Case22 7yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0011342

(Lens dislocation, Mild intellectual disability, Mild developmental delay)

HPOsFreeText Patient had marfanoid features and was diagnosed on the basis of dislocated lens and mild developmental delay. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet.

CaseNotHPOs n/a

NotHPOsFreeText n/a

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.919G>A (p.Gly307Ser), 2. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), comp het

ClinVar 1. 117, 2. 198388

gnomAD 1. MAF=0.00041539(Other), no homozygotes, 2. MAF= 0.00002683(European(non-Finnish)), no homozygotes

CaseAddInfo patient also carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia.

CasePMIDs n/a

Case16 3yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256

(Lens dislocation, Mild intellectual disability)

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

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

ClinVar 117

gnomAD MAF= 0.00041539(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case5 14yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

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

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText no other sequelae

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.325T>C (p.Cys109Arg), compound heterozygous

ClinVar 1. 120, 2. 212878

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0001631(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case23 5yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0002751, HP:0000766

(Lens dislocation, Mild intellectual disability, Kyphoscoliosis, Abnormality of the sternum)

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.430G>A (p.Glu144Lys), 2. IVS1+1G>A, compound heterozygous

ClinVar 1. 122, 2. n/a

CAID 2. need more info

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

Case13 8yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0000767

(Lens dislocation, Pectus excavatum)

HPOsFreeText borderline intellectual disability. Diagnosis was based on dislocated lenses. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient had a partial response to the treatment. Homocystine levels were sharply reduced on pyridoxine and folate treatment, but did not levels did not fall below 20μmol (nv <60μmol) on this treatment alone.

CaseNotHPOs n/a

NotHPOsFreeText n/a

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2(CBS):c.430G>A (p.Glu144Lys), 2. NM_000071.2(CBS):c.1111G>A (p.Val371Met), compound heterozygous

ClinVar 1. 122, 2. 212862

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. MAF= 0.00006219(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case27 6yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0001256, HP:0002616, HP:0006280, HP:0002583

(Lens dislocation, Mild intellectual disability, Aortic root dilation, Chronic pancreatitis, Colitis)

HPOsFreeText Patient diagnosed on the basis of presenting marfanoid features. Patient had chronic pancreatitis requiring TPN and colitis requiring colostomy. Final CT scan of patient looking like multi-infarct dementia. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs n/a

NotHPOsFreeText n/a

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

CaseMethod1 PCR

CaseMethod2 Sanger

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

Variant 1. NM_000071.2:c.684C>A (p.Asn228Lys), 2. IVS11+1G>A, comp het

ClinVar 1. n/a, 2 n/a

CAID 1. CA410600617, 2. not enough info

gnomAD 1. MAF=0.00001759(European(non-Finnish)), no homozygotes, 2. n/a

CaseAddInfo n/a

CasePMIDs n/a

Case# PB5, Saudi Arabia

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

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

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

Variant NM_000056.4(BCKDHB):c.574G>A (p.Gly192Arg)

ClinVar 96596

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB6, Saudi Arabia

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

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

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

Variant NM_000056.4(BCKDHB):c.817A>C (p.Thr273Pro)

ClinVar 96610

VariantEvidence none

CaseAddInfo consanguineous family

Case# PB4, Saudi Arabia

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

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

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

Variant NM_000056.4(BCKDHB):c.502C>T (p.Arg168Cys)

ClinVar 96586

VariantEvidence none

CaseAddInfo consanguineous family

CasePMIDs previously studied in 17922217

Case# PB3, Saudi Arabia

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

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

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

Variant NM_000056.3:c.286del

CAID CA658820633

VariantEvidence null

CaseAddInfo consanguineous family

Case# PA5

Variant NM_000709.3:c.809C>A

CAID CA406012999

VariantEvidence none

Case# PA4

Variant NM_000709.3(BCKDHA):c.661_664delTACG (p.Tyr221Glnfs)

ClinVar 203638

Case# PB2, Saudi Arabia

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

CasePreviousTesting Blood spot newborn screen/presented symptoms in Hospital

CaseMethod1 PCR

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

Variant NM_000056.3:c.197G>C

CAID CA364658947

VariantEvidence none

CaseAddInfo consanguineous family

Case# PA3

Variant NM_000709.3(BCKDHA):c.647-1G>C

ClinVar 431985

gnomAD 0.000009079( European (Non-Finnish)), 0.000004103 (Overall)

CasePMIDs described previously in 19715473

Case# PA2

Variant NM_000709.3:c.409G>A(p.Glu137Lys)

CAID CA406007842

VariantEvidence none

Case# PA1

Variant NM_000709.3(BCKDHA):c.347A>G (p.Asp116Gly)

ClinVar 93354

VariantEvidence none

CaseWA: Female, 5 yrs onset, French-Canadian

CasePresentingHPOs: HP:0002013, HP:0001944, HP:0001289, HP:0002367, HP:0001942, HP:0031962, HP:0001987, HP:0003236, HP:0001946, HP:0002919, HP:0000651, HP:0012120 (Vomiting, Dehydration, Confusion, Visual hallucinations, Metabolic acidosis, Elevated serum anion gap, Hyperammonemia, Elevated serum creatine kinase, Ketosis, Ketonuria, Diplopia, Methylmalonic aciduria)

HPOsFreeText: Low incorporation of 14C-propionate (4.1 nmol propionate/mg protein/18 h; control mean 10.8, SD 3.7) with no response to hydroxycobalamin

CaseNotHPOs: HP:0002151 (Increased serum lactate)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous with unremarkable family history, Treatment with carnitine and restricted protein intake normalized symptoms, Sequencing of the mother revealed Variant 2 without Variant 1 confirming compound heterozygosity

CasePreviousTesting: Metabolic acidosis values w/ elevated anion gap (pH = 6.96, bicarbonate 3.5 mmol/L and pCO2 15.9 mm Hg, anion gap 25.5 mmol/L); Mild hyperammonemia (107 μmol/L; ref. < 50); Elevated creatine kinase (from 498 IU/L initially up to 3062 IU/L, ref. < 150); Organic acid profiles were analyzed via gas chromatography–mass spectrometry with Table 1 showing relevant organic acid values; Proband was negative for propionyl-coA carboxylase deficency (811 pmol/min/mg protein with control mean 1123, PCCA and PCCB variants were negative) and ruled out MUT/cobalamin issues as well; Fusion experiments showed negative results for mut, cblA, and cblB complementation but no increase in activity when fused with MCEE confirming the pathway blockage

CaseGenotypingMethod: Extracted DNA from blood was amplified and three coding exons/splice site junctions of MCEE were Sanger sequenced. A deletion/duplicaiton analysis yeilded normal results. To search for an intronic sequence variant, total RNA was extracted and reverse-transcribed to confirm a 92-bp insertion between Exons 2 and 3. Resulting sequencing of this genomic area revealed a deep intronic variant that created a new consensus donor splice site that leads to a premature stop codon.

Variant1: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

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

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

Variant2: NM_032601.3:c.379-644A>G

CAID: CA892631472, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA892631472

gnomAD: Not in gnomAD

Case42 sex unknown, Spain

CasePresentingHPOs HP:0006846, HP:0000707

(Acute encephalopathy, Neurological abnormality)

HPOsFreeText Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 35(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 268(nv 2–14 mm/mol creatinine).

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A433V variant creates an MwpI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved.

Variant NM_000159.3(GCDH):c.1298C>T (p.Ala433Val), homozygous

ClinVar 556228

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs see notes on previous studies

Case1 sex unknown, Spain

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

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

HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate 3336(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 825(nv 2–14 mm/mol creatinine).In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

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

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

ClinVar 2083

gnomAD MAF= 0.0004013(African), no homozygotes

CaseAddInfo Sibling(Case 2) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2120mmol/mol creatinine and 3-OH-glutarate was 543mmol/mol creatinine.

CasePMIDs n/a

Case24 sex unknown, Spain

CasePresentingHPOs HP:0000707

(Neurological abnormality)

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 1673(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 795(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A304T variant destroys an AluI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. The L309W variant creates an EcoP15 site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.910G>A (p.Ala304Thr), 2. NM_000159.3:c.926T>G (p.Leu309Trp), compound heterozygous

ClinVar 1. 554907, 2. n/a

CAID 2. CA404319538

gnomAD 1. MAF=0.00006163(African), no homozygotes, 2. MAF= 0.000008816(European(non-Finnish)), no homozygotes CaseAddInfo n/a

CasePMIDs n/a

Case13 sex unknown, Spain

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

(Non-ambulatory, Nonverbal, Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 1288(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 75(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R402W variant destroys a MspI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), homozygous

ClinVar 2085

gnomAD MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case27 sex unknown, Spain

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

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

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 2(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 18(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 10.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3(GCDH):c.1198G>A (p.Val400Met), homozygous

ClinVar 2088

gnomAD MAF= 0.0002769(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case38 sex unknown, Spain

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

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

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 4(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 43(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 9. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The Y155H variant creates a NcoI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3:c.463T>C(p.Tyr155His) , 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

ClinVar 1. n/a, 2. 2089

CAID 1. CA404317601

gnomAD 1. MAF=0.000008791(European(non-Finnish)), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs see notes on previous studies

Case10 sex unknown, Spain

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

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

HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 778(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 264(nv 2–14 mm/mol creatinine).

