CaseOPM-1: Male, Taiwan, Birth diagnosis

HPOsFreeText: GAA (MS/MS) enzyme activity at 0.97 umol/hr/L

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.1935C>A (p.Asp645Glu)

ClinVar: 4029 https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

gnomAD: East Asian 1.729e-3, Overall 1.240e-4 http://gnomad.broadinstitute.org/variant/17-78086721-C-A

Variant2: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: One Pompe Mutation, Nomenclature indicates Variants 1 and 2 are in cis and the other allele is Wildtype

CaseIP2-6: Female, Taiwan, Birth diagnosis

HPOsFreeText: GAA (MS/MS) enzyme activity at 0.02 umol/hr/L, Serum CK at 709 U/L

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.1935C>A (p.Asp645Glu)

ClinVar: 4029 https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

gnomAD: East Asian 1.729e-3, Overall 1.240e-4 http://gnomad.broadinstitute.org/variant/17-78086721-C-A

Variant2: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: Infantile Onset Pompe Disease, Nomenclature indicates that Variant 1 and 2 are in cis and the patient is homozygous for this allele, 2 more patients also have the same genotype

Case60

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.1445C>G (p.Pro482Arg)

CAID: CA401366794 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.1445C%3EG

gnomAD: Not in gnomAD

Variant2: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

CaseAddInfo: Adult Late Onset Pompe Disease, 1 person more with the same genotype

CaseLOPD-12: 2 weeks diagnosis

HPOsFreeText: GAA activity 2.0 (nmol · h−1 · mg−1), Mean percentage of normal 2.8%

GenotypingMethod: Newborn Screening Panels

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Chromosomal code not provided and typo likely

Variant2: NP_000143.2:p.V350 mol/L

ClinVar: N/A

gnomAD: N/A

CaseAddInfo: Late Onset Pompe Disease

Case19: Male, 57 years report

HPOsFreeText: 8 years of ERT completed, 6 Minute Walking Test at 273 meters, Forced Vital Capacity at 77%

GenotypingMethod: GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 http://www.ncbi.nlm.nih.gov/clinvar/variation/4027

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.1819_1836del (p.Gly607_His612del )

CAID: CA658795266 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.1819_1836del

gnomAD: Not in gnomAD

CaseAddInfo: Late Onset Pompe Disease

CaseCII-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 1515 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.194T>C (p.Ile65Thr)

ClinVar: 636 https://www.ncbi.nlm.nih.gov/clinvar/variation/636/

gnomAD: 0.0005574, https://gnomad.broadinstitute.org/variant/12-102894893-A-G?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.1065+1G>A

ClinVar: 102501 https://www.ncbi.nlm.nih.gov/clinvar/variation/102501/

gnomAD: 0.00004622, http://gnomad.broadinstitute.org/variant/12-103238113-C-T

CaseAII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 375 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

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

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseBII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 270 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.688G>A (p.Val230Ile)

ClinVar: 102784 https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/

gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?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

Case 10 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.658_660delAAG (p.Lys220del)

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) also homozygous for variant

Case 4 (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.467G>A (p.Gly156Asp)

ClinVar: 554696

CAID: CA340133108

gnomAD: not in gnomAD

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info given, sibling (fetus) carrier of both variants. variant 2 is not in the table of 31 variants (Table 1).

Case61(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.599G > A (p.Trp200Ter)

ClinVar: n/a

CAID: n/a

gnomAD: 0.000008829 (European non-Finnish)

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.W203X paternal variant

Case 21 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.467G > A (p.Gly156Ala)

ClinVar: n/a

in ClinVar it says that this nucleotide change corresponds to p.Gly156Asp (p.G156D), which is the paternal variant listed in case 4 that I mentioned was not also listed in Table 1 (list of all 31 variants found). I am wondering if p.G156A is a typo in case 21 Table 2 and Variant 18 Table 1

CAID: CA340133108

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for p.G156A (possible typo??) maternal variant

Case52(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.658_660delAAG (p.Lys220del)

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

Variant2: NM_015506.2(MMACHC):c.365A > T (p.His121Leu)

ClinVar: n/a

CAID: n/a

gnomAD: n/a

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.K220del maternal variant

Case 26 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.440_441delGT

ClinVar: n/a

CAID: CA312741

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for p.W203X paternal variant

Case32 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.666C > A (p.Tyr222Ter)

ClinVar: 496436

CAID: CA827827

gnomAD: 0.00006537 (South Asian)

Variant2: NM_015506.2(MMACHC):c.80A>G (p.Gln27Arg)

ClinVar: 552467

CAID: CA827620

gnomAD: not in gnomAD

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.Y222X maternal variant

Case 17 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.445_446insA (p.Cys149Ter)

ClinVar: n/a

CAID: n/a

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.567dupT (p.Ile190Tyrfs*13)

ClinVar: 556708

CAID: CA522810899

gnomAD: [0.0001024] (https://gnomad.broadinstitute.org/variant/1-45974604-G-GT) (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for c.567dupT paternal variant

CaseF1P: Female, 8 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family 1, Variant is demonstrated to activate a cryptic splice site and abolish the canon splice site leading to a premature termination and nonsense-mediated decay

CasePreviousTesting: Blood phenylalanine before treatment was 1174 μmol/l, Blood tyrosine before treatment was 33 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.169-2A>G

ClinVar: 555212 https://www.ncbi.nlm.nih.gov/clinvar/variation/555212/

gnomAD: 0.00003267, http://gnomad.broadinstitute.org/variant/12-103288698-T-C

CaseF6P: 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, Predicted to undergo NMD

CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was N/A 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(PAH):c.526C>T (p.Arg176Ter)

ClinVar: 102723 https://www.ncbi.nlm.nih.gov/clinvar/variation/102723/

gnomAD: 0.00008012, http://gnomad.broadinstitute.org/variant/12-103249094-G-A

Case3b: Female, 9 d at initiation of follow up, East Indian ancestry, sibling of Case 3a (Family 1)

HPOsFreeText: NBS C4-acylcarnitine 2.1 umol/L, Plasma C4-acylcarnitine 2.47 umol/L, urine C4-acylcarnitine 21.66 mmol/mol creatinine, Urine C4/C3 ratio 42

NotHPOsFreeText: normal urine isobutyrylgycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3b (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.867C>A (p.His289Gln)

ClinVar: 5358

CAID: CA117441

gnomAD: not in gnomAD

CaseAddInfo: homozygous mutations, no data for SCAD gene variants

Case8: Male, 6 wks at initiation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 1.8 umol/L, plasma C4 acylcarnitine 1.52 umol/L, in vitro probe isoC4-acylcarnitine 0.187 umol/ g protein, in vitro probe C4-acylcarnitine 0.573 umol/g protein, elevated urine C4-acylcarnitine 25.09 mmol/mol creatinine, Urine C4/C3 ratio 88

NotHPOsFreeText: normal urine isobutyryglycine

CaseAddInfo: unremarkable clinical condition

Case8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2(ACAD8):c.512C>G (p.Ser171Cys)

ClinVar: 95589

CAID: CA223125

gnomAD: 0.02252 (European non-Finnish)

Variant2: NM_014384.2(ACAD8):c.455T>C (p.Met152Thr)

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygote specified allele 1 and 2, but not maternal and paternal. Potential splice-site alteration at exon 3(+3A>G). ACADS (SCAD-deficient) gene variants 625G>A/625G>A.

Case765: Female, 9 years report, Spain

CasePresentingHPOs: HP:0003153, HP:0001256, HP:0007359, HP:0012000 (Cystathioninuria, Mild mental retardation, Partial seizures, EEG with generally recognized spikes)

HPOsFreeText: Elevated urine cystathionine (750 umol/g creatine; reference <46) and Elevated tHcys in urine (61 umol/g creatine; reference <20), Elevated plasma tHcys (19 umol/l; reference <7.5), Elevated plasma cystathionine (10 umol/l; reference =0), Post treatment normal urine cystathionine (34 umol/g creatine)

CaseNotHPOs: HP:0003345 (Glutathione synthetase deficiency)

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

CaseREU3: Male, 6 yrs report, United Kingdom

CasePresentingHPOs: HP:0001337, HP:0001263, HP:0000717, HP:0001382, HP:0012120 (Tremor, Global developmental delay, Autism, Joint hypermobility, Methylmalonic aciduria)

HPOsFreeText: Malonic aciduria

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant

CasePreviousTesting: All participants had undergone multiple standard and specialized biochemical tests, invasive procedures (e.g. muscle and/or skin biopsy, lumbar puncture) and targeted gene testing; MRI head not performed

CaseGenotypingMethod: 16 broad classes of IEM was target enriched and sequenced. Any suspected pathogenic variants were confirmed with Sanger sequencing.

