family 1-III:2

CaseHPOs: HP:0003563 (decreased LDL cholesterol)

CaseNotHPOs: HP:0000819 (Diabetes mellitus)

CasePreviousTesting: TC 98 mg/dl, LDL-C 14 mg/dl, HDL-C 79 mg/dl, TG 2 mg/dl (see additional values in Table 1). Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

ClinVar: N/A

CAID: CA346011071

gnomAD: 0.000008796 (European non-Finnish)

Case#: Family 1- II:2, female, 49 years

CaseHPOs: HP:0003563 (decreased LDL cholesterol)

CaseNotHPOs: HP:0001397, HP:0000819 (liver steatosis, diabetes)

CasePreviousTesting: TC 143 mg/dl, LDL-C 20 mg/dl, HDL-C 120 mg/dl, TG 18 mg/dl (see additional values in Table 1). ApoB100 <10 mg/dl (normal range 49-88) (Supplemental data) Normal ranges- total cholesterol (TC) 92-234 mg/dl, LDL-cholesterol (LDL-C) 136-174 mg/dl, HDL-cholesterol (HDL-C) 60-95 mg/dl), triglyceride (TG) 35-132 mg/dl.

Variant: NM_000384.2:c.2533C>T (p.Gln845Ter), heterozygous

ClinVar: N/A

CAID: CA346011071

gnomAD: 0.000008796 (European non-Finnish)

FamilyName: Family 1

FamilyPresentingHPOS: HP:0001257, HP:0000639, HP:0001251

FamilyNotHPOs:

CountryOrigin: India

Ethnicity: n/a

Race: n/a

FamilyPreviousTesting: MRI showed brain hypomyelination.

FamilyGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Affected: 3

Unaffected:

Segregations:

PublishedLOD:

eLOD:

AddSegregationInfo:

ProbandLabel: III-1, Female, 27 yo

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

FamilyAddInfo:

FamilyPMIDs:

Case#: Family 1, Individual III-3, Male, 8yo, dx at 6mo

CasePresentingHPOs: HP:0000639, HP:0012389, HP:0001270, HP:0002078, HP:0002070, HP:0001260, HP:0007256

CaseNotHPOs:

CasePreviousTesting: MRI

CaseGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

VariantEvidence:

CaseAddInfo: Wheelchair bound at 8 yo.

CasePMIDs:

FamilyName: Family 3 (individuals 6 and 7)

FamilyPresentingHPOS: HP:0000639, HP:0012736, HP:0001252, HP:0001257

FamilyNotHPOs:

CountryOrigin: Saudi Arabia

Ethnicity: n/a

Race: n/a

FamilyPreviousTesting: MRI showed brain hypomyelination

FamilyGenotypingMethod: combination of homozygosity mapping and WES, autozygosity mapping

Affected: 3

Unaffected:

Segregations:

PublishedLOD:

eLOD:

AddSegregationInfo: consanguineous family

ProbandLabel: IV-6 (individual 6), Female, 6yo, dx at 1mo

Variant: NM_177400.2(NKX6-2):c.487C>G (p.Leu163Val)

ClinVar: 430623, https://www.ncbi.nlm.nih.gov/clinvar/variation/430623/

gnomAD: n/a

CasePresentingHPOs:

CasePresentingHPOTerm:

CaseNotHPOs:

AddCaseInfo:

VariantEvidence:

Case#: 2, female 4 days (onset), 4 y 3 mo (current), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012088, HP: 0011968, HP: 0001276, HP: 0001941, HP: 0002543, HP: 0011342 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, hypertonia, acidosis, abnormal globus pallidus MRI signals, mild global developmental delay)

HPOsFreeText: Poor response to light and sound, abnormal MRI signals in frontal lobes, Blood ammonia: 95 uM, Hemoglobin: 117 g/L, Leucin: 745.01 uM, Valine: 526.40 uM, Isoleucine: 181.06 uM, Alloisoleucine: 69.45 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo:

CasePreviousTesting: n/a

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000709.3(BCKDHA): c.659C>T (p.Ala220Val)

ClinVar: 93367

CAID: n/a (because this doesn't need to be included if it is in ClinVar right?)