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

ClinVar 1. 2083, 2. 2085

gnomAD 1. MAF=0.0004013(African), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

CaseAddInfo Sibling (Case 11) was asymptomatic. GC-MS measured glutarate of 2083(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 262(nv 2–14 mm/mol creatinine)

CasePMIDs n/a

Case3 sex unknown, Spain

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

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

HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 1773(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 340(nv 2–14 mm/mol creatinine).In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

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

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

ClinVar 2083

gnomAD MAF= 0.0004013(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case21 sex unknown, Spain

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

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

HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 204(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 143(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 2.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A195T variant destroys a BanI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

Variant 1. NM_000159.3:c.583G>A (p.Ala195Thr), 2. NM_000159.3(GCDH):c.356C>T (p.Ser119Leu), compound heterozygous

ClinVar 1. n/a, 2. 288248

CAID 1. CA404318183

gnomAD 1. not in gnomAD, 2. MAF=0.0001984(Ashkenazi Jewish), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case29 sex unknown, Spain

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

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

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 5(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 114(nv 2–14 mm/mol creatinine).

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3(GCDH):c.1198G>A (p.Val400Met), homozygous

ClinVar 2088

gnomAD MAF= 0.0002769(Other), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case18 sex unknown, Spain

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

(Non-ambulatory, Nonverbal, Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 4097(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 212(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was <0.5.

CaseMethod1 SSCP

CaseMethod2 Sanger

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

Variant 1. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

ClinVar 1. 2085, 2. 370106

gnomAD 1. MAF=0.0007566(European(Finnish)), no homozygotes, 2. MAF= 0.00005646(Latino), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case5: male, Lebanon, neonatal screening 7 days

CasePresentingHPOs: HP:0045045, HP:0002155

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment of 150-200 mg L-carnitine/kg body weight and has shown normal development until 10 months.8 months: elevated serum triglycerides and GOT.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.51 umol/l and 0.72 umol/l; upper 99th percentile 0.29 umol/l) and C5/C2 acylcarnitine ratio (0.04 and 0.06; upper 99th percentile 0.02). 8 months: elevated serum triglycerides (673 mg/dl; ref <205) and GOT (57 U/l; ref <35).

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced. Sibling and parents: only exons 1, 4, and 10 were analyzed.

Variant: 1. NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys) 2. NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile)

ClinVar: 1. 9203; 2. 9202

gnomAD: 1. Latino 0.0004797, Overall 0.0002404, no homozygotes; 2. South Asian 0.002678; Overall 0.0008097, no homozygotes

VariantEvidence: In vitro expression of c.1159G>A in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stability. c. 443C>T decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

CaseAddInfo: 3 year old brother had a similar metabolite profile, but was not picked up by newborn screening (different cut-off values were used). Parents were normal. Patient also had c.38G>A polymorphism.

CasePMIDs:

CaseOS-104_II-1: Male, Birth onset, Turkey

CasePresentingHPOs: HP:0001992, HP:0001324, HP:0002317 (Organic aciduria, Muscular hypotonia, Unsteady gait)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263, HP:0001252 (Global developmental delay, Muscle weakness)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, Two younger brothers are unaffected, The variant results in a frameshift that extends the WT protein to 408 AAs and affects the C-terminal peptidase domain

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; Metabolite pattern of brother was unremarkable; Values of excreted AAs are in Table 1; Ultrasound, electromyography, and NMR tomography of the musculature from the lower extremities showed unremarkable results; Routine histological, histochemical, enzyme histochemical, and immunohistochemical studies did not reveal any significant myopathological abnormalities

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.1102_1103AC[3] (p.Pro369fs)

ClinVar: 18109, https://www.ncbi.nlm.nih.gov/clinvar/variation/18109/

gnomAD: Not in gnomAD

CaseOS-120_II-1: Female, Birth onset, German/Italian

CasePresentingHPOs: HP:0001992, HP:0011343 (Organic aciduria, Moderate global developmental delay)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Younger brother is unaffected; Proband is confirmed compound heterozygous as mother is heterozygous for R353C but father is unavailable

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; Neuropediatric evaluation performed

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.

Variant1: NM_000666.3(ACY1):c.699A>C (p.Glu233Asp)

ClinVar: 18111, https://www.ncbi.nlm.nih.gov/clinvar/variation/18111/

gnomAD: 0.0001846, https://gnomad.broadinstitute.org/variant/3-52021204-A-C

Variant2: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

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

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

Case2: Male, 1y 7m, Chinese

HPOsFreeText: (at 11 days) 1.69 C4 umol/L, 0.19 C4/C2, 2.38 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case2 (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:

Case7: Male, 6m, Chinese

CasePresentingHPOs: HP:0002248, HP:0001290, HP:0008872, HP:0002572 (haematemesis, hypotonia, feeding difficulties in infancy, recurrent vomiting)

HPOsFreeText: (at 19 days) 1.01 C4 umol/L, 0.38 C4/C2, 1.61 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case7 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.444G>T (p.Pro148=)

ClinVar: n/a

CAID: CA6372946

gnomAD: 0.0002772 (Other)

Variant2: NM_014384.2:c.1176G>T (p.Arg392Ser)

ClinVar: n/a

CAID: CA6373249

gnomAD: 0.0001088 (East Asian)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

Case1 Female, 1mo diagnosis, Korean

CasePresentingHPOs HP:0003235

(Increased blood methionine)

HPOsFreeText increased pre-treatment blood homocysteine and post-treatment total homocysteine, patient treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

CaseNotHPOs HP:0001083, HP:0001249

(Ectopia lentis, Intellectual disability)

NotHPOsFreeText Marfan syndrome, vascular occlusion

CasePreviousTesting pretreatment/posttreatment methionine: 1,239/123 μM(nv 7-47), pretreatment/posttreatment homocysteine: 28/0 μM(nv 0-5), posttreatment total homocysteine 144 μM(nv 5-15). Diagnosis upon neonatal screen

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced

Variant 1. NM_001320298.1:c.461T>A(p.Leu154Gln), 2. NM_000071.2(CBS):c.770C>T (p.Thr257Met), compound heterozygous

ClinVar 1. n/a, 2. 188927

CAID 1. CA410601512

gnomAD 1. not in gnomAD, 2. MAF=0.0001396(Other), no homozygotes

CaseAddInfo L154Q variant from father, T257M from mother. Additional R18C variant inherited from father, but protein from this SNP retains normal expression, 30-70% of enzyme activity and was found to have a 1/100 frequency in the study's control population

CasePMIDs n/a

Case4 Female, 7yo diagnosis, Korean

CasePresentingHPOs HP:0001083, HP:0001249, HP:0003235

(Ectopia lentis, Intellectual disability, Increased blood methionine)

HPOsFreeText Marfan syndrome, vascular occlusion, increased pre-treatment blood homocysteine and post-treatment total homocysteine, patient treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting pretreatment/posttreatment methionine: 24/575 μM(nv 7-47), pretreatment/posttreatment: 34/0 μM(nv 0-5), posttreatment total homocysteine 194 μM(nv 5-15)

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced

Variant 1. NM_000071.2(CBS):c.1006C>T (p.Arg336Cys), 2. NM_000071.2(CBS):c.1058C>T (p.Thr353Met), compound heterozygous

ClinVar 1. 92423, 2. 131

gnomAD 1. MAF=0.00004417(European(non-Finnish)), no homozygotes, 2. MAF=0.0002916(African), no homozygotes

CaseAddInfo R336C variant was paternally inherited, T353M variant was maternally inherited

CasePMIDs n/a

Case#: Patient 2, caucasian, 3 days (onset)

CasePresentingHPOs:

HPOFreeText: 3 days: hypoglycemia, poor feeding, lethargy, hypothermia. MRI: bilateral areas of subacute ischemia, increased T1 signal in lentiform nuclei consistent with global hypoxia. 1 year MRI: evolving areas of ischemia, thinning of gyri, delayed myelination of corpus callosum. 4 years: developmental delay, epilepsy. 6 years: unable to crawl or walk recurrent ear infections, chronic sinusitis, left eye extropia, microcephaly.

CaseNotHPOs: Normal neonatal EEG

CasePreviousTesting: 3 days: increased 2-methylbutyrylglycine (urine), 2-methylbutyrylcarnitine in plasma (C5-carnitine 1.4-2.4 uM, ref <0.4 uM)., elevated short chain carnitine to free carnitine (1.0, ref <0.5), normal blood amino acids. SBCAD enzyme activity in fibroblasts: 0.1 nmol/min/mg, ref. 0.16-0.29 nmol/min/mg).

CaseGenotypingMethod: Genomic DNA sequencing of all exons and part of flanking introns.

Variant: 1. NM_001609.3(ACADSB):c.303+3A>G 2. NM_001609.3(ACADSB):c.763C>T (p.Leu255Phe)

ClinVar: 1. 448980 2. 9200

gnomAD: 1. Not in gnomAD 2. Not in gnomAD

VariantEvidence: Skipping of exon 3 confirmed by mRNA analysis and minigene assay.This leads to a shifted reading frame with a PTC and likely NMD (when mRNA from patient 2's fibroblasts, who is het. for the variant, was analyzed, they saw no product from the mutant allele). CIS OR TRANS??

CaseAddInfo: Sister was also diagnosed with SBCADD prenatally and has been treated since birth. She has no clinical symptoms.

CasePMIDs: 10832746

Case#: Patient 1, Somalia, birth

CasePresentingHPOs: HP:0002104, HP:0001250, HP:0001263, HP:0008947

HPOFreeText: At birth, GC/MS of urine showed elevated 2-methylbutyrylglycine and 2-ethylhydracrylic acid, mildly elevated lactate. Plasma carnitine profile normal. NBS blood spot: high normal acylcarnitine profile (0.39 uM C5-acylcarnitine, ref <0.4 uM). 6 weeks: apena. 6 months: seizures, decline around 10 months, normal CT cerebrum. 7 months: protein-restricted diet. 8 months: normal EEG, infantile spasms. 9 months: global developmental delay, hypotonia. 10 months: sparse eye contact.