Variant: NM_001243279.3:c.1453A>C (p.Ser485Arg)

CAID: CA397148172, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397148172

gnomAD: Not in gnomAD

CaseGM01566: Female, 16 years report, Caucasian, Europe

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a compound heterozygote for this variant, 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: CTH, 1-BP DEL, 1220C AKA: NM_001902.5:c.1064del (p.Thr355Ilefs*19)

ClinVar: 2938 https://www.ncbi.nlm.nih.gov/clinvar/variation/2938/

gnomAD: European (Non-Finnish) 1.551e-4, Overall 8.845e-5 https://gnomad.broadinstitute.org/variant/1-70904381-AC-A

CaseBI2K: N/A

CasePresentingHPOs: HP:0001875, HP:0001644, HP:0003756 (Neutropenia, Dilated cardiomyopathy, Skeletal myopathy)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseGenotypingMethod: Five genes noted to have high heart and skeletal muscle expression were sequenced and ORFs created. After PCR amplification and direct sequencing of the TAZ gene (G4.5.), a unique missense variant was found in this proband.

CasePreviousTesting: N/A

CaseAddInfo: N/A

Variant: NM_000116.5(TAZ):c.239-1G>C

ClinVar: 11102, https://www.ncbi.nlm.nih.gov/clinvar/variation/11102/

gnomAD: Not in gnomAD

Case3: Female, 1y 5m, Chinese

HPOsFreeText: (at 21 days) 1.96 C4, 0.17 C4/C2, 2.09 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case3 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

CaseAddInfo:

Case6: Male, 8y 11m, Chinese, part of Family 1

CasePresentingHPOs: HP:0000750, HP:0001328 (speech delay, learning disability)

HPOsFreeText: (at 8y 8m) 1.07 C4 umol/L, 0.13 C4/C2, 1.20 C4/C3

Case6 (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: older brother of patient 5. Had not undergone expanded NBS at birth but presented with symptoms by age 8 and was diagnosed later since his younger sister has IBDHD. Trans heterozygous, inherited one allele from each parent

Case1: Male, 5 years onset, African

CasePresentingHPOs: HP:0410020, HP:0003750, HP:0030234 (Fish odor, Muscle fatigue, Highly elevated creatine phosphokinase)

HPOsFreeText: Increased fish odor under stress or effort, Elevated plasma creatine kinase (1066 U/L; reference 30–270), Riboflavin (10 mg/day) had no effect, High N,N-dimethylglycine in urine (449 mmol DMG/mol; over 20x normal)

CaseNotHPOs: HP:0001249, HP:0040126, HP:0003138, HP:0040087, HP:0010919, HP:0010901, HP:0003614, HP:0001871, HP:0001410 (Intellectual disability, Abnormal serum cobalamin level, Increased blood urea nitrogen, Abnormal serum folate, Abnormality of homocysteine metabolism, Abnormality of methionine metabolism, Trimethylaminuria, Hematological abnormality, Liver dysfunction)

NotHPOsFreeText: Normal serum cobalamin (222 pmol/L; reference 150–400) and urea (5 mmol/L; reference 2.5–7.5), Normal plasma folate (9.7 nmol/L; reference 4–15) and homocysteine (12 μmol/L; reference 8–18)

CasePMIDs: 10767172, 10102904

CaseAddInfo: Consanguinity of the parents is unknown, Brothers, sisters, and the two sons of the patient were without signs or symptoms, Patient is homozygous for this mutation

CasePreviousTesting: Nuclear magnetic resonance (NMR) spectroscopy, Conventional metabolic screening techniques, Gas chromatography (GC) analysis, Analysis of the very-long-chain fatty acids and a carnitine ester profile in serum, Amino acid and organic acid analyses of blood and urine

CaseGenotypingMethod: cDNA was prepared from the patient and control fibroblast cultures. PCR amplification was performed and the DMGDH gene was sequenced. After the mutation was confirmed, the area around it was again amplified and sequenced.

Variant: NM_013391.3:c.326A>G (p.His109Arg)

ClinVar: 4742 https://www.ncbi.nlm.nih.gov/clinvar/variation/4742/

gnomAD: African 4.737e-3, Overall 5.205e-4 https://gnomad.broadinstitute.org/variant/5-78351682-T-C

CaseEPI4Kn2: Female, 1 month onset

CasePresentingHPOs: HP:0002521, HP:0011167, HP:0032794, HP:0000618, HP:0003089, HP:0000473, HP:0003487, HP:0032988, HP:0008936, HP:0001276, HP:0010864 (Hypsarrhythmia, Focal tonic seizure, Myoclonic seizure, Blindness, Hamstring contractures, Torticollis, Babinski sign, Persistent head lag, Muscular hypotonia of the trunk, Hypertonia, Severe intellectual disability)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263 (Global developmental delay)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: Currently on vigabatrin, topiramate, and oxcarbazepine; Previously on phenobarbitone and levetriacetam; Bifrontal central frequent discharges on EEG; Normal brain imaging; No confirmed genetic or metabolic diagnosis, and no history of congenital TORCH infection, premature birth (before 32 weeks gestation), neonatal hypoxic-ischemic encephalopathy or neonatal seizures, meningitis/encephalitis, stroke, intra-cranial hemorrhage, significant head trauma, or evidence of acquired epilepsy

CaseGenotypingMethod: Exome sequencing was performed from primary DNA in parental leukocytes. Coding regions of the genome were sequenced in a trio in order to determine which loci bearing de novo mutations were present according to specifications. All candidate de novo variants were confirmed with Sanger sequencing of the proband and parents.

Variant: NM_004171.4(SLC1A2):c.244G>C (p.Gly82Arg)

ClinVar: 254265, https://www.ncbi.nlm.nih.gov/clinvar/variation/254265/

gnomAD: Not in gnomAD

CaseFZ2: Male, Finland, 2.9 yrs deceased

CasePresentingHPOs: HP:0001511, HP:0008897, HP:0001999, HP:0000973, HP:0100678, HP:0000963, HP:0010648, HP:0001388, HP:0100790, HP:0001374, HP:0001181, HP:0001762, HP:0002650, HP:0000938, HP:0000270, HP:0002645, HP:0012443, HP:0025356, HP:0008872, HP:0001252, HP:0001348, HP:0000518, HP:0002677, HP:0000325, HP:0011220, HP:0000337, HP:0000411, HP:0000369 (Intrauterine growth retardation, Postnatal growth retardation, Abnormal facial shape, Cutis laxa, Premature skin wrinkling, Thin skin, Dermal translucency, Joint laxity, Hernia, Congenital hip dislocation, Adducted thumb, Talipes equinovarus, Scoliosis, Osteopenia, Delayed cranial suture closure, Wormian bones, Abnormality of brain morphology, Psychomotor retardation, Feeding difficulties in infancy, Muscular hypotonia, Brisk reflexes, Cataract, Small foramen magnum, Triangular face, Prominent forehead, Broad forehead, Protruding ear, Low-set ears)

HPOsFreeText: Typical facial gestalt, Reduced collagen type 1 and 3 production

CaseNotHPOs: HP:0000252, HP:0005116, HP:0000486 (Microcephaly, Arterial tortuosity, Strabismus)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed de novo in this and two other cases 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. qPCR was used to exclude the presence of a exonic deletion and 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.412C>T (p.Arg138Trp)

ClinVar: 217259 https://www.ncbi.nlm.nih.gov/clinvar/variation/217259/

gnomAD: Not in gnomAD

CaseFZ5: Male, Mexico, 4 yrs report

CasePresentingHPOs: HP:0001511, HP:0008897, HP:0001999, HP:0000973, HP:0100678, HP:0000963, HP:0010648, HP:0001388, HP:0001374, HP:0001181, HP:0001762, HP:0002650, HP:0000938, HP:0000270, HP:0025356, HP:0001252, HP:0001348, HP:0000518, HP:0000325, HP:0011220, HP:0000337, HP:0000411, HP:0000369, HP:0000252 (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, Talipes equinovarus, Scoliosis, Osteopenia, Delayed cranial suture closure, Psychomotor retardation, Muscular hypotonia, Brisk reflexes, Cataract, Triangular face, Prominent forehead, Broad forehead, Protruding ear, Low-set ears, Microcephaly)

HPOsFreeText: Typical facial gestalt

CaseNotHPOs: HP:0005116, HP:0000486, HP:0100790, HP:0002645, HP:0012443 (Arterial tortuosity, Strabismus, Hernias, Wormian bones, Abnormality of brain morphology)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed de novo in this case with one other maternally-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. qPCR was used to exclude the presence of a exonic deletion and 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>T (p.Arg138Leu)

ClinVar: 217261 https://www.ncbi.nlm.nih.gov/clinvar/variation/217261/

gnomAD: Not in gnomAD

CaseLE25: Male, 7 yrs report

CasePresentingHPOs: HP:0000639 (Nystagmus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants confirmed in-trans via parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.634G>A (p.Val212Met)

CAID: CA397135749, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397135749

gnomAD: 0.00004778, https://gnomad.broadinstitute.org/variant/16-89167723-G-A

Variant2: NM_001243279.3(ACSF3):c.1470G>C (p.Glu490Asp)

ClinVar: 377432, https://www.ncbi.nlm.nih.gov/clinvar/variation/377432/

gnomAD: 0.001502, https://gnomad.broadinstitute.org/variant/16-89211778-G-C

CaseLE17: Male, 7 yrs report

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants not confirmed in-trans due to lack of parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.774_775del (p.Trp259Glyfs*10)

CAID: CA1139532418, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139532418

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

CaseE: Male, French, Germany

CasePresentingHPOs: HP:0010896, HP:0010897 (Hypersarcosinemia, Hypersarcosinuria)

HPOsFreeText: Elevated blood Sarcosine (192 μmol/l; reference 0-9), Elevated urine Sarcosine (645 μmol/mmol; reference 0-36)

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Phase of the variants are unknown

CasePreviousTesting: N/A

CaseGenotypingMethod: DNA was extracted from the probands and immediate family. The whole coding region and the exon-intron boundaries of the SARDH gene was then amplified and sequenced.