gnomAD: not in gnomAD

Case#: 7, female, 2 y 5 m (current), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012751, HP: 0012696 (elevated A keto acids in urine, abnormal signals in cerbral ganglia, abnormal thalamic MRI signal intensity)

HPOsFreeText: leucin: 621.72 uM, valine: 594.15 uM, isoleucine: 225.21 uM, Alloisoleucine: 76.62 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: detected by newborn screening, unsure cis or trans

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_183050.3:c.482T>G (p.Val161Gly), NM_183050.3:c.508C>T (p.Arg170Cys)

ClinVar: not found, 96590

CAID: CA364657700, CA224301

gnomAD: not found, 0.00001759 (European, non-Finnish)

Case# Subject 5, F, 7yo onset, Hispanic

CasePresentingHPOs HP:0001270, HP:0000750, HP:0005184, HP:0001250, HP:0008942, HP:0003236, HP:0001664, HP:0004756, HP:0011675, HP:0001943, HP:0002151, HP:0003201, HP:0001249, HP:0002913, HP:0003324, HP:0001695, HP:0006956

HPOcont: Motor Delay, Speech Delay, Prolonged QTc interval, Seizures, Elevated CPK, Torsade de pointes, Ventricular tachycardia, Arrhythmia, Hypoglycemia, Elevated Lactate, Acute rhabdomyolysis, Intellectual Disability, Myoglobinuria, Generalized Muscle Weakness, Cardiac Arrest, Enlarged lateral ventricles

HPOFreeText: speech and motor delay, prolonged QTc interval, seizures, prior to her acute presentation. (7 years) acute rhabdomyolysis, high CPK and myoglobinuria. (13 years) muscle weakness, cardiac arrest, torsade de pointes from prolonged QTc interval, ventricular tachycardia with recurrent pulseless arrest and arrhythmia, able to ambulate.

CaseNotHPOs n/a

CasePreviousTesting highest CPK (60,000 U/L), 953 U/L for AST, 540 U/L for ALT, and CPK-MB of 291 U/L.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, parents confirmed heterozygotes

CasePMIDs n/a

Case# F1_IV:5, M, 6.5yo report, Saudi Arabia

CasePresentingHPOs HP:0001263, HP:0008947, HP:0001257, HP:0000486, HP:0000639, HP:0004326, HP:0000252

HPOcont: Global developmental delay, Infantile muscular hypotonia, Spasticity, Strabismus, Nystagmus, Cachexia, Microcephaly

Free text: "At 4.5 years of age, he was cachectic with a weight of 8.1 kg (−5.2 SD), short with a length of 89 cm (−3.7 SD), and microcephalic with a head circumference of 46 cm (−3.2 SD). He was inattentive and had no visual tracking ability as well as bilateral strabismus and nystagmus. He had severe axial hypotonia and appendicular hypertonia with spasticity."

CaseNotHPOs HP:0001250

NotHPOcont: Seizures

CasePreviousTesting "Plasma lactate, ammonia, uric acid, lipid profile, tandem mass spectrometry (MS), urine organic acids, plasma amino acids, and congenital disorder of glycosylation screenings did not reveal any abnormality. Chromosomal analysis and microarray were unremarkable. Glycosaminoglycans and oligosaccharides in the urine were normal. Lysosomal enzyme analysis was unremarkable. HEXB and SMN1 mutation analysis did not reveal pathogenic mutations. Brain MRI showed mild diffuse brain atrophy, and MRS (magnetic resonance spectroscopy) showed a mild reduction of the N-acetylaspartate peak but a normal lactate peak. Skeletal survey showed diffuse osteopenia."

CaseMethod1 Exome sequencing

CaseMethod2 Sanger

CaseGenotypingMethod autozygome filtering after exome sequencing, confirmed with sanger

Variant NM_032504.1(UNC80):c.3793C>T (p.Arg1265Ter)

ClinVar 219188

gnomAD 0.00004175(Latino), 0.000006613(Overall)

CaseAddInfo His first-cousin parents had two sons who died at 4 and 6 years of age with a reportedly identical phenotype of profound static encephalopathy and no seizures. The index individual has two living brothers and two sisters who are all healthy