CaseNotHPOs: Normal chromosome analysis, cytomegalovirus (CMV) negative, normal hearing and vision, no skin changes.

CasePreviousTesting: SBCAD enzyme activity in fibroblasts: 0.17 +/- 0.01 nmol/min/mg, ref. 0.54-0.79 nmol/min/mg).

CaseGenotypingMethod: Genomic DNA sequencing of all exons and part of flanking introns.

Variant: NM_001609.3(ACADSB):c.303+3A>G

ClinVar: 448980

gnomAD: Not in gnomAD

VariantEvidence: Skipping of exon 3 confirmed by mRNA analysis and minigene assay.This leads to a shifted reading frame with a PTC and likely NMD (when mRNA from patient 2's fibroblasts, who is het. for the variant, was analyzed, they saw no product from the mutant allele).

CaseAddInfo:

CaseKO: Male, 22 yrs report, Serbia

CasePresentingHPOs: HP:0002076, HP:0002017, HP:0000505, HP:0002357, HP:0003474, HP:0004302, HP:0001269, HP:0012229, HP:0011288, HP:0002321, HP:0000622 (Migraine, Nausea and vomiting, Visual impairment, Dysphasia, Sensory impairment, Functional motor deficit, Hemiparesis, CSF pleocytosis, EEG with parietal sharp slow waves, Vertigo, Blurred vision)

HPOsFreeText: Mechanosensitivity

CaseNotHPOs: HP:0011182, HP:0001251, HP:0001250 (Interictal epileptiform activity, Ataxia, Seizure)

NotHPOsFreeText: N/A

CaseAddInfo: No evidence of headache attacks with focal neurological deficits in any other family member, but the patient’s father was found to suffer from migraine without aura

CasePreviousTesting: Responsive to treatment with ibuprofen; Mild head trauma is a trigger; Neuroimaging during attacks was normal; Screen for variants in CACNA1A, ATP1A2, SCN1A, and PRRT2 was negative

CaseGenotypingMethod: All exons and exon-intron boundaries of the SLC1A3 gene were seuqenced and a variant was found that segregates with the phenotype.

Variant: NM_004172.5:c.1159A>C (p.Thr387Pro)

CAID: CA359482299, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359482299

gnomAD: Not in gnomAD

CaseJE: Male, 10 yrs report,

CasePresentingHPOs: HP:0002131, HP:0004374, HP:0001319, HP:0001270, HP:0001350, HP:0002076, HP:0010547, HP:0001272, HP:0002381, HP:0002181, HP:0011182, HP:0045084, HP:0001289, HP:0002078, HP:0007034, HP:0007772, HP:0011289 (Episodic ataxia, Hemiplegia/hemiparesis, Neonatal hypotonia, Motor delay, Slurred speech, Migraine, Muscle flaccidity, Cerebellar atrophy, Aphasia, Cerebral edema, Interictal epileptiform activity, Limb myoclonus, Confusion, Truncal ataxia, Generalized hyperreflexia, Impaired smooth pursuit, EEG with temporal sharp slow waves)

HPOsFreeText: Left visual field neglect, Episodic left hemifield distortion

CaseNotHPOs: HP:0000639, HP:0000570, HP:0007670, HP:0000267 (Nystagmus, Impaired saccades, Abnormal vestibulo-ocular reflex, Cranial asymmetry)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed heterozygous de novo via parental testing and confirmed paternity; No family member has any neurological signs or symptoms

CasePreviousTesting: Previously screened for CACNA1A and ATP1A2 with negative results; Episodic migraine attacks led to progressive right-sided headache and left-sided symptoms such as weakness and visual field neglect; Comprehensive metabolic workup revealed no abnormality in the CSF, serum, and urine; MRI showed a diffuse right-sided cortical hyperintensity most prominent in fluid-attenuated inversion recovery (FLAIR); EEG showed subclinical seizure activity in the left frontal temporal cortex and diffuse slowing on the right

CaseGenotypingMethod: DNA was extracted from blood samples. All exons and flanking intronic regions of SLC1A3 were PCR-amplified and directly sequenced. These were confirmed via resequencing.

Variant: NM_004172.5(SLC1A3):c.869C>G (p.Pro290Arg)

ClinVar: 9441, https://www.ncbi.nlm.nih.gov/clinvar/variation/9441/

gnomAD: Not in gnomAD

CaseV1 Male, 6yr report, Dutch

CasePresentingHPOs HP:0025116, HP:0001941, HP:0002098, HP:0000737, HP:0010818, HP:0010851, HP:0000486, HP:0002464, HP:0001288, HP:0000750, HP:0000238, HP:0001263, HP:0100021

(Fetal distress, Acidosis, Respiratory distress, Irritability, Generalized tonic seizures, EEG with burst suppression, Squint, Spastic dysarthria, Gait difficulties, Speech delay, Hydrocephalus, Developmental delay, Cerebral palsy)

HPOsFreeText born at 35wk gestation. (neonatal, pre-treatment:) apgar score 1min:6, 5min:7; acidosis, respiratory distress, irritability, generalized tonic fits(onset at 1h old), burst suppression EEG, resistant to ACD's. (4do:) first pyridoxine trial, trial dose/route=50mg i/v, complete cessation of seizures, apnoea, hypotonia/sleepiness, hypotension, initial maintenance daily dose=50mg. (infancy/childhood:) squint, spastic dysarthria, gait problems, speech delay/difficulties, IQ:60-70, hydrocephalus on MRI requiring ventriculoperitoneal shunt. (PMID:16159904:) developmental delay, cerebral palsy

CaseNotHPOs HP:0001557, HP:0003270, HP:0002013, HP:0011169, HP:0001336, HP:0002521, HP:0025116

(Abnormal Intrauterine movements, Abdominal distension, Vomiting, Clonic seizures, Myoclonic jerk, Hypsarrhythmia, Fetal distress)

NotHPOsFreeText (neonatal, pre-treatment:) abdominal distension, clonic or myoclonic jerks, hypsarryhythmia, or other EEG changes. (infancy/childhood:) recurrence of seizures with febrile illness. (PMID:16159904:) intrauterine seizures, signs of fetal distress, for example, meconium stained amniotic fluid or abnormal cardiotocography

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 6.9, 1.5(nv<0.15μM), plasma pipecolic acid: 5.3(nv<2.5μM), CSF AASA: 1(nv <0.1μM), plasma AASA: 2.4(nv<0.2μM), urine AASA: 12(nv<1 mmol/mol creatinine).

Variant 1. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), 2. NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), compound heterozygous

ClinVar 1. 17994, 2. 17995

gnomAD 1.MAF= 0.0006123(European(Non-Finnish)), no homozygotes, 2. MAF=0.0001385(Other), no homozygotes

CaseAddInfo nonconsanguineous parents

CasePMIDs 17721876, 17088338, 16159904

CaseP1 Male, 4.5yr report, Austrian

CasePresentingHPOs HP:0010818, HP:0010851, HP:0001290, HP:0011343, HP:0007359, HP:0001942, HP:0002376, HP:0001290

(Generalized tonic seizures, EEG with burst suppression, Hypotonia, moderate GDD, focal seizures, Metabolic acidosis, Developmental regression, Hypotonia)

HPOsFreeText born 40wk gestation. (neonatal, pre-treatment) apgar scores at 1min:8, 5min:9, 10min: 10, generalized tonic fits at <1d old and burst suppression EEG. (3d:) introduced pyridoxine therapy, 100mg I/v trial dose/route, complete cessation of seizures, apnoea(3d), hypotonia, sleepiness, initial maintenance daily dose of 10 mg/kg. (infancy/childhood:) hypotonia, moderate IQ delay. (4d:) withdrew from pyridoxine trial then focal seizures recurrenced 3 weeks after(definite PDE). (PMID: 0894227) gestational toxicosis, birth weight 3,260g, myoclonic jerks of both arms with hours of birth.Paroxysms of polyspike-wave-activity on EEG, normal cranial imaging,CSF analysis

CaseNotHPOs n/a

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 3.4(nv<0.15μM), urine AASA: 168 before treatment(nv<1 mmol/mol creatinine). Blood lactate: 4.0mM and CSF lactate: 4.2mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 4.7(nv 0.7-2.6mmol/liter), AASA in plasma 2.6(nv<0.2mmol/liter), urine AASA 17(nv<1mmol/molcreatinine). (PMID: 0894227) CSF analysis, organic acids in urine, amino acids in serum, and VLCFAs were normal. Plasma PA at 1st week 49µmol/L(before treatment)(nv 1-3.2), at 1-6mo 14.3µmol/L, 6-12mo 10.1µmol/L, CSF PA at 0-1yr 3.38µmol/L.