Variant1: NM_007101.3:c.1540C>T (p.Arg514Ter)

ClinVar: 39451 https://www.ncbi.nlm.nih.gov/clinvar/variation/39451/

gnomAD: Latino 2.154e-4, Overall 1.120e-4 https://gnomad.broadinstitute.org/variant/9-136570084-G-A

Variant2: NM_007101.3:c.2167C>T (p.Arg723Ter)

ClinVar: 39450 https://www.ncbi.nlm.nih.gov/clinvar/variation/39450/

gnomAD: African 9.899e-5, Overall 5.729e-6 http://gnomad.broadinstitute.org/variant/9-136536816-G-A

CaseD: Male, French, Quebec

CasePresentingHPOs: HP:0010896, HP:0010897 (Hypersarcosinemia, Hypersarcosinuria)

HPOsFreeText: Elevated blood Sarcosine (229 μmol/l; reference 0-9), Elevated urine Sarcosine (1213 μmol/mmol; reference 0-36)

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: DNA was extracted from the probands and immediate family. The whole coding region and the exon-intron boundaries of the SARDH gene was then amplified and sequenced.

Variant: NM_007101.3:c.860C>T (p.Pro287Leu)

ClinVar: 39449 https://www.ncbi.nlm.nih.gov/clinvar/variation/39449/

gnomAD: European (Finnish) 1.692e-4, Overall 1.032e-4 http://gnomad.broadinstitute.org/variant/9-136594942-G-A

CaseDO2: Male, Italy, 1 day onset

CasePresentingHPOs: HP:0001252, HP:0002045, HP:0002033, HP:0001958, HP:0001987, HP:0002151, HP:0001942, HP:0003648, HP:0001640, HP:0001644, HP:0001667, HP:0003324, HP:0001270, HP:0001510, HP:0001875, HP:0002098, HP:0001649, HP:0000969, HP:0001712, HP:0012666, HP:0003535, HP:0001397, HP:0001706 (Muscular hypotonia, Hypothermia, Poor suck, Nonketotic hypoglycemia, Hyperammonemia, Increased serum lactate, Metabolic acidosis, Lacticaciduria, Cardiomegaly, Dilated cardiomyopathy, Right ventricular hypertrophy, Generalized muscle weakness, Motor delay, Growth delay, Neutropenia, Respiratory distress, Tachycardia, Edema, Left ventricular hypertrophy, Severely reduced ejection fraction, 3-Methylglutaconic aciduria, Hepatic steatosis, Endocardial fibroelastosis)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001875 (Neutropenia)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: Birth weight of 2830 g; Unremarkable family history; See "Results" for exact metabolic values

CaseGenotypingMethod: Genomic DNA was isolated from whole blood and the TAZ gene was amplified and directly sequenced.

Variant: NM_000116.4:c.541+1G>A

CAID: CA415183775, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA415183775

gnomAD: Not in gnomAD

CaseDO1: Male, Italy, 3 days onset

CasePresentingHPOs: HP:0011968, HP:0001254, HP:0001252, HP:0002045, HP:0001640, HP:0012664, HP:0002119, HP:0001943, HP:0002910, HP:0003236, HP:0001942, HP:0002151, HP:0003542, HP:0100493, HP:0008315, HP:0011936, HP:0003648, HP:0003344, HP:0003535, HP:0001508, HP:0001270, HP:0001649, HP:0001875, HP:0001644, HP:0002375, HP:0001706, HP:0001397 (Poor feeding, Lethargy, Muscular hypotonia, Hypothermia, Cardiomegaly, Reduced ejection fraction, Ventriculomegaly, Hypoglycemia, Elevated hepatic transaminase, Elevated serum creatine kinase, Metabolic acidosis, Increased serum lactate, Increased serum pyruvate, Hypoammonemia, Decreased plasma free carnitine, Decreased plasma total carnitine, Lacticaciduria, 3-Methylglutaric aciduria, 3-Methylglutaconic aciduria, Failure to thrive, Motor delay, Tachycardia, Neutropenia, Dilated cardiomyopathy, Hypokinesia, Endocardial fibroelastosis, Hepatic steatosis)

HPOsFreeText: N/A

CaseNotHPOs: HP:0002240, HP:0002919 (Hepatomegaly, Ketonuria)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: Birth weight of 2780 g; Three maternal great-uncles and two maternal second cousins died in the first years of life; See "Results" for exact metabolic values;

CaseGenotypingMethod: Genomic DNA was isolated from whole blood and the TAZ gene was amplified and directly sequenced.

Variant: NM_000116.5(TAZ):c.589G>A (p.Gly197Arg)

ClinVar: 11105, https://www.ncbi.nlm.nih.gov/clinvar/variation/11105/

gnomAD: Not in gnomAD

Case2: Female, Iran, 18 mo (age at diagnosis)

CasePresentingHPOs: HP:0003324, HP:0001254, HP:0004789, HP:0002039, HP:0002015, HP:0002098, HP:0001508, HP:0002360, HP:0001298 (generalized muscle weakness, lethargy, milk intolerance, anorexia, swallowing difficulty, breathing difficulties, failure to thrive, sleep disturbance, encephalopathy)

HPOsFreeText: unspecified abnormalities in sitting and speech

Case (Level 2)

CasePreviousTesting: elevated propionylcarnitines (4.24 umol/L), Urine MMA (BT) 2200 umol/mmol creatinine, Urine MMA (AT) 40.0 umol/mmol creatinine

CaseMethod1: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.2125-3C>G

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

CaseAddInfo: consanguineous parents. Treated for MMA with L-carnitine, biotin, and vitamin B12. Died at the age of 3.5 y. homozygous mutation.

Case3: Female, Iran, 3 d (age at diagnosis)

CasePresentingHPOs: HP:0002883, HP:0001254, HP:0004789, HP:0002039, HP:0001290, HP:0001941, HP:0001508, HP:0001298, HP:0002019 (rapid breathing, lethargy, milk intolerance, anorexia, hypotonia, acidosis, failure to thrive, encephalopathy, constipation)

Case (Level 2)

CasePreviousTesting: elevated propionylcarnitine (61 umol/L), Urine MMA (BT) 1950 umol/mmol creatinine, Urine MMA (AT) 35.0 umol/mmol creatinine.

CaseMethod1: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.2125-3C>G

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

CaseAddInfo: Consanguineous parents. Treated for MMA with L-carnitine, sodium benzoate, and vitamin B12. Currently 6 y, with moderately delayed development. Deceased infant sibling with similar symptoms, not genotyped. homozygous mutation.

GroupPresentingHPOs: HP:0002013, HP:0001263 (vomiting, developmental delay)

HPOsFreeText: increased urinary excretion of methylmalonate and methylcitric acids. Elevated propionylcarnitine.

NumberMales: 0

NumberFemales: 3

CountryOrigin: Iran

AgeRange: 3 d-22 mo (age at diagnosis)

TotalNumber: 3

FamilyInfo: 3

NoFamily: 0

GroupAddInfo: All probands are products of consanguineous marriages.

Group (Level 2)

VariantCount: 3

NonVariant: 0

OtherVariant: 0

GroupPreviousTesting: urine organic acid analysis with urease treatment extraction with gas chromatography-mass spectrometry, after showing high levels of propionylcarnitine (umol/L) through tandem mass spectrometry

GroupMethod1: PCR

GroupGenotypingMethod: Genomic DNA was extracted from peripheral blood samples by the salting out method. MUT gene was analyzed by PCR and sequencing of both DNA strands of the entire coding region and highly-conserved exon-intron splice junctions. Reference sequence is NM_000255.3. Amplification was confirmed by electrophoresis, and products of the sequencing reaction were analyzed by DNA Sequencher 4.7. The phase of the mutation was confirmed by sequencing DNA from the patients parents.