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD MAF= 0.0006123(European(Non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs 10894227 (Patient 2), 17068770 (Patient 11)

CaseF5S: 21 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant has been shown to abolish canonical splice donor site and lead to a null protein

CasePreviousTesting: Blood phenylalanine before treatment was 1698 μmol/l, Blood tyrosine before treatment was 37 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.842+1G>A

ClinVar: 599 https://www.ncbi.nlm.nih.gov/clinvar/variation/599/

gnomAD: 0.00007752, http://gnomad.broadinstitute.org/variant/12-103246592-C-T

CaseF5P: 18 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family 5, Variant has been shown to abolish canonical splice donor site and lead to a null protein

CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was 36 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.842+1G>A

ClinVar: 599 https://www.ncbi.nlm.nih.gov/clinvar/variation/599/

gnomAD: 0.00007752, http://gnomad.broadinstitute.org/variant/12-103246592-C-T

CaseF1S: 5 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: 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 1431 μmol/l, Blood tyrosine before treatment was 35 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

CaseF2P: 2 yrs report, India

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Family is consanguinous, Parents were confirmed heterozygous, Variant may not undergo NMD however would be missing essential domains and is predicted to be null

CasePreviousTesting: Blood phenylalanine before treatment was 1619 μmol/l, Blood tyrosine before treatment was 60 μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

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

Variant: NM_000277.3:c.1177_1178insT (p.Asn393Ilefs*2)

CAID: CA16020958 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA16020958

gnomAD: Not in gnomAD

Case1: Amish

HPOsFreeText: GA1 confirmed

Case (Level 2)

CasePreviousTesting: GA1 confirmed

CaseMethod1: PCR

CaseMethod2: MaeII restriction digest

CaseGenotypingMethod: same as Amish group

Variant: NM_000159.3(GCDH):c.1262C>T (p.Ala421Val)

ClinVar: 2082

gnomAD: 0.0002867 (European non-Finnish)

CaseAddInfo: homozygous, founder allele in Amish of Lancaster County from immigrant from Switzerland to US in early 18th century. 4 non-Amish patients were found heterozygous for this allele with central European ancestry.

CaseBH: Male, Somalia, 8 yrs report

CasePresentingHPOs: HP:0003026, HP:0001511, HP:0000973, HP:0008936, HP:0000023, HP:0008780, HP:0000519, HP:0000639, HP:0011493, HP:0001263, HP:0001999, HP:0000337, HP:0000325, HP:0000494, HP:0000160, HP:0000977, HP:0001181, HP:0002119, HP:0005116 (Short long bone, Intrauterine growth retardation, Cutis laxa, Truncal hypotonia, Inguinal hernia, Congenital bilateral hip dislocation, Developmental cataract, Nystagmus, Central opacification of the cornea, Global developmental delay, Abnormal facial shape, Broad forehead, Triangular face, Downslanted palpebral fissures, Narrow mouth, Soft skin, Adducted thumb, Ventriculomegaly, Arterial tortuosity)

HPOsFreeText: At age 8 years, his height was 96 cm (Z=−5.8) and weight was 11.6 kg (Z=−7.26); Head circumference was 45.4 cm, (Z=−5.0) which is the 50th centile for a 10-month-old boy; Walked with support

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous fourth cousins, Had an older sister and younger brother who were developmentally appropriate and well grown

CasePreviousTesting: N/A

CaseGenotypingMethod: PYCR1 and ALDH18A1 were Sanger sequenced in the proband which revealed a single variant. Chromosomal SNP microarray showed no regions of homozygosity or any other deletions or duplications. Whole Exome Sequencing of genomic DNA from the proband was performed for confirmation again only revealing the single heterozygous missense variant in ALDH18A1. Copy-number analysis was performed and identified no significant variation. Sequencing of the parents revealed a de novo inheritance pattern.

Variant: NM_002860.3:c.377G>A (p.Arg126His)

CAID: CA377706756 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377706756

gnomAD: Not in gnomAD

Patient8: Male, 6yo, Family C (fig. 2)

CasePresentingHPOs: HP:0000486, HP:0000651 (squint, diplopia)

HPOsFreeText: acute neonatal IVA, treated with IVA special formula and oral L-carnitine, elevated isovalerylglycine, C5-carnitine = 6.8 µmol/l, normal development for age, weight = 128cm, weight = 28kg, normal chest, cardiovascular, and abdominal exams

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: diagnosed at 3do via NBS, consanguineous family, family history and multiple sibling deaths

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

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

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

gnomAD: n/a

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

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

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

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

Patient4: Male, 2.5yo

CasePresentingHPOs: HP:0002033, HP:0001254, HP:0001987, HP:0001873, HP:0002013 (poor sucking, lethargy, hyperammonaemia, thrombocytopenia, vomiting)

HPOsFreeText: acute neonatal IVA, treated with IVA special formula along with sodium benzoate and glycine (benzoate and glycine discontinued after 1yr), elevated isovalerylglycine, C5-carnitine = 17.4 µmol/l, birth weight = 3kg, able to sit at 6mo, walked at 13mo, began to babble at 17mo, did not have bladder/bowel control until 2.5yo, current weight = 14kg, current height = 86.5cm

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: symptom onset at 5do, diagnosis at 30do via clinical presentation, consanguineous family

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.863C>T (p.Ala288Val) listed in paper as c.872C>T (p.Ala291Val)

ClinVar: 281076, https://www.ncbi.nlm.nih.gov/clinvar/variation/281076/

gnomAD: n/a

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

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

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

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

Patient1: Male, 4yo, Twin A, Family A (fig. 2)

CasePresentingHPOs:

HPOsFreeText: acute neonatal IVA, treated with IVA special formula, elevated isovalerylglycine in urine organic acids, C5-carnitine = 6.15 µmol/l, at 2yo stopped formula and switched to vegetarian diet with L-carnitine supplements, admitted every 3-4mo due to metabolic crisis, at 4yo began formula again along with vegetarian diet and L-carnitine supplements, sat alone at 6mo, walked alone at 1yo, spoke first word at 1yo, unremarkable systemic examination at 4yo

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: diagnosed at 3 days old via NBS (positive family history and 3 sibling deaths), consanguineous family

CasePMIDs: PMID: 24516753

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.1184G>A (p.Arg395Gln) listed in paper as c.1193G>A (p.R398Q)

ClinVar: 529434, https://www.ncbi.nlm.nih.gov/clinvar/variation/529434/

gnomAD: n/a

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

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

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

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

Case#: GA5, Southern Italy, 40 years (onset), gender unknown

CaseHPOs: HP:0000662, HP:0012026 (night blindness, (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances at age 40 years. Plasma ornithine levels could be normalized by diet alone. Not responsive to Vitamin B6 treatment.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 805 umol/L (normal <100)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.1307T>A (p.Ile436Asn)

ClinVar: 56115

gnomAD: The maximum population minor allele frequency in gnomAD = 0.00002662 (European non-Finnish); no homozygotes in any population.

VariantEvidence: The variant was expressed in S. cerevisae with a deletion of CargB, the year ortholog of OAT, that cannot grow in media with ornithine as the sole nitrogen source. Whereas expression of wild type OAT allows yeast to grow in media with ornithine as the sole nitrogen source, no growth was observed when the variant was expressed. OAT enzymatic activity was measured and was <10% normal, and OAT protein was barely detectable on Western blot.

Case#: GA3, Turkey, 5 years (onset), gender unknown

CaseHPOs: HP:0012026 (hyperornithinemia)

CaseHPOsFreeText: Presented with visual disturbances at 5 years of age. No further details.

CaseNotHPOs: Neonatal encephalopathy

CasePreviousTesting: No previous DNA testing noted. Plasma ornithine at diagnosis 650umol/L (normal <100)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Sequence analysis of the OAT gene from fibroblast or lymphocyte cDNA and genomic DNA. Variant: NM_000274.3(OAT):c.991C>T (p.Arg331Ter) (homozygous)

ClinVar: 56141

gnomAD: The maximum population minor allele frequency in gnomAD is 0.0001446 (Latino); no homozygotes in any population.

Family#: GA-07, Lebanese Maronite

FamilyHPOs: HP:0012026

FamilyHPOText: “Clinical presentation typical of gyrate atrophy”; no further details.

FamilyGenotypingMethod: RNAse A protection assay using 2 probes to cover the entire OAT cDNA, narrowed the site of the variant to the 5’ end of the gene. DNA sequence analysis revealed c.3G>A (p.Met1?). Parents are confirmed heterozygous, based on RFLP analysis.

FamilyPreviousTesting: Elevated plasma ornithine; Fibroblast OAT activity was undetectable

Variant: NM_000274.3(OAT):c.3G>A (p.Met1?)

ClinVar: 146

gnomAD: Not in gnomAD

Proband: GA-07, Case 7, female, Lebanese, 32 (at report)

CasePreviousTesting: Plasma ornithine, on normal diet: 771uM/l (normal 75+/-25). Fibroblast OAT activity was undetectable (ornithine value from Kaiser-Kupfer, M. I., and D. Valle. 1986. Progress in Retinal Research. p179-206)

CaseAddInfo: Parents are confirmed heterozygotes.

Sibling: GA-07, Case 16, male, Lebanese, 33 (at report)

SiblingPreviousTesting: Plasma ornithine, on normal diet: 800uM/l (normal 75+/-25). Fibroblast OAT activity was undetectable (ornithine value from Kaiser-Kupfer, M. I., and D. Valle. 1986. Progress in Retinal Research. p179-206)

Points: 1 point

Case1: Male, 3 months diagnosis/death, Egypt, African

CasePresentingHPOs: HP:0001999, HP:0011968, HP:0001531, HP:0001270, HP:0001252, HP:0003468, HP:0001636, HP:0001274 (Dysmorphic facial features, Poor feeding, Failure to thrive in infancy, Motor delay, Muscle hypotonia, Abnormal vertebrae, Tetraology of Fallot, Agenesis of corpus callosum)

HPOsFreeText: Agenesis of the cingulate gyrus

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Parents are consanguinous, Proband is homozygous for this mutation, Died a few days after hospital admission in infancy

CasePreviousTesting: Increased levels of S-2-carboxypropyl-cysteamine and S-2-carboxypropyl-cysteine, Fibroblast and liver homogenates of patient 1 showed normal hydratase activities towards methacrylyl-CoA (as well as crotonyl-CoA and tiglyl-CoA),