Case1: Female, Iran, 22 mo (age at diagnosis)

CasePresentingHPOs: HP:0001250, HP:0001290, HP:0001941, HP:0002019, HP:0002355, HP:0001344 (seizures, generalized hypotonia, acidosis, constipation, difficulty walking, absent speech)

HPOsFreeText: congenital malformations

Case (Level 2)

CasePreviousTesting: elevation of propionylcarnitine (9.8 umol/L0, Urine MMA (BT) 2800 umol/mmol creatinine, Urine MMA (AT) 47.0 umol/mmol creatinine

CaseMethod1: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.2125-3C>G

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

CaseAddInfo: consanguineous parents, treated for MMA with phenobarbital, L-carnitine, and vitamin B12. Died at 3 y of age. homozygous mutation.

Case1: Male, 3 months onset, China, Asian

CasePresentingHPOs: HP:0011968, HP:0001290, HP:0001263, HP:0001508, HP:0000023, HP:0002793, HP:0004691, HP:0001999, HP:0000369, HP:0000218, HP:0000954, HP:0006802, HP:0100952, HP:0002079, HP:0002151, HP:0012736, HP:0002421 (Poor feeding, Generalized hypotonia, Psychomotor delay, Poor weight gain, Inguinal hernia, Abnormal pattern of respiration, 2-3 toe syndactyly, Dysmorphic facies, Low-set ears, High-arched palate, Transverse palmar crease, Abnormality of the anterior horn cells, Enlarged lateral sulcus, Thinning of the corpus callosum, Increased serum lactate, Profound global developmental delay, Poor head control)

HPOsFreeText: 3 kg birth weight, Breath-holding spells, The parameters at 5 months were as follows: weight, 4 kg (<0.4th percentile); length, 58 cm (<0.4th percentile), head circumference, 36.5 cm (<0.4th percentile), Enlarged anterior portion of bilateral ventricles and thinning surrounding whiter, Abnormal infant EEG

CaseNotHPOs: HP:0001946, HP:0003542, HP:0000364, HP:0003457 (Ketosis, Increased serum pyruvate, Hearing abnormality, EMG abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous, parental heterozygosity is confirmed, Both variants are predicted to destroy normal splicing sites and cause a null protein with Variant 1 skipping exon 4 and Variant 2 skipping exon 12

CasePreviousTesting: Mild elevation of hydroxyl-C4-carnitine (0.79; reference: 0.03–0.70), Normal venous blood lactate at 3 months (1.1 mmol/L; reference 0.44–1.78 mmol/L) and elevated at 5 months (3.2 mmol/L; reference: 1.42–1.90 mmol/L), Ketone and pyruvate levels at 5 months were normal, Karyotype analysis was performed to confirm normality. Low-coverage massively parallel CNV sequencing was used to confirm any copy number variation, which showed normal results.

CaseGenotypingMethod: Genomic DNA was extracted from lymphocytes and whole exome sequencing was performed. The identified variants were filtered for pathogenicity and confirmed via Sanger sequencing. cDNA sequence analysis was also performed to determine the effect of these variants on the protein.

Variant1: NM_014362.3:c.304+3A>G (p.=)

CAID: CA913203579 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203579

gnomAD: Not in gnomAD

Variant2: NM_014362.3:c.1010_1011+3delTGGTA

CAID: CA2027408 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_014362.3%3Ac.1010_1011%2B3delTGGTA

gnomAD: Not in gnomAD

Case2: Male, Belgium

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0003798, HP:0001558, HP:0001623, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Arthrogryposis, Decreased fetal movement, Breech presentation, Ophthalmoplegia)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased 10 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(LMOD3):c.138dup (p.Ser47Glnfs)

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

Case4: Male, Japan, Asian

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 4 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.231G>A (p.Trp77*)

CAID: CA353478954 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.231G%3EA

gnomAD: Not in gnomAD

Case13a: Male, Pakistan

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001623, HP:0001561, HP:0000602, HP:0002808 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Breech presentation, Polyhydramnios, Ophthalmoplegia, Kyphosis)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 3 months, Has a sibling with same genotype/phenotype

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.1099_1100delAA (p.Asn367Glnfs*11)

ClinVar: 162218 https://www.ncbi.nlm.nih.gov/clinvar/variation/162218/

gnomAD: South Asian 4.575e-4, Overall 5.625e-5 https://gnomad.broadinstitute.org/variant/3-69168405-GTT-G

Case1a: Female, Algeria

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001622, HP:0002804, HP:0003798 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Preterm delivery, Arthrogryposis, Nemaline bodies)

HPOsFreeText: Bilateral femoral fractures, Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period, Parents are consanguineous

CasePreviousTesting: N/A

CaseGenotypingMethod: Linkage analysis combined with homozygosity mapping was used to identify candidate chromosomal loci. Whole exome sequencing in this family revealed likely pathogenic mutations in LMOD3 which agreed with the aforementioned analysis and was consistent with autosomal recessive inheritance.

Variant: NM_198271.4(LMOD3):c.138dup (p.Ser47Glnfs)

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

Case7: Female, Japan, Asian

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 1 yr 7 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.

Variant1: NM_198271.4:c.349C>T (p.Gln117*)

CAID: CA353477271 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.349C%3ET

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1218delA (p.Lys406Asnfs*11)

CAID: CA909806380 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.1218delA

gnomAD: Not in gnomAD

Case11b: Male, Sweden

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

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

Case1b: Female, Algeria

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001622 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Preterm delivery)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period, Parents are consanguineous

CasePreviousTesting: N/A

CaseGenotypingMethod: Linkage analysis combined with homozygosity mapping was used to identify candidate chromosomal loci. Whole exome sequencing in this family revealed likely pathogenic mutations in LMOD3 which agreed with the aforementioned analysis and was consistent with autosomal recessive inheritance.

Variant: NM_198271.4(LMOD3):c.138dup (p.Ser47Glnfs)

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

CaseKLC: Male, 42 yrs death, Japan, Asian

CasePresentingHPOs: HP:0001394, HP:0002078, HP:0000651, HP:0008353, HP:0003763, HP:0100785, HP:0001276, HP:0030904, HP:0030906, HP:0030903 (Cirrhosis, Truncal ataxia, Diplopia, Neutral hyperaminoaciduria, Bruxism, Insomnia, Hypertonia, Glabellar reflex, Suck reflex, Grasp reflex)

HPOsFreeText: Monoamino-monocarboxylic aciduria, Transient stupor

CaseNotHPOs: HP:0000992, HP:0011123, HP:0040129 (Cutaneous photosensitivity, Dermatitis, Abnormal nerve conduction velocity)

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);

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_883TG[1] (p.Val295fs)

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

CaseKLD: Female, 6 yrs report, Japan, Asian

CasePresentingHPOs: HP:0001047, HP:0002028, HP:0004325, HP:0004322, HP:0008353, HP:0001397, HP:0001249 (Atopic dermatitis, Chronic diarrhea, Decreased body weight, Short stature, Neutral hyperaminoaciduria, Hepatic steatosis, Intellectual disability)

HPOsFreeText: Lowered concentrations of valine, methionine, isoleucine, tyrosine, phenylalanine, and tryptophan with generalized mild hypoaminoacidemia

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are first-cousin consanguineous, Max LOD score is 1.45 for family, Pedigree in Figure 1aD

CasePreviousTesting: Oral loading tests demonstrated impaired absorption of tryptophan from the gut, while the absorption of proline was intact; Absence of hyperaminoaciduria was confirmed by urine analyses of the pedigree members

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 missense mutation that perfectly segregated with the phenotype.

CasePMIDs: 2582682, 11394870

Variant: NM_001003841.3:c.169C>T (p.Arg57Cys)

CAID: CA3182581 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182581

gnomAD: 0.0002181, https://gnomad.broadinstitute.org/variant/5-1201934-C-T

CaseCA5: Male, 9 months death

CasePresentingHPOs: HP:0001644, HP:0001875, HP:0001508, HP:0003535, HP:0002014, HP:0008872, HP:0003146 (Dilated cardiomyopathy, Neutropenia, Failure to thrive, 3-Methylglutaconic aciduria, Diarrhea, Feeding difficulties in infancy, Hypocholesterolemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: The TAZ gene was PCR amplified in three fragments and directly sequenced in the mother and proband.

Variant: NM_000116.4:c.629T>G (p.Leu210Arg)

CAID: CA415184340, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA415184340

gnomAD: Not in gnomAD

CaseCA3: Male, 6 months diagnosis

CasePresentingHPOs: HP:0001644, HP:0001875, HP:0001508, HP:0003535, HP:0003756, HP:0030319, HP:0003551 (Dilated cardiomyopathy, Neutropenia, Failure to thrive, 3-Methylglutaconic aciduria, Skeletal myopathy, Facial weakness, Difficulty climbing stairs)

HPOsFreeText: N/A

CaseNotHPOs: HP:0003107 (Abnormal circulating cholesterol concentration)

NotHPOsFreeText: N/A

CaseAddInfo: Cardiac transplant 11 months after presentation; Variant also found in mother and grandmother

CasePreviousTesting: N/A

CaseGenotypingMethod: The TAZ gene was PCR amplified in three fragments and directly sequenced in the mother and proband.

Variant: NM_000116.5(TAZ):c.589G>A (p.Gly197Arg)

ClinVar: 11105, https://www.ncbi.nlm.nih.gov/clinvar/variation/11105/

gnomAD: Not in gnomAD

CaseSK: Male, Pakistan, Birth onset

CasePresentingHPOs: HP:0008846, HP:0001562, HP:0002987, HP:0012453, HP:0001623, HP:0001518, HP:0003561, HP:0002209, HP:0011359, HP:0000963, HP:0100678, HP:0000973, HP:0100679, HP:0000348, HP:0002007, HP:0005280, HP:0000463, HP:0003196, HP:0000430, HP:0000233, HP:0000490, HP:0007759, HP:0000218, HP:0000347, HP:0005328, HP:0002828, HP:0002098, HP:0009110, HP:0000883, HP:0011682, HP:0001655, HP:0100545, HP:0007727, HP:0002033, HP:0002015, HP:0001250, HP:0000023, HP:0001525 (Severe intrauterine growth retardation, Oligohydramnios, Elbow contracture, Bilateral wrist flexion contracture, Breech presentation, Small for gestational age, Birth length less than 3rd percentile, Sparse scalp hair, Dry hair, Thin skin, Wrinkled skin, Cutis laxa, Lack of skin elasticity, High forehead, Frontal bossing, Depressed nasal bridge, Anteverted nares, Short nose, Underdeveloped nasal alae, Thin vermilion border, Deeply set eye, Opacification of the corneal stroma, High-arched palate, Micrognathia, Progeroid facial appearance, Multiple joint contractures, Respiratory distress, Diaphragmatic eventration, Thin ribs, Perimembranous ventricular septal defect, Patent foramen ovale, Arterial stenosis, Opacification of the corneal epithelium, Poor suck, Dysphagia, Seizures, Inguinal hernia, Severe failure to thrive)

HPOsFreeText: Clenched fists, Birth weight was 1.52 kg (<3rd centile), his length was 38 cm (<3rd centile) and his OFC was 29.5 cm (<3rd centile). His Apgar scores were six and nine at 1 and 5 min respectively, Parchment paper‐like textured skin, Prominent cheek jowls, Absent Bowman's membrane, Increased cellularity in the substantia propia, Decreased amount of elastin compared to controls, Less-deefined collagen fibers, Amounts of collagen type I and III were qualitatively decreased

CaseNotHPOs: N/A

NotHPOsFreeText: Normal lung parenchyma

CaseAddInfo: Born to consanguineous first-cousin once removed parents

CasePreviousTesting: Maternal TORCH analysis showed no signs of an acute infection; Amniocentesis showed a normal male karyotype (46,XY), and amniotic fluid virology studies showed no detectable virus; Fetal echocardiography was normal; Fibroblast analysis showed cell proliferation was severely diminished along with abnormally decreased collagen production; A heterozygous variant in PYCR1 was also found (c.329C > T) but is predicted benign and no functional expression alteration of PYCR1 was found.

CaseGenotypingMethod: The exons and exon-intron boundaries of ALDH18A1 were subject to mutation screening via direct sequencing and PCR amplification. A homozygous canonical splice-site variant was found with both parents heterozygous for the same mutation. cDNA was applied to test for functional alteration of the transcript which yielded, rathert than the WT 706 bp protein, a shortened protein ranging from 492-583 bp. These two transcripts either lead to a large deletion of c.1757–1970 or a premature termination codon predicted to undergo NMD.

Variant: NM_002860.4(ALDH18A1):c.1923+1G>A

ClinVar: 29727 https://www.ncbi.nlm.nih.gov/clinvar/variation/29727/

gnomAD: Not in gnomAD

Case2: Male, White, 18 yrs report

CasePresentingHPOs: HP:0010864, HP:0000717, HP:0002019, HP:0002300, HP:0001250, HP:0012072 (Severe Intellectual disability, Autism, Constipation, Mutism, Seizures, Aciduria)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627, HP:0000175 (Abnormal heart morphology, Cleft palate)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous, Has 22q11.2 deletion so phenotypes other than urinary excretion may result from that

CasePreviousTesting: Urine analysis at 25 years of age showed an increase of AAA (226 mmol/mol creatinine; ref <14) and KAA (68 mmol/mol creatinine; ref not detected)

CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced. SSCP analysis confirmed the presence of the 22q11.2 deletion.

Variant1: 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

Variant2: NM_018706.7(DHTKD1):c.2318C>T (p.Pro773Leu)

ClinVar: 420289 https://www.ncbi.nlm.nih.gov/clinvar/variation/420289/

gnomAD: 0.0001423, https://gnomad.broadinstitute.org/variant/10-12155062-C-T

Case3: Female, 5 yrs report

CasePresentingHPOs: HP:0012072 (Aciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo:

CasePreviousTesting: Partial biotinidase deficiency (19%) was confirmed; Urine AAA (552 mmol/mol creatinine; ref <91) and KAA (251 mmol/mol creatinine) were clearly increased. At 5 years of age, urine AAA and KAA as well as plasma AAA were persistently elevated.

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

Variant1: 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

Variant2: NM_018706.7(DHTKD1):c.1309G>T (p.Glu437Ter)

ClinVar: 574714 https://www.ncbi.nlm.nih.gov/clinvar/variation/574714/

gnomAD: 0.0001316, https://gnomad.broadinstitute.org/variant/10-12136221-G-T

CaseST: Female, 2 days onset

CasePresentingHPOs: HP:0002521, HP:0010841, HP:0012000, HP:0032842, HP:0011468, HP:0007289, HP:0100704, HP:0000639, HP:0001601, HP:0012820, HP:0002835, HP:0001252, HP:0001257, HP:0001263, HP:0002079, HP:0011757, HP:0003429 (Hypsarrhythmia, Multifocal epileptiform discharges, EEG with generalized spikes, Generalized-onset epileptic spasm, Facial tics, Limb fasciculations, Cerebral visual impairment, Nystagmus, Laryngomalacia, Bilateral vocal cord paralysis, Aspiration, Muscular hypotonia, Spasticity, Global developmental delay, Hypoplasia of the corpus callosum, Posterior pituitary hypoplasia, CNS hypomyelination)

HPOsFreeText: Lack of normal sleep or wake features on EEG

CaseNotHPOs: HP:0002650 (Scoliosis)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo heterozygous

CasePreviousTesting: Currently on vigabatrin, levetiracetam, Rufinamide and ketogenic diet, previously on phenobarbatol, ACTH, Cannabidiol oil and Prednisolone; MRS with small lactate peaks in the basal ganglia and supratentorial white matter

CaseGenotypingMethod: Whole exome sequencing revealed a pathogenic heterozygous c.254T>C (p.Leu85Pro) variant in the SLC1A2 gene, which was classified as de novo using parental testing.

Variant: NM_004171.4(SLC1A2):c.254T>C (p.Leu85Pro)

ClinVar: 254266, https://www.ncbi.nlm.nih.gov/clinvar/variation/254266/

gnomAD: Not in gnomAD

CaseAC007_II-1: Male, 5 yrs onset, Liberia, Black

CasePresentingHPOs: HP:0001992, HP:0002373, HP:0010864, HP:0000729, HP:0000750, HP:0002539, HP:0002282 (Organic aciduria, Febrile seizure, Severe intellectual disability, Autistic behavior, Delayed speech and language development, Cortical dysplasia, Gray matter heterotopia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are reportedly non-consanguineous, Proband is confirmed homozygous for this variant without parental confirmation via restriction fragment analysis

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

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. Restriction digest analysis was performed to confirm homozygosity.