CasePMIDs: 7122152

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant: NM_014362.3:c.220-9T>G

ClinVar: 1144 https://www.ncbi.nlm.nih.gov/clinvar/variation/1144/

gnomAD: Not in gnomAD

Case2: Male, Caucasian, 9 months onset

CasePresentingHPOs: HP:0011968, HP:0001270, HP:0001251, HP:0002376, HP:0002121, HP:0000737, HP:0002317, HP:0002599, HP:0002078, HP:0012389, HP:0001310, HP:0001337, HP:0001254, HP:0001942, HP:0002329, HP:0001308, HP:0002599, HP:0001332, HP:0002181, HP:0002134 (Poor feeding, Delayed motor milestones, Ataxia, Developmental regression, Absence seizures, Irritability, Unsteady gait, Head titubation, Truncal ataxia, Appendicular hypotonia, Dysmetria, Tremor, Lethargy, Metabolic acidosis, Drowsiness, Tongue fasciculation, Head titubation, Dystonia, Cerebral edema, Abnormality of the basal ganglia)

HPOsFreeText: Head bobbing at 4 months, Rolled over at 5 mo but lost the ability at 10 mo, Reaching out and grasping objects at 4 mo but lost the ability at 13 mo, Eye rolling episodes at 9 months, Lost ability to finger feed at 10 months, Inability to sit unsupported, At 14 months blood pH was 7.29 with a base deficit of 15.8 mmol/L, Sluggish papillary responses, Pooling of secretions in the mouth, No improvement on treatment with thiamine or a combination of vitamin C, vitamin E, and ubiquinone, Signal abnormalities in the globus pallidus and the midbrain

CaseNotHPOs: HP:0000639, HP:0002151, HP:0001987, HP:0003116, HP:0012443 (Nystagmus, Increased serum lactate, Hyperammonemia, Abnormal echocardiogram, Abnormality of brain morphology)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were nonconsanguinous, Proband is compound heterozygous for these mutations with parental testing

CasePreviousTesting: Pyruvate dehydrogenase and pyruvate carboxylase in cultured human skin fibroblasts, Activities of respiratory chain complexes in a muscle biopsy, Marked reduction of complex I (patient 0.089, controls 0.104–0.268) and a borderline reduction of complex IV (patient 0.013, controls 0.014–0.034), Organic acid analysis during ketotic episodes showed excessive excretion of 3-hydroxybutyrate and acetoacetate and moderate excretion of lactate, 2-hydroxyisovalerate, 2-oxoisocaproate, dicarboxylic acids (C6, C8, C10), and methylmalonate, with normal levels of methylcitrate as opposed to normal levels when well, Urine amino acid analysis, Elevated levels of hydroxy-C4-carnitine (patient 0.45-1.73 μM, controls <0.4 μM) even when not ketotic

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant1: NM_014362.4:c.365A>G (p.Tyr122Cys)

ClinVar: 1145 https://www.ncbi.nlm.nih.gov/clinvar/variation/1145/

gnomAD: Latino 4.338e-4, Overall 6.373e-5 https://gnomad.broadinstitute.org/variant/2-191155151-T-C

Variant2: NM_014362.3:c.79-3C>G

ClinVar: 1146 https://www.ncbi.nlm.nih.gov/clinvar/variation/1146/

gnomAD: Not in gnomAD

Case1873(W.C.) Male, 37yo report, Irish

CasePresentingHPOs HP:0002625, HP:0000766, HP:0002942, HP:0006682, HP:0005625, HP:0002353

(Deep vein thrombosis, Sternal anomaly, Thoracic kyphosis, Ventricular extrasystoles, Osteoporosis of vertebrae, EEG abnormality)

HPOsFreeText Patient had single episode of deep vein thrombosis of left leg at 30yo. No further clinical sequelae related to homocystinuria.

(PMID: 20329304): Patient was born normally at 36wks gestation weighing 2.9kg. By 9 and half years old he was well developed and nourished, mentally normal at IQ 93. He did have pronounced malar flush, some grey hair of normal texture, slightly depressed sternum, mild kyphosis of upper thoracic spine. Exam of major systems was normal save for occasional ventricular extrasystole. Roengenogram showed marked osteoporosis of spine, but normal long bones. EEG showed non-specific diffuse abnormality.

CaseNotHPOs HP:0001083

(Lens dislocation)

NotHPOsFreeText lenses were found to not be displaced upon exam at 9 and a half years old.

CasePreviousTesting Plasma homocysteine was 450μM pretreatment. Pyroxidine treatment reduced those levels to trace amounts. In patient fibroblasts, no CBS protein was detect on Western blot and CBS assay detected no activity. (PMID: 20329304): "Full hemogram, routine urine analysis, liver function tests, serum ion and iron-binding capacity, plasma magnesium, serum calcium, inorganic phosphate, fasting blood sugars, blood urea nitrogen, and bone marrow examination were all normal". Heavy homocysteine spot shown on chromatogram of urinary amino acids.

CaseMethod1 PCR

CaseMethod2 Sanger

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

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

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

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

CAID 1. CA410600501

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

CaseAddInfo Mother had edema of both legs with no other features of pre-eclampsia during the last six weeks of pregnancy.

CasePMIDs 20329304

Case2267(g) Caucasian, Hispanic

CasePresentingHPOs HP:0003571 (Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting none reported

Variant NM_000532.4(PCCB):c.1218_1231delGGGCATCATCCGGCinsTAGAGCACAGGA (p.Gly407Argfs)

ClinVar 38875

gnomAD not in gnomAD

CaseAddInfo parents tested heterozygous

CasePMIDs n/a

Case467 Caucasian

CasePresentingHPOs HP:0003571 (Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting none reported

Variant 1. NM_000532.4(PCCB):c.1218_1231delGGGCATCATCCGGCinsTAGAGCACAGGA (p.Gly407Argfs), 2. NM_000532.4:c.1222del (p.Ile408SerfsTer?)

ClinVar 1.38875, 2. n/a

CAID 2. unregistered

gnomAD 1. not in gnomAD

CaseAddInfo parents NOT tested, phase unknown

CasePMIDs n/a

CaseCHN2.1: Canada, 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.532C>T (p.Arg178Ter)

CAID: CA3182753, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182753

gnomAD: 0.0004414, https://gnomad.broadinstitute.org/variant/5-1212468-C-T

Variant2: NM_001003841.3:c.1213G>A (p.Glu405Lys)

CAID: CA3183103, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3183103

gnomAD: 0.0001203, https://gnomad.broadinstitute.org/variant/5-1219057-G-A

CaseCHN1.1: Canada, White

CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants segregate with the disease, Has a sibling with the same variant and 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.

Variant1: NM_001003841.3:c.196G>A (p.Gly66Arg)

CAID: CA359061114 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359061114

gnomAD: Not in gnomAD

Variant2: NM_001003841.3:c.982C>T (p.Arg328Cys)

CAID: CA3182972, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182972

gnomAD: 0.0002479, https://gnomad.broadinstitute.org/variant/5-1216767-C-T

CaseAHN16.1: 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.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

Case9: Male, Turkey, 24 yrs report,

CasePresentingHPOs: HP:0002251, HP:0001321, HP:0001161, HP:0025356, HP:0002474, HP:0000708, HP:0001488, HP:0002317, HP:0000646, HP:0000486 (Aganglionic megacolon, Cerebellar hypoplasia, Hand polydactyly, Psychomotor retardation, Expressive language delay, Behavioral abnormality, Bilateral ptosis, Unsteady gait, Strabismus)

HPOsFreeText: Dysgnathia

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous, Parents are consanguineous, cDNA amplification of the exons 8 and 9 in this patient revealed an insertion of 64 base pairs due to the use of a cryptic donor site leading to a premature stop codon and a likely null allele; Proband has two healthy sisters

CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; A metabolic work-up revealed alpha-ketoadipic aciduria and alpha-aminoadipic aciduria; A non-verbal intelligence test yielded a slightly decreased value; A single metabolic decompensation in adulthood was ascribed to Helicobacter pylori and its eradication improved the patient’s well-being.

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

Variant: NM_018706.6:c.1671+1G>A

CAID: CA5407905 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407905

gnomAD: 0.0001399, https://gnomad.broadinstitute.org/variant/10-12139996-G-A

Case8: Female

CasePresentingHPOs: HP:0001270, HP:0001252, HP:0011342, HP:0007479 (Motor delay, Muscular hypotonia, Mild motor developmental delay, Congenital nonbullous ichthyosiform erythroderma)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Consanguineity is suspected, Proband is homozygous

CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Urine AAA and KAA were elevated. Oxidation of radiolabeled AAA in fibroblasts was deficient.

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

CasePMIDs: 1112064, 1112065

Variant: NM_018706.7(DHTKD1):c.2134C>T (p.Arg712Ter)

ClinVar: 572241 https://www.ncbi.nlm.nih.gov/clinvar/variation/572241/

gnomAD: 0.00003267, https://gnomad.broadinstitute.org/variant/10-12149994-C-T

Case2 unknown sex, Netherlands, Dutch

CasePresentingHPOs HP:0001250, HP:0001263

(Seizures, Developmental delay)

HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 4do, first administered pyridoxine 6mo, age at trial 1.7yr, initial dose:100mg, maintenance dose:100mg/day, delayed development(PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"

CaseNotHPOs n/a

NotHPOsFreeText intrauterine seizures

CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 4.7(nv <1mmol/mol cr), α‐AASA plasma 0.9(nv <0.2μmol/l), pipecolic acid urine 0.27(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 5.8(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)

Variant 1. NM_001202404.1:c.1321T>A (p.Cys441Ser), 2. NM_001182.4(ALDH7A1):c.834G>A (p.Val278=)

ClinVar 1. n/a, 2. 18002

CAID 1. CA360721136

gnomAD 1. not in gnomAD, 2. not in gnomAD(C and not G at that position?)