Variant: NM_000666.3(ACY1):c.1156C>T (p.Arg386Cys)

ClinVar: 712435, https://www.ncbi.nlm.nih.gov/clinvar/variation/712435/

gnomAD: 0.01775 (3 homozygotes), https://gnomad.broadinstitute.org/variant/3-52023020-C-T

CaseAC014_II-1: Female, 3 yrs report, Lebanon

CasePresentingHPOs: HP:0001992, HP:0025356 (Organic aciduria, Psychomotor retardation)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, Proband is confirmed homozygous for this variant via parental testing, Siblings are healthy

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

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.1132C>T (p.Arg378Trp)

ClinVar: 493363, https://www.ncbi.nlm.nih.gov/clinvar/variation/493363/

gnomAD: 0.00001499 in ExAC, https://gnomad.broadinstitute.org/variant/3-52022996-C-T?dataset=exac

CasePAII-1: Female, 18 yrs onset

CasePresentingHPOs: HP:0000147, HP:0040292, HP:0002083, HP:0003401, HP:0001251, HP:0000640, HP:0006855, HP:0006744 (Polycystic ovary disease, Left hemiplegia, Migraine without aura, Paresthesia, Ataxia, Gaze-evoked nystagmus, Cerebellar vermis atrophy, Adrenocortical carcinoma)

HPOsFreeText: N/A

CaseNotHPOs: HP:0000505 (Visual impairments)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, Mother has similar symptoms but declined to be clinically examined

CasePreviousTesting: Episodes triggered by menstruation but also by stress and preceded by a sensorimotor march; EEG and electroneurography were normal; Pathologic CAG expansions in CACNA1A and conventional mutations in CACNA1A, ATP1A2, and SCN1A were ruled out; Treatment with ACZ (250 mg twice daily) prevented hemiplegic spells and interictal GEN receded; MRS demonstrated low combined glutamate and glutamine peak that responded to ACZ treatment during an episode

CaseGenotypingMethod: Targeted genotyping analysis was performed.

Variant: NM_004172.5:c.379_383del (p.Tyr127Aspfs*60)

CAID: CA1139532263, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139532263

gnomAD: Not in gnomAD

Case25014: Female, 31 yrs onset, United States

CasePresentingHPOs: HP:0002527, HP:0002064, HP:0002460, HP:0002395, HP:0007350, HP:0003487, HP:0000012, HP:0006938, HP:0100658, HP:0000518, HP:0002322, HP:0010784, HP:0012104, HP:0006913 (Falls, Spastic gait, Distal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Urinary urgency, Impaired vibration sensation at ankles, Cellulitis, Cataract, Resting tremor, Uterine neoplasm, Parietal cortical atrophy, Frontal cortical atrophy)

HPOsFreeText: 5/7 disability score, Chronic microvascular disease

CaseNotHPOs: HP:0001317, HP:0002464, HP:0100543, HP:0000973 (Abnormal cerebellum morphology, Spastic dysarthria, Cognitive impairment, Cutis laxa)

NotHPOsFreeText: N/A

CaseGenotypingMethod: Exome sequencing data of 160 index patients with autosomal dominant spastic paraplegia and 275 index patients with autosomal recessive or sporadic spastic paraplegia was examined. 95 patients were screened through panel sequencing. Any determined ALDH18A1 mutations were confirmed by Sanger sequencing.

CasePreviousTesting: N/A

CaseAddInfo: Case is sporadic

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

CaseGSHSP44: Female, 44 yrs onset, Australia/UK

CasePresentingHPOs: HP:0040083, HP:0002317, HP:0002064, HP:0002460, HP:0002395, HP:0007350, HP:0003487, HP:0000012, HP:0012104, HP:0006913, HP:0001761, HP:0031520, HP:0006827 (Toe walking, Unsteady gait, Spastic gait, Distal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Urinary urgency, Parietal cortical atrophy, Frontal cortical atrophy, Pes cavus, Groin pain, Atrophy of the spinal cord)

HPOsFreeText: 4/7 disability score, Hip replacement

CaseNotHPOs: HP:0001317, HP:0002464, HP:0100543, HP:0000973, HP:0006938 (Abnormal cerebellum morphology, Spastic dysarthria, Cognitive impairment, Cutis laxa, Impaired vibration sensation at ankles)

NotHPOsFreeText: N/A

CaseGenotypingMethod: Exome sequencing data of 160 index patients with autosomal dominant spastic paraplegia and 275 index patients with autosomal recessive or sporadic spastic paraplegia was examined. 95 patients were screened through panel sequencing. Any determined ALDH18A1 mutations were confirmed by Sanger sequencing.

CasePreviousTesting: N/A

CaseAddInfo: Case is sporadic

Variant reported as c.1949G>T which does not exist in current transcripts

Variant: NM_002860.3:c.1955C>T (p.Ser652Phe)

CAID: CA377700120 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377700120

gnomAD: Not in gnomAD

Case53: 4 mo (at biopsy), Arab/Turkish, female

CaseNotHPOs: metabolic acidosis, homocystinuria (HP:0001942, HP:0002156)

NotHPOsFreeText: normal synthesis of adenosylcobalamin and methylcobalmin (suggests patient does not have cblX disease).

Case 53 (Level 2)

CasePreviousTesting: same as group. found 1.0 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_005334.2:c.4475C>T (p.Pro1492Leu)

ClinVar: n/a

CAID: CA415114585

gnomAD: n/a

CaseAddInfo: Originally identified as mut0 type patient through somatic cell complementation. But NGS instead identified a novel heterozygous mutation in HCFC1, which is detailed above. Based on clinical presentation it was determined unlikely that the identified variant is related to the patients MMA.

Case52: 3 wks (at biopsy), Irish/Italian

CasePresentingHPOs: methylmalonic acidemia (HP:0002912)

HPOsFreeText: SIDS, elevation in C3 carnitine (post mortem blood spot)

Case 52 (Level 2)

CasePreviousTesting: same as group. found 2.0 nmol/mg protein/18 h propionate incorporation, 2.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_001177599.1:c.273A>T (p.Arg91Ser)

ClinVar: n/a

CAID: CA353555085

gnomAD: n/a

CaseAddInfo: Originally identified as mut0 type patient through somatic cell complementation. But NGS instead identified a novel heterozygous mutation in SUCLG2. Unknown relevance of variant to patient's phenotype.

Case51: 3 wks (at biopsy), Irish/Italian

CasePresentingHPOs: metabolic acidosis-severe, methylmalonic acidemia-mild, lactic acidosis, sensorineural hearing loss (HP:0001942, HP:0002912, HP:0003128, HP:0000407)

Case 51 (Level 2)

CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 0.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_003849.3:c.433G>A (p.Glu145Lys)

ClinVar: n/a

CAID: CA347515756

gnomAD: 0.00001761 (European non-Finnish)

Variant2: NM_003849.3:c.511A>C (p.Asn171His)

ClinVar: n/a

CAID: CA347515593

gnomAD: n/a

CaseAddInfo: Originally identified as mut0 type patient through somatic cell complementation. But NGS instead identified two novel heterozygous mutations in the SUCLG1 gene (detailed above). Mutations are likely causative of patient's phenotype.

Case48: 8 mo (at biopsy), Indian

Case 48 (Level 2)

CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 1.1 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.2179C>T (p.Arg727Ter)

ClinVar: 218998

CAID: CA347913

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut0 type, homozygous mutations.

Case47: 2 y 7 mo (at biopsy), Barbadian

Case 47 (Level 2)

CasePreviousTesting: same as group. found 0.4 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.2150G>T (p.Gly717Val)

ClinVar: 1881

CAID: CA249729

gnomAD: 0.0006810 (African)

CaseAddInfo: mut- type, homozygous mutations. reportedly non-consanguineous

Case46: 1 y (at biopsy), White

Case 46 (Level 2)

CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 0.9 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.1962_1963delTC (p.Arg655Terfs)

ClinVar: 552144

CAID: CA658821515

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case44: 13y (at biopsy), Arab

Case 44 (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.1 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.1871A>G (p.Gln624Arg)

ClinVar: n/a

CAID: CA3846720

gnomAD: 0.00003266 (South Asian)

CaseAddInfo: mut0 type, homozygous mutations.

Case43: 20 y (at biopsy), Lebanese

Case 43 (Level 2)

CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.1 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.1741C>T (p.Arg581Ter)

ClinVar: 554675

CAID: CA364395893

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case45: no age or ethnicity recorded

Case 45 (Level 2)

CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.6 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.1891delG (p.Ala631GlinfsTer17)

ClinVar: n/a

CAID: CA351288

gnomAD: 0.00002896 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case42: 1 y 7 mo (at biopsy), Hmong

Case 42 (Level 2)

CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 9.0 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.1663G>A (p.Ala555Thr)

ClinVar: 203850

CAID: CA312769

gnomAD: 0.0003262 (East Asian)

CaseAddInfo: mut- type, homozygous mutations. Additional heterozygous mutations in CUBN gene (Variant 1: NM_001081.3:c.3500G>T, CAID: CA376148913 , gnomAD: 0.00005014, East Asian ) (Variant 2: NM_001081.3:c.6211A>G, CAID: CA5423765 , gnomAD: 0.001003, East Asian )

Case41: 6 mo (at biopsy), Pakistani

Case 41 (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.1560G>C (p.Lys520Asn)

ClinVar: n/a

CAID: CA364397073

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case40: Middle Eastern

Case 40 (Level 2)

CasePreviousTesting: same as group. found 1.8 nmol/mg protein/18 h propionate incorporation, 1.6 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.1420C>T (p.Arg474Ter)

ClinVar: 554873

CAID: CA138795916

gnomAD: 0.00003267 (South Asian)

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case39: 1 y (at biopsy), Asian

Case 39 (Level 2)

CasePreviousTesting: same as group. found 1.4 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.1280G>A (p.Gly427Asp)

ClinVar: 218990

CAID: CA347873

gnomAD: 0.0004011 (East Asian)

CaseAddInfo: mut0 type, homozygous mutations. documented non-consanguinity.

Case38: 9 y (at biopsy), German/Polish

Case 38 (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.1106G>A (p.Arg369His)

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut0 type, homozygous mutations.

Case37: 18 mo (at biopsy), Moroccan

Case 37 (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.683G>A (p.Arg228Gln)

ClinVar: n/a

CAID: CA3847070

gnomAD: 0.00002905 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case36: 14 mo (at biopsy), Hispanic

Case 36 (Level 2)

CasePreviousTesting: same as group. found 0.7 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.406G>T (p.Val136Phe)

ClinVar: n/a

CAID: CA364404792

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case35: 5 y (at biopsy), Hispanic

Case 35 (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.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case33: 9 mo (at biopsy), Hispanic

Case 33 (Level 2)

CasePreviousTesting: same as group. found 1.0 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.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case32: 10 y (at biopsy), Arab

Case 32 (Level 2)

CasePreviousTesting: same as group. found 1.0 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.278G>A (p.Arg93His)

ClinVar: 1880

CAID: CA249728

gnomAD: 0.0004777 (European- Finnish)

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case34: 3.5 wks (at biopsy), White/Hispanic

Case 34 (Level 2)

CasePreviousTesting: same as group. found 1.6 nmol/mg protein/18 h propionate incorporation, 1.8 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.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

CaseSA4P: Female, 12 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001987, HP:0002167 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Hyperammonemia, Neurological speech impairment)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Has mother with confirmed variant and similar phenotypes

CasePreviousTesting: Leucine load test showed leucine sensitivity; Protein/leucine restriction 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

CaseB1: United States, White

CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants segregate with the disease, Has a brother (B2) also homozygous for variant and positive for amino acid profile

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.

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

CaseAHN8.1: 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:c.277G>A (p.Gly93Arg)

CAID: CA3182636 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182636

gnomAD: 0.0001195, https://gnomad.broadinstitute.org/variant/5-1208935-G-A

Variant2: NM_001003841.3(SLC6A19):c.1173+2T>G

ClinVar: 449553 https://www.ncbi.nlm.nih.gov/clinvar/variation/449553/

gnomAD: 0.0006791, https://gnomad.broadinstitute.org/variant/5-1217062-T-G

CaseAHN6.3: 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(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

CaseAHN15.1: 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.850G>A (p.Gly284Arg)

CAID: CA3182918, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182918

gnomAD: 0.00005440, https://gnomad.broadinstitute.org/variant/5-1214143-G-A

Patient2: Female, 5yo, Thai

CasePresentingHPOs: HP:0011968, HP:0001254, HP:0100806, HP:0001876, HP:0001290, HP:0001942, HP:0001987, HP:0002342 (poor feeding, lethargy, sepsis, pancytopenia, hypotonia, metabolic acidosis, hyperammonemia, moderate mental retardation)

HPOsFreeText: acute neonatal IVA, hemoglobin = 11g/dL, WBC = 3100/mm^3, platelets = 47,000/mm^3, sepsis treated with parenteral antibiotics and IV fluid, bicarbonate = 14mmol/L, anion gap = 18mmol/L, ammonia = 97µmol/L, began metabolic treatment at 14mo but was non-compliant, developmental quotient = 48, treated with low-protein diet and leucine-free formula (150–250mg/kg per day of l‐glycine, and 100mg/kg per day of l‐carnitine), urine isovalerylglycine = 153

CaseNotHPOs:

NotHPOsFreeText: ammo

CaseAddInfo: non-consanguineous family, diagnose with sepsis at 14 days old, lost to follow up at 5yo

CasePMIDs:

CasePreviousTesting: urine organic acid analysis with GC/MS (PMID: 27082169)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted from peripheral blood, IVD coding exons and flanking introns amplified with PCR (primer in table 1), PCR products purified and sequenced with Big Dye Primer Cycle Sequencing Kit and ABI 210 Genetic Analyzer

Variant1: c.457–3_2CA>GG / no ClinVar or CAID

Variant2: NM_001354598.2:c.194C>G (p.Ala65Gly)

CAID: CA391744802, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391744802

gnomAD: n/a

CaseIW: Female, 10 yrs report,

CasePresentingHPOs: HP:0002078, HP:0000486, HP:0002080, HP:0001350 (Truncal ataxia, Strabismus, Intention tremor, Slurred speech)

HPOsFreeText: Hypoperfusion of cerebellum and brainstem at 8 yrs

CaseNotHPOs: HP:0001270 (Motor delay)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are healthy and non-consanguineous and have no family history of neurological symptoms; Proband is confirmed de novo heterozygous via parental testing

CasePreviousTesting: Treatment with acetazolamide helped with symptoms

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes and subject to whole exome sequencing. Variants were filtered according to likely pathogenicity and presence in previously reported causative genes associated with ataxia, cerebellar atrophy, and other neurodegenerative diseases.The SLC1A3 variant was confirmed via Sanger seuqencing in the proband and absent in her parents.

Variant: NM_004172.5:c.383T>G (p.Met128Arg)

CAID: CA359477326, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359477326

gnomAD: Not in gnomAD

Case2928: Female, 2 years diagnosis, Czech

CasePresentingHPOs: HP:0001270, HP:0001263, HP:0003153, HP:0001250, HP:0002240, HP:0000980, HP:0000613, HP:0001744 (Motor delay, Psychomotor retardation, Cystathioninuria, Seizures, Hepatomegaly, Paleness, Photophobia, Splenomegaly)

HPOsFreeText: Elevated total homocysteine (34.0 μM/l; reference 5.1–13.9), Elevated cystathionine (4.4 μM/l; reference 0.04–0.34), Normal total cysteine (250 μmol/l; reference 203–369), Responsive to B6 treatment, Birth weight was 3000 g

CaseNotHPOs: HP:0000315, HP:0000939, HP:0000818, HP:0001977 (Ocular abnormality, Osteoporosis, Abnormality of the endocrine system, Abnormal thrombosis)

NotHPOsFreeText: N/A

CaseAddInfo: Patient is compound heterozygous for these mutations

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.

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

Variant Too Long

Variant2: NP_001893.2:p.Gly57_Gln196del

ClinVar:

gnomAD:

CaseOS-124_II-1: Male, Birth onset, Turkey

CasePresentingHPOs: HP:0001992, HP:0001263, HP:0002275, HP:0001252, HP:0002079, HP:0001320, HP:0002188, HP:0003396, (Organic aciduria, Global developmental delay, Poor motor coordination, Muscular hypotonia, Hypoplasia of the corpus callosum, Cerebellar vermis hypoplasia, Delayed CNS myelination, Syringomyelia,

HPOsFreeText: Syringomyelia length of 3.5 cm

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Parents are consanguineous, Older sister are unaffected, This variant results in a splicing alteration in the acceptor site of Exon 6, skipping exon 6 (amino acid residues 121 to 146) and causing a premature stop codon; 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; MRI of the head and spine was performed at age 3 mo

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.360-1G>A

ClinVar: 18112, https://www.ncbi.nlm.nih.gov/clinvar/variation/18112/

gnomAD: 0.00001767, https://gnomad.broadinstitute.org/variant/3-52020270-G-A

CaseFamily1,III-1: male, Family 1

HPOsFreeText: same as family

CaseAddInfo: affected sibling with same variant (fetus with unknown gender)

Case (Level 2)

CasePreviousTesting: same as family

CaseMethod1: same as family

CaseGenotypingMethod: same as family

Variant1: NM_015506.2(MMACHC):c.271dupA

ClinVar: 1421

CAID: CA090937

gnomAD: .002800 (Ashkenazi Jewish)

Variant2: NM_015506.2:c.468_469delCT

ClinVar: n/a

CAID: n/a

gnomAD: n/a

CaseAddInfo: Variant one said to be associated with early onset disease.