CaseAddInfo Parents heterozygous for either allele=variants in trans in the patient. Two unaffected siblings, one with neither variant and the other with one copy of the p.Cys441Ser variant

CasePMIDs 17088338 , 16159904

CaseBI-1: 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.1222C>T (p.Arg408Trp)

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

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

Variant2: NM_000277.3(PAH):c.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

CaseEI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 430 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.1066-11G>A

ClinVar: 607 https://www.ncbi.nlm.nih.gov/clinvar/variation/607/

gnomAD: 0.0004116, https://gnomad.broadinstitute.org/variant/12-103237568-C-T

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

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

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

CaseAI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 330 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.143T>C (p.Leu48Ser)

ClinVar: 608 https://www.ncbi.nlm.nih.gov/clinvar/variation/608/

gnomAD: 0.001025, https://gnomad.broadinstitute.org/variant/12-102912816-A-G?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

CaseDI-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 365 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.561G>A (p.Trp187Ter)

ClinVar: 102736 https://www.ncbi.nlm.nih.gov/clinvar/variation/102736/

gnomAD: 0.00001760, https://gnomad.broadinstitute.org/variant/12-103249059-C-T

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

CaseAII-5: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 440 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

CaseAII-3: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 370 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

Case5: Female, 3.5 (report), European

CasePresentingHPOs: HP:0002194, HP:0000750, HP:0002370, HP:0002136, HP:0002066, HP:0002360, HP:0025401, HP:0012168, HP:0000252, HP:0000316, HP:0000426, HP:0000369, HP:0000347, HP:0002299, HP:0006801

HPOFreeText: Normal neonatal course. By 8 months could not crawl, subsequent gross motor development delayed. Speech and language delay. By 3.5 years showed balance problems, poor coordination, abnormal wide based gait with ataxia. Sleep disturbance , staring, behavioral issues since 1 year. Dysmorphic features noted at 3.5 years. Brain dysgenesis and partial seizure disorder.

CaseNotHPOs: No skeletal abnormaliites, no organomegaly.

CasePreviousTesting: Followup C5 carnitine 2.58 nM/ml (ref <0.63). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts. Chromosome and fragile X testing normal as well as sequencing of exons 2 and 3 of MECP2. Plasma amino acids normal as well as Angelmann syndrome testing and microarray testing.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: NM_001609.3(ACADSB):c.303+1G>A (homozygous)

ClinVar: 203367

gnomAD: Other 0.0005549

VariantEvidence: Canonical splice site variant. Discrupts canonical splicing signal of intron 3.

CaseAddInfo:

CasePMIDs:

Case2: European

CasePresentingHPOs:

HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 1.89 nM/ml (ref <0.63). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: 1. NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile) 2. NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys)

ClinVar: 1. 9202 2. 9203

gnomAD: 1. South Asian 0.002678 2. Latino 0.0004797

VariantEvidence: 1. Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro 2. In vitro expression of c.1159G>A in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stabilit

CaseAddInfo: No info on cis or trans. Also heterozygous for p.R13K polymorphism.

CasePMIDs:

Case4:

CasePresentingHPOs:

HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 2.58 nM/ml (ref <0.63). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: NM_001609.3(ACADSB):c.303+1G>A (homozygous)

ClinVar: 203367

gnomAD: Other 0.0005549

VariantEvidence: Canonical splice site variant. Discrupts canonical splicing signal of intron 3.

CaseAddInfo:

CasePMIDs:

CaseSA3P: Female, 16 months onset, European

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo via parental teting and confirmed paternity

CasePreviousTesting: 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

CaseSA5P: Female, 3 months onset, European

CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001249, HP:0001250 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Intellectual disability, Seizure)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001987 (Hyperammonemia)

NotHPOsFreeText: N/A

CaseAddInfo: Has father with confirmed variant and similar phenotypes

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

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

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

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

gnomAD: Not in gnomAD

CaseSA2P: Female, 3 months onset, European

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo via parental teting and confirmed paternity

CasePreviousTesting: Leucine load test showed leucine sensitivity in some patients; 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

CaseF-4 female, 2mo onset, Ethnicity: Southern Indian, Muslim

CasePresentingHPOs HP:0006846, HP:0001254, HP:0001987, HP:0002154, HP:0045045, HP:0003571

(Acute encephalopathy, Lethargy, Hyperammonemia, Elevated blood glycine, Elevated acylcarnitines, Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1540C>T (p.Arg514Ter)

ClinVar 217893

gnomAD MAF=0.00005015(South Asian), no homozygotes

CaseAddInfo consanguineous, abnormality in family history noted

CasePMIDs n/a

CaseF-25 female, 4do onset, Ethnicity: North Indian, Muslim

CasePresentingHPOs HP:0006846, HP:0001254, HP:0002098, HP:0001942, HP:0045045, HP:0003571

(Acute encephalopathy, Lethargy, Respiratory distress, Poor feeding, Metabolic acidosis, Elevated acylcarnitines, Propionicacidemia)

HPOsFreeText Serum ammonia 86.4micromolar

CaseNotHPOs n/a

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1498+2T>C

ClinVar 217895

gnomAD not in gnomAD

CaseAddInfo consanguineous, no abnormalities in family history noted

CasePMIDs n/a

CaseF-2 male, 14mo onset, Ethnicity: North Indian, Hindu

CasePresentingHPOs HP:0001263, HP:0003571

(Developmental delay, Propionicacidemia)

HPOsFreeText normal plasma amino acids, acylcarnitines 13.9(normal <3.6nmol/mL), normal development by 6.5 years

CaseNotHPOs HP:0001942, HP:0001987

(Metabolic acidosis, Hyperammonemia)

CasePreviousTesting Also screened for variants in PCCA

Variant NM_000532.4(PCCB):c.1210G>A (p.Glu404Lys)

ClinVar 217891

gnomAD MAF= 0.00003266(South Asian), no homozygotes

CaseAddInfo nonconsanguineous, no abnormality in family history noted

CasePMIDs n/a

Case: BIODEF 306, male, Caucasian, 7 days (per BIODEF website)

CasePresentingHPOs: HP:0008297, HP:0040210

Increased primapterin levels in urine.

CaseNOTHPOs:

CasePreviousTesting: n/a

CaseGenotypingMethod: Assumed PCR of exons 2-4 of PCBD1 followed by direct sequencing. Psuedogenes were not assessed.

Variant: NM_000281.3(PCBD1):c.289G>A (p.Glu97Lys)

ClinVar ID: 91907

Homozygous

gnomAD: MAF (Euro-NF)= 2.320E-5 in hets only, no homozygous. http://gnomad.broadinstitute.org/variant/10-72643733-C-T

AddCaseInfo: Parents noted as consanguineous on the BIODEF website.

VariantEvidence: Expression of recombinant protein in bacteria revealed that the E97K are present in the insoluble fraction compared to wildtype which is found in the soluble. The little amount retained of each in the soluble fraction showed that they retained activity. Dehydratase activity of the patients duodenal mucosa cells showed reduced activity of he E97K (17% activity) mutant compared to wildtype , indicating that this mutation severely reduces the activity of PCBD1.

Patient16: Group 3

CasePresentingHPOs: same as group 3

CasePreviousTesting: same as group 3

CaseGenotypingMethod: same as group 3

Variant1: NM_001159508.1:c.149G>C (p.Arg50Thr) listed in paper as (p.Arg21Pro)

CAID: CA391743853, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391743853

gnomAD: n/a

Variant2: NM_002225.4:c.851G>A

CAID: CA7480763, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA7480763

**In ClinVar as: NM_002225.3(IVD):c.860G>A (p.Arg287Gln), https://www.ncbi.nlm.nih.gov/clinvar/variation/555453/ **

gnomAD: 0.00001770, http://gnomad.broadinstitute.org/variant/15-40707154-G-A

Patient18: Group 3

CasePresentingHPOs: same as group 3

CasePreviousTesting: same as group 3

CaseGenotypingMethod: same as group 3

Variant1: NM_002225.3:c.1136T>C (p.p.Ile349Thr) **listed in paper as (p.Phe350Ser)

CAID: CA391723904, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391723904

gnomAD: n/a

Variant2: IVS3+5G>T no ClinVar or CAID

Patient8: Group 2

CasePresentingHPOs: same as group 2

CasePreviousTesting: same as group 2

CaseGenotypingMethod: same as group 2

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

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

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

Variant2: NM_002225.3:c.262G>T

CAID: CA391745812, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391745812

gnomAD: n/a

Patient4: Female, 3yo sibling to patient 5

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 4.0 μmol l−1, IVA incorp (%) = 80, IVG in urine mmol permol creatinine = 242, Ammonium (μmol l−1) = 31, pH = 7.37, Protein intake (g kg−1 per day) = 1.5, treated with carnitine supplements, PDI/IQ in follow-up = 92

CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS, diagnosed at 26 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.4(IVD):c.1205T>C (p.Ile402Thr)

ClinVar: 529433, https://www.ncbi.nlm.nih.gov/clinvar/variation/529433/

gnomAD: n/a

Variant2: NM_001159508.1:c.500T>C

CAID: CA391717541, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391717541

gnomAD: n/a

Patient7: Male, 2yo

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 1.6 μmol l−1, IVG in urine mmol permol creatinine = 272, IVA incorp (%) = 72, Ammonium (μmol l−1) = 51, pH = 7.39, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 93

CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 28 days, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.706G>A

CAID: CA268780419, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268780419

gnomAD: 0.00003187, http://gnomad.broadinstitute.org/variant/15-40705199-G-A

Patient14: Male, 24yo

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259, HP:0001987, HP:0001941

(poor feeding, vomiting, dehydration, lethargy, coma, hyperammonemia, acidosis)

HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 4.3 μmol l−1, IVA incorp (%) = 12, IVG in urine mmol permol creatinine = 16594, Ammonium (μmol l−1) = 126, pH = 7.17, Protein intake (g kg−1 per day) = 0.7, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 88

CaseNotHPOs:

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed via clinical findings at 1yo, hospitalized outside of detection period

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: c.1-?_c.295+? (Delexons 1–3) no ClinVar or CAID

Variant2: NM_002225.4(IVD):c.1184G>A (p.Arg395Gln) listed in paper as (p.Arg395His)

CAID: CA268781747, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268781747

ClinVar: 529434, https://www.ncbi.nlm.nih.gov/clinvar/variation/529434/

gnomAD: 0.00001415, http://gnomad.broadinstitute.org/variant/15-40710365-G-A

Patient11: Female, 19yo, sibling to patient 10

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

HPOsFreeText: intermittent isovaleric acidemia, IVA incorp (%) = 13, IVG in urine mmol permol creatinine = 3488, Ammonium (μmol l−1) = 47 pH = 7.33, Protein intake (g kg−1 per day) = 1.0, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 85, sweaty feet odor

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Diagnosed via clinical findings at 2yo

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.3(IVD):c.884T>C (p.Leu295Pro)

ClinVar: 555464, https://www.ncbi.nlm.nih.gov/clinvar/variation/555464/

gnomAD: n/a

Variant2: NM_002225.3:c.1211A>G

CAID: CA391724518, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391724518

gnomAD: n/a

Patient13 Male, 9yo

CasePresentingHPOs: HP:0011968, HP:0001254, HP:0001259, HP:0001987

(poor feeding, lethargy, coma, hyperammonemia)

HPOsFreeText: acute isovaleric acidemia, C5 (DBS) = 16.3 μmol l−1, IVA incorp (%) = 5.5, IVG in urine mmol permol creatinine = 3352, Ammonium (μmol l−1) = 606, pH = 7.26, Protein intake (g kg−1 per day) = 0.8, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 87, sweaty feet odor

CaseNotHPOs: HP:0002013, HP:0001944 (vomiting, dehydration)

NotHPOsFreeText:

CaseAddInfo: diagnosed via clinical findings at 20 days old, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.158G>C listed in clinvar as NM_002225.4(IVD):c.149G>C (p.Arg50Pro)

CAID: CA274129, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA274129

ClinVar: 188922, https://www.ncbi.nlm.nih.gov/clinvar/variation/188922/

gnomAD: 0.00001591, http://gnomad.broadinstitute.org/variant/15-40699841-G-C

Case# P1, 4day onset, Turkish

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

CasePreviousTesting negative for NAGS and CPS1 genes.

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

Variant NM_001739.1:c.123G>A

CAID CA397038622

VariantEvidence truncated protein

CaseAddInfo consanguineous

Case# P7, 5day onset, Bangladesh

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

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

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

Variant NM_001739.1(CA5A):c.721G>A (p.Glu241Lys)

ClinVar 388645

gnomAD 0.002694 (South Asian), 0.0003177 (Overall)

VariantEvidence CA5A variant in Sf9 insect cells exhibited 26.1% of WT enzyme activity (Fig 2d).

CaseAddInfo consanguineous

Case23 Female, 5.2yo report, Ethnicity: Russian

CasePresentingHPOs HP:0003571, HP:0012523, HP:0001531, HP:0001944, HP:0001259, HP:0001250

(propionicacidemia, oral aversion, failure to thrive in infancy, dehydration, coma, seizures)

HPOsFreeText feeding refusal, failure to thrive, dehydration, coma, seizures(7do). 55 IQ on Culture-Free-Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosis by newborn screening. PCC activity in patient fibroblasts was 0.5% of control.

Variant NM_000532.4:c.803T>G (p.Leu268Trp), homozygous

ClinVar n/a

CAID CA354644558

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

Case8 Male, 9.8yo report, Ethnicity:Turkish

CasePresentingHPOs HP:0012523, HP:0001508, HP:0002013, HP:0008947, HP:0002789, HP:0002045, HP:0002014, HP:0003571

(propionicacidemia, oral aversion, failure to thrive, vomiting, infantile hypotonia, tachypnea, hypothermia, diarrhea)

HPOsFreeText feeding refusal, failure to thrive, vomiting, hypotonia, tachypnea, hypothermia, diarrhea (4do). 73 IQ on Culture Free Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screening

Variant NM_000532.4:c.429+3_6delAAGT (p.Asp125_Lys143del), homozygous

ClinVar n/a

CAID to register

gnomAD not in gnomAD

CaseAddInfo parental consanguinity

CasePMIDs n/a

Case10: Male, Ecuador

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001558, HP:0000602, HP:0001622, HP:0001371, HP:0001623, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia, Preterm delivery, Contractures, Breech presentation, Arthrogryposis)

HPOsFreeText: Bilateral femoral fractures

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 6 weeks

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.976G>C (p.Gly326Arg)

CAID: CA353473660 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.976G%3EC

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1372C>T (p.Gln458*)

CAID: CA353470920 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.1372C%3ET

gnomAD: Not in gnomAD

Case6: Female, Japan, Asian

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0001789, HP:0000252, HP:0001622, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movement, Hydrops fetalis, Microcephaly, Preterm delivery, Contractures)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 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: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

Case3: Female, Portugal

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0001558, HP:0001561, HP:0001371 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Decreased fetal movement, Polyhydramnios, Contracture)

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.154del (p.Met52*)

CAID: CA909810717 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.154delA

gnomAD: Not in gnomAD

Case12a: Male, Afghanistan

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0002804, HP:0001558, HP:0001622, HP:0001623, HP:0003798 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Arthrogryposis, Decreased fetal movement, Preterm delivery, Breech presentation, Nemaline bodies)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in 2 months, Has 2 siblings 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

Case14a: Female, Australia

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0001622, HP:0002804, HP:0003798, HP:0001558, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Nemaline bodies, Decreased fetal movements, Ophthalmoplegia)

HPOsFreeText: Atrophic myofibers, Percutaneous endoscopic gastrostomy performed, Nocturnal noninvasive ventilation

CaseNotHPOs: HP:0001627, HP:0002540 (Cardiac abnormality, Inability to walk)

NotHPOsFreeText: N/A

CaseAddInfo: Typical congenital nemaline myopathy, Alive at 10 yrs, Parents are not 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.

Variant1: NM_198271.4:c.1103_1105del (p.Asn368del)

ClinVar: 162216 https://www.ncbi.nlm.nih.gov/clinvar/variation/162216/

gnomAD: Not in gnomAD

Variant2: NM_198271.4:c.1201C>T (p.Arg401Ter)

ClinVar: 162217 https://www.ncbi.nlm.nih.gov/clinvar/variation/162217/

gnomAD: African 4.137e-5, Overall 7.135e-6 https://gnomad.broadinstitute.org/variant/3-69168305-G-A

Case5: Female, Japan, Asian

CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0100309 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movements, Subdural hemorrhage)

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 2 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.300_304delGACTC (p.Thr101Argfs*4)

CAID: CA913203453 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203453

gnomAD: Not in gnomAD

Variant1: NM_198271.4:c.601_602delGA (p.Asp201Glnfs*9)

CAID: CA913203454 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203454

gnomAD: Not in gnomAD

CaseAN: Male, 78 yrs report, Germany, White

CasePresentingHPOs: HP:0003774, HP:0001638, HP:0000822, HP:0002099, HP:0012125, HP:0001297, HP:0002134, HP:0002549, HP:0000738, HP:0000739, HP:0000746, HP:0002322, HP:0002172, HP:0012120 (Stage 5 chronic kidney disease, Cardiomyopathy, Hypertension, Asthma, Prostate cancer, Stroke, Abnormality of the basal ganglia, Deficit in phonologic short-term memory, Hallucinations, Anxiety, Delusions, Resting tremor, Postural instability, Methylmalonic aciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Mother had dementia, Proband is diagnosed with Parkinson's disease, Sanger sequencing confirmed compound heterozygous as unaffected sons are heterozygous for one variant each

CasePreviousTesting: Montreal Cognitive Assessment (MoCA) score of 17/30 in 2013; Mild MMA-uria, together with increased plasma levels of propionyl-carnitine, was demonstrated in 2016 via metabolic investigation (values in Table 1)

CaseGenotypingMethod: Whole genome sequencing data was analyzed using a pipeline restricted to 681 genes known to cause IEM. Heterozygous mutations in MCEE were identified.

Variant1: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

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

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

Variant2: NM_032601.3:c.419del (p.Lys140Argfs*6)

CAID: CA1702578, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1702578

gnomAD: 0.00007076, https://gnomad.broadinstitute.org/variant/2-71337211-CT-C

CaseCA4: Male, 6 months death

CasePresentingHPOs: HP:0001644, HP:0001508 (Dilated cardiomyopathy, Failure to thrive)

HPOsFreeText: N/A

CaseNotHPOs: N/A

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 obligate heterozygotes, III.2, a heterozygous carrier, and III.4.