CaseT23159: Female, 2 days onset

CasePresentingHPOs: HP:0200134, HP:0011167, HP:0010818, HP:0032667, HP:0031475, HP:0032816, HP:0010841, HP:0010845, HP:0006808, HP:0002079, HP:0012753, HP:0002059, HP:0007266, HP:0002273, HP:0011471, HP:0000121, HP:0000141, HP:0000696, HP:0001662, HP:0002045, HP:0000253, HP:0000341, HP:0001525, HP:0001007, HP:0002751, HP:0001371, HP:0001182 (Epileptic encephalopathy, Focal tonic seizure, Generalized tonic seizure, Myoclonic status epilepticus, Nonconvulsive status epilepticus, Neonatal multifocal myoclonic seizure, Multifocal epileptiform discharges, EEG with generalized slow activity, Cerebral hypomyelination, Hypoplasia of the corpus callosum, T2 hypointense basal ganglia, Cerebral atrophy, White matter dysmyelination/demyelination, Tetraparesis, Gastrostomy tube feeding in infancy, Nephrocalcinosis, Amenorrhea, Delayed eruption of permanent teeth, Bradycardia, Hypothermia, Progressive microcephaly, Narrow forehead, Severe failure to thrive, Hirsutism, Kyphoscoliosis, Flexion contracture, Tapered finger)

HPOsFreeText: Thinning of cortical gray matter

CaseNotHPOs: HP:0001272 (Cerebellar atrophy)

NotHPOsFreeText: Hypomyelination of cerebellum and brain stem

CaseAddInfo: Proband confirmed de novo heterozygous by parental sequencing

CasePreviousTesting: Currently on carbamazepime, lamotrigine and lacosamide; previously on pyridoxine, clonazepam, acetazolamide, valproate, phenobarbitone, phenytoin, prednisolone, vigabatrin, topiramate and ketogenic diet

CaseGenotypingMethod: About 10% of the original 290 genes where a single de novo variant had been identified was chosen for targeted sequencing in a new cohort. Most of these individuals had been tested for mutations of known and novel candidate genes as well as pathogenic copy-number variants. These genes were sequenced in the parents and proband to look for de novo variants.

Variant: NM_004171.4(SLC1A2):c.254T>C (p.Leu85Pro)

ClinVar: 254266, https://www.ncbi.nlm.nih.gov/clinvar/variation/254266/

gnomAD: Not in gnomAD

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

HPOsFreeText: elevated blood levels of propionylcarnitine (C3) (median 13.56 umol/L), and elevated C3 to acetylcarnitine (C2) ratio (median 0.85). elevated urine methylmalonate levels (median 598.96 mmol/mol creatinine). 28/73.7% displayed recurrent vomiting (HP:0002572). 28/73.7% displayed disturbances of consciousness (HP:0004372). 23/60.5% displayed feeding difficulties in infancy (HP:0008872), 20/52.6% displayed respiratory distress (HP:0002098), 20/52.6% displayed failure to thrive (HP:0001508), 20/52.6% displayed dystonia (HP:0001332), 14/36.8% displayed mental retardation, 12/31.6% displayed convulsions.

GroupNotHPOs: normal plasma total homocysteine

NotHPOsFreeText:

NumberMales: 27

NumberFemales: 16

CountryOrigin: China

Ethnicity: Chinese

AgeRange: 33d- 10.3 y at last follow up

TotalNumber 43

FamilyInfo: 43

NoFamily: 0

GroupAddInfo: 9 identified by NBS, 34 recruited after being suspected of inherited metabolism disorders. 42 families from 14 provinces of the Mainland of China. 8 died during acute metabolic crisis, 7 lost to follow up, 28 alive at end of study.

Group (Level 2)

VariantCount: 43 (35 had two mutant alleles)

NonVariant: 0

OtherVariant: 0

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

GroupMethod1: PCR

GroupGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes from patients and their parents. Exonic and 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.

Case1: Male, Chinese, 11 mo (at end of study)

Case1HPOs: HP:0012736 (profound psychomotor retardation)

HPOsFreeText: 10 mo at onset, poor neurological outcome

NotHPOsFreeText: not responsive to vitamin B12

Case1 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

CaseAddInfo: homozygous mutations

Case4: Male, Chinese, 2.8 y (end of study)

HPOsFreeText: poor neurologic outcome, neonatal onset

NotHPOsFreeText: not responsive to vitamin B12

Case4 (Level 2):

CasePreviousTesting: NBS

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 552079

CAID: CA3847064

gnomAD: 0.0002008 (East Asian)

CaseAddInfo: homozygous mutations

Case5: Female, Chinese, 1.6 y (onset)

HPOsFreeText: 1.6 y onset

NotHPOsFreeText: Not responsive to vitamin B12

Case5 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: homozygous mutations, lost to follow up

Case3: Female, Chinese, 4 mo (end of study)

HPOsFreeText: Responsive to vitamin B12

Case3 (Level 2):

CasePreviousTesting: NBS

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.599T>C (p.Ille200Thr)

ClinVar: n/a

CAID: CA364404381

gnomAD: n/a

CaseAddInfo: homozygous mutations, asymptomatic

Case2: Male, Chinese, 3 mo (age at death)

HPOsFreeText: Neonatal onset

NotHPOsFreeText: Not responsive to vitamin B12

Case2 (Level 2):

CasePreviousTesting: NBS (newborn screening)

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000255.3:c.482G>T (p.Gly161Val)

ClinVar: n/a

CAID: CA364404636

gnomAD: n/a

CaseAddInfo: homozygous mutations, novel mutation

CaseAL1: Male, 14 yrs report

CasePresentingHPOs: HP:0012120 (Methylmalonic aciduria)

HPOsFreeText: Malonic acidemia/uria

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Born to non-consanguineous Ashkenazi Jewish parents; Proband is confirmed homozygous via parental testing

CasePreviousTesting: Newborn screening identified these probands, with subsequent urine organic acid analysis by gas chromatography mass spectroscopy confirming CMAMMA; Initial urine MMA level was 891 μmol/mmol creatinine; Confirmatory testing showed a urine MMA of 745 μmol/mmol creatinine (normal <25) and MA of 60 μmol/mmol creatinine (normal <6); Plasma MMA level was 18 μmol/l (normal <0.5); No other organic acid abnormality was detected. Carnitine levels, acylcarnitine profiles, plasma amino acids, ammonia, blood gas values, total homocysteine, folate and vitamin B12 levels were all within reference ranges, and the mothers were not vitamin B12 deficient; MCD activity in fibroblasts were within the reference range

CaseGenotypingMethod: Genomic DNA was isolated from fibroblasts and all exons and flanking introns of MLYCD, along with ACSF3, were subject to Sanger sequencing.

Variant: NM_001243279.3:c.1411C>T (p.Arg471Trp)

ClinVar: 31137, https://www.ncbi.nlm.nih.gov/clinvar/variation/31137

gnomAD: 0.007046, https://gnomad.broadinstitute.org/variant/16-89211719-C-T

CaseWG2098: 3 yrs onset

CasePresentingHPOs: HP:0001251, HP:0004302, HP:0001260, HP:0002313, HP:0012120 (Ataxia, Functional motor deficit, Dysarthria, Spastic paraparesis, Methylmalonic aciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband has normal 14C-propionate incorporation, suggesting normal MCEE protein activity level; The high gnomAD frequency and homozygotes suggests this is likely a benign polymorphism

CasePreviousTesting: Normal MRI; Propionate Incorporation w/o hydroxycobalamin at 7.0 nmols/mg protein/18hr; Propionate Incorporation with hydroxycobalamin at 8.2 nmols/mg protein/18hr; Adenosylcobalamin synthesis percentage at 12.7%; Elevated methylmalonic values of 621 µmol/mmol creatinine (reference 0.8-5.2 µmol/mmol creatinine)

CaseGenotypingMethod: Genomic DNA was extracted from patient fibroblasts, sequenced, and the three MCEE/thirteen MUT exons were analyzed and amplified. Any reported mutations were resequenced from fresh PCR product.

Variant: NM_032601.4(MCEE):c.178A>C (p.Lys60Gln)

ClinVar: 203812, https://www.ncbi.nlm.nih.gov/clinvar/variation/203812/

gnomAD: 0.01463 (10 homozygotes), https://gnomad.broadinstitute.org/variant/2-71351536-T-G

CaseDOIII-3: Female, 12 yrs report, White

CasePresentingHPOs: HP:0001531, HP:0002020, HP:0001942, HP:0001944, HP:0002789, HP:0002013, HP:0002014, HP:0002919, HP:0012120 (Failure to thrive in infancy, Gastroesophageal reflux, Metabolic acidosis, Dehydration, Tachypnea, Vomiting, Diarrhea, Ketonuria, Methylmalonic aciduria)

HPOsFreeText: Elevated methylcitric acid

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are first-cousin consanguineous, Son is healthy but second daughter shares phenotypes with the proband and shows clear methylmalonic aciduria, Proband and her sister are confirmed homozygous for this variant via parental testing

CasePreviousTesting: Serum methylmalonic acid was 1314 ng/ml (normal < 32); Vitamin B12 levels were normal (927 pg/ml, normal 200–1100); Vitamin B12 injections improved patient condition; At 12.5 yrs carnitine, plasma AAs, blood counts, and basic metabolic panels are normal but methylmalonic acid remains high at 180–1456 mmol/mol creatinine; Fibroblasts showed normal AdoCbl synthesis, contrary to expected from MMAA or MMAB variants; MUT and MMAB were sequenced with no variation found

CaseGenotypingMethod: Genomic DNA was isolated and PCR-amplified before directly sequencing all exons and flanking intronic sequences of the MCEE gene. Restriction enzyme digest confirmed the phase of the variant in the proband and the parents.

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

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

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