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

Case# P1, Male, Chinese, 5 months

CasePresentingHPOs HP:0006986, HP:0002373, HP:0008947, HP:0001249

CaseMethod1 PCR

CaseGenotypingMethod PCR of sevon exons of QDPR gene

Variant NM_000320.2:c.661C>T(p.R221X), NM_000320.2:c.515C>T(p.P172L)

CAID CA2868005, CA2868085

gnomAD (Latino) 0.00002978, (Ashkenazi Jewish) 0.0001019

VariantEvidence null

CasePMIDs 19099731

Case1: Male, 15 months onset, Iran

CasePresentingHPOs: HP:0006579, HP:0001324, HP:0001336, HP:0000639, HP:0002134, HP:0002282, HP:0002453, HP:0002540, HP:0002463, HP:0006801, HP:0001252, HP:0011443, HP:0001251, HP:0001310, HP:0000565, HP:0001510 (Neonatal jaundice, Muscle weakness, Myoclonus, Nystagmus, Abnormality of the basal ganglia, Heterotopia, Abnormality of the globus pallidus, Inability to walk, Language impairment, Hyperactive deep tendon reflexes, Muscular hypotonia, Abnormality of coordination, Ataxia, Dysmetria, Esotropia, Growth delay)

HPOsFreeText:

CaseNotHPOs: HP:0012443, HP:0012447 (Abnormality of brain morphology, Abnormal myelination)

NotHPOsFreeText:

CaseAddInfo: No parental consanguinity,

CasePreviousTesting: Plasma amino acids and plasma acylcarnitine profile were normal. The organic acid in the urine showed an elevated 3‐hydroxyisovaleric acid (110 mmol/mol creatinine, normal <44 mmol/mol creatinine). Serum biotinidase activity was normal. Blood lactate and ammonia were normal in repeated measurements.

CaseGenotypingMethod: Patient had the IVD exons and exon-intron boundaries analyzed using PCR/Sanger sequencing to follow up on suspected IVA, with no variants found. Whole Exome Sequencing was performed to determine the correct genetic cause of the disorder by evaluating all known exons and their flanking regions. This found two heterozygous missense mutations in HIBCH consistent with the diagnosis. Trio PCR/Sanger sequencing confirmed parental heterozygosity and the variants in the patient.

Variant1: NM_014362.3:c.641C>T (p.Thr214Ile)

CAID: CA349890265 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.641C%3ET

gnomAD: Not in gnomAD

Variant2: NM_014362.3:c.913A>G (p.Thr305Ala)

CAID: CA62635843 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.913A%3EG

gnomAD: European (Non-Finnish) 1.767e-5, Overall 7.978e-6 https://gnomad.broadinstitute.org/variant/2-191077780-T-C

CaseST-8: Female, 1 day onset, Germany

CasePresentingHPOs: HP:0006579, HP:0001643, HP:0001410, HP:0001319, HP:0006236, HP:0001786 (Prolonged neonatal jaundice, Patent ductus arteriosus, Decreased liver function, Neonatal hypotonia, Slender metacarpals, Narrow foot)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001250 (Seizure)

NotHPOsFreeText: N/A

CaseAddInfo: Family is non-consanguineous, Proband is compound heterozygous for these variants

CasePreviousTesting: See Group

CaseGenotypingMethod: See Group

Variant1: NM_001123.3:c.893C>A (p.Ala298Asp)

CAID: CA377399006, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399006

gnomAD: Not in gnomAD

Variant2: NM_001123.3:c.925C>T (p.Gln309Ter)

CAID: CA377398330, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377398330

gnomAD: Not in gnomAD

CaseST-6: Male, 1 day onset, Morocco

CasePresentingHPOs: HP:0006579, HP:0001249, HP:0001270, HP:0001324, HP:0004322, HP:0000256, HP:0000316, HP:0006236, HP:0001786, HP:0008070, HP:0000708, HP:0002355, HP:0003202, HP:0002071 (Prolonged neonatal jaundice, Intellectual disability, Motor delay, Muscle weakness, Short stature, Macrocephaly, Hypertelorism, Slender metacarpals, Narrow foot, Sparse hair, Behavioral abnormality, Difficulty walking, Skeletal muscle atrophy, Abnormality of extrapyramidal motor function)

HPOsFreeText: N/A

CaseNotHPOs: HP:0001250 (Seizure)

NotHPOsFreeText: N/A

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

CasePreviousTesting: See Group

CaseGenotypingMethod: See Group

Variant: NM_001123.3:c.685_687delinsCC (p.Thr229ProfsTer16)

CAID: CA1139768931, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139768931

gnomAD: Not in gnomAD

Case4: Female, 2 wks at initation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.0 umol/L, Plasma C4-acylcarnitine 1.52 umol/L

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case4 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.443C>T (p.Pro148Leu)

ClinVar: n/a

CAID: CA6372945

gnomAD: not in gnomAD

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygote, indicated alleles 1 and 2 but not specified maternal and paternal, potential splice site variant of ACAD8 at exon3 (+3A>G)

Case3a: Male, 5d at initiation of follow up, East Indian Ancestry, sibling of Case 3b (family 1)

HPOsFreeText: NBS C4-acylcarnitine 2.4 umol/L, Plasma C4-acylcarnitine 1.14 umol/L, in vitro probe isoC4-acylcarnitine 0.133 umol/ g protein,

NotHPOsFreeText: normal urine isobutyrylglycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3a (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

Case9: Male, 2 mo at initiation of follow up, Hispanic ancestry

HPOsFreeText: NBS C4-acylcarnitine 1.8 umol/L, Plasma C4-acylcarnitine 3.28, umol/L, in vitro probe isoC4-acylcarnitine 0.074 umol/g protein, urine C4-acylcarnitine 7.86 mmol/mol creatinine, Urine C4/C3 ratio 63

NotHPOsFreeText: normal urine isobutyrylglycine

CaseAddInfo: unremarkable clinical condition

Case9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.233T>C (p.Met78Thr)

ClinVar: 430160

CAID: CA6372883

gnomAD: n/a

CaseAddInfo: homozygous variants, no potential splice site alterations, no data for ACADS (SCAD-deficient) gene variants

Case2: Female, 3 m at initiation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.5 umol/L, plasma C4-acylcarnitine 10.00 umol/L, isoC4-acylcarnitine 0.120 umol/g protein, in vitro prob C4-acylcarnitine 0.220 umol/ g protein

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2(ACAD8):c.289G>A (p.Gly97Arg)

ClinVar: 281037

CAID: CA6372897

gnomAD: 0.0002175 (East Asian)

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygous, potential splice-site alteration on ACAD8 at Exon 3 (+3A>G), homozygous for two common ACADS (SCAD-deficient) gene variants (625G>A/625G>A) which has 22% frequency in general population and correlates with increased accumulation of butyrylcarnitine

Case# 18804, Spanish, 3yo report

CaseHPOs asymmptomatic

Variant NM_000709.3:c.647C>T, NM_000709.3:c.889C>T

CAID CA9461230(c.647), CA9461294(889)

gnomAD c.647=0.0001332(African), 0.00002463(Overall), c.889=0.00006534(African), 0.00001624(Overall)

VariantEvidence reduced BCKD activity to 30% of normal in patient fibroblasts

CaseAddInfo in trans

Case# 20493, Spanish, 1yo reported

CasePresentingHPOs HP:0008344

CasePreviousTesting categorized into classical and variant phenotypes based on BCKD deficiency assessed by measuring the L-[1-14C] leucine decarboxylation rate by intact cells in absence of BCKD kinase inhibitors (Duran, et al., 1978), plasma amino acid levels, and mode of clinical presentation

CaseMethod1 Direct Sequencing

CaseMethod2 PCR

CaseGenotypingMethod direct sequencing of PCR fragments obtained after amplification of the entire coding sequence of BCKDHA, BCKDHB or DBT genes. sequenced both strands (forward and reverse) of corresponding exons and their intronic flanking sequence for confirmation.

Variant NM_000709.3:c.757G>A, NM_000709.3:c.848G>A, NM_000709.3:c.898G>A

CAID CA9461255(757), [CA406013082(848)&CA406013351(898)]

gnomAD c.757=0.00006681(European(Non-Finnish)), 0.00003236(Overall)

VariantEvidence Patient fibroblasts had <1% of normal BCKD activity

CaseAddInfo parents genotypes confirmed (in trans)

Case# 5888, Spanish, 10mo death

Variant NM_000709.3(BCKDHA):c.940C>T (p.Arg314Ter), NM_000709.3(BCKDHA):c.1037G>A (p.Arg346His)

ClinVar 224072(c.940), 93336(c.1037)

gnomAD c.940=0.000008958(European (Non-Finnish)), 0.000004064(Overall)

CaseAddInfo not confirmed in trans

Case# 16243, Spanish, 5yo reported

CasePresentingHPOs HP:0008344, HP:0001315

CasePreviousTesting categorized into classical and variant phenotypes based on BCKD deficiency assessed by measuring the L-[1-14C] leucine decarboxylation rate by intact cells in absence of BCKD kinase inhibitors (Duran, et al., 1978), plasma amino acid levels, and mode of clinical presentation

CaseMethod1 Direct Sequencing

CaseMethod2 PCR

CaseGenotypingMethod direct sequencing of PCR fragments obtained after amplification of the entire coding sequence of BCKDHA, BCKDHB or DBT genes. sequenced both strands (forward and reverse) of corresponding exons and their intronic flanking sequence for confirmation.

Variant NM_000709.3(BCKDHA):c.117delC (p.Arg40Glyfs), NM_000709.3(BCKDHA):c.117dupC (p.Arg40Glnfs)

ClinVar 93342(del), 166741(dup)

gnomAD del=0.0007494(African), 0.0001696(Overall)

CaseAddInfo in trans

CasePMIDs duplication variant in 8037208

CaseLE12: Female, 23 yrs report

CasePresentingHPOs: HP:0002725 (Systemic lupus erythematosus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant 1 homozygous, with variant 2 in-cis with one copy confirmed 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.1553C>A (p.Ala518Asp)

CAID: CA8238286, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8238286

gnomAD: 0.00006153, https://gnomad.broadinstitute.org/variant/16-89212397-C-A

Variant2: NM_001243279.3:c.473C>T (p.Pro158Leu)

CAID: CA8237662, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8237662

gnomAD: 0.0002823, https://gnomad.broadinstitute.org/variant/16-89167562-C-T