CaseOPOPD-67: Female, Taiwan, Birth diagnosis

HPOsFreeText: GAA (MS/MS) enzyme activity at 0.93 umol/hr/L

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.1726G>A (p.Gly576Ser)

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

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

Variant2: NM_000152.4:c.2236T>G (p.Trp746Gly)

ClinVar: 556431 https://www.ncbi.nlm.nih.gov/clinvar/variation/556431/

gnomAD: East Asian 6.410e-4, Overall 3.186e-5 http://gnomad.broadinstitute.org/variant/17-78090813-T-G

CaseAddInfo: One Pompe Mutation allele and One Pseudodeficency Mutation allele, 2 other patients have this genotype

CaseOPM-1: Male, Taiwan, Birth diagnosis

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

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

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

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

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

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

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

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

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

CaseIP2-6: Female, Taiwan, Birth diagnosis

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

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

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

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

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

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

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

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

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

Subject II-4: female

CasePresentingHPOs:

HPOsFreeText: normal GAA enzyme values

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: carrier status, clinically asymptomatic

CasePMIDs:

CasePreviousTesting: DBS

CaseGenotypingMethod: GAA genotyping

Variant: NM_000152.4(GAA):c.2560C>T (p.Arg854Ter)

ClinVar: 4034, https://www.ncbi.nlm.nih.gov/clinvar/variation/4034/

gnomAD: 0.0002090, http://gnomad.broadinstitute.org/variant/17-78092070-C-T

Case64

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

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

Variant1: NM_000152.4:c.1655T>C (p.Leu552Pro)

ClinVar: 279811 https://www.ncbi.nlm.nih.gov/clinvar/variation/279811/

gnomAD: European (Non-Finnish) 7.053e-5, Overall 3.188e-5 http://gnomad.broadinstitute.org/variant/17-78085800-T-C

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

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

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

CaseAddInfo: Adult Late Onset Pompe Disease

Patient3: 53yo

CasePresentingHPOs: HP:0002870

HPOsFreeText: hyperCKemia, GAA = 16%, BMI = 27.7, left vertebral artery dominant, temporo-insular lacunes

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 24yr disease duration

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.-32-13T>G

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

gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

CaseLOPD-12: 2 weeks diagnosis

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

GenotypingMethod: Newborn Screening Panels

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

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

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

Chromosomal code not provided and typo likely

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

ClinVar: N/A

gnomAD: N/A

CaseAddInfo: Late Onset Pompe Disease

Patient18: Male, Northern China

CasePresentingHPOs:

HPOsFreeText: IOPD

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo:

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

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

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

gnomAD: 0.0001721, http://exac.broadinstitute.org/variant/17-78086721-C-A

Variant2: NM_000152.4(GAA):c.796C>T (p.Pro266Ser)

ClinVar: 556117, https://www.ncbi.nlm.nih.gov/clinvar/variation/556117/

gnomAD: n/a

NM_002458:c.7975C>T

Unable to identify variant for following reasons: 1) NM_002458 is forMUC5B not ITGA2B 2) ITGA2B c.7975 is outside the references in allele registry

CaseCII-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 1515 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

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

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

CaseAII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 375 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

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

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

CaseBII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 270 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?dataset=gnomad_r3

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

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

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

Case3:

CasePresentingHPOs:

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

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 0.25 nM/ml (ref 0.33). 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.621G>A (p.Trp207Ter) 2. unknown

ClinVar: 299075

gnomAD:

VariantEvidence: Genomic DNA showed heterozygosity for this variant, but cDNA indicated homozygosity. The variant on the second allele must result in loss of transcription, abnormal splicing, unstable RNA, or deletion containing exon 5.

CaseAddInfo:

CasePMIDs:

CaseF1P: Female, 8 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

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

CaseGenotypingMethod: N/A

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

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

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

CaseF6P: 1 yr report, India

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Family is consanguinous, Predicted to undergo NMD

CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was N/A μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

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

Variant: NM_000277.3(PAH):c.526C>T (p.Arg176Ter)

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

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

Monoallelic, AD

Case#: Muriello case

CaseHPOs: HP:0003235 (hypermethioninemia)

CaseHPOsFreeText: Elevated methionine on newborn screen. Intermottent elevations of ALT (66 and 88 U/L) with normal AST, alkaline phosphatase and total bilirubin.

CaseNotHPOsFreeText: Normal plasma homocysteine

CasePreviousTesting: Plasma methionine 0.81 mg/dL (54 μmol/L) at 1 day, 1.08 mg/dL (73 μmol/L) at 16 days (normal < 0.8 mg/dL). Methionine concentration was 175, 185, 192, 136, 75 μmol/L (reference range 9–43 μmol/L) at ages 3.5 weeks, 2 months, 3 months, 5 months, and 12 months, respectively. Normal plasma homocysteine, normal tyrosine. Normal S-adenosylmethionine, and S-adenosylhomocysteine.

CaseGenotypingMethod: WES

Variant: NM_000429.2:c.776C>T (p.Ala259Val) (heterozygous)

ClinVar: 279845

gnomAD: The highest population minor allele frequency in gnomAD is 0.00006437 (African)

VariantEvidence: In the dimerization domain, like p.R264H. 80% reduction of the MAT activity

CaseAddInfo: The variant is maternally inherited. The mother had a mild elevation of methionine of 50 μmol/L (normal range 10–42) at 27 years of age; this was normal on repeat at 28 years old (33 umol/L) Transaminases were normal on both occasions, but she had a history of elevated liver enzymes as a child including a hepatitis-like illness, which lasted months.

CasePMIDs:

Points: 0.5 This patient and her mother are heterozygous for a missense variant in MAT1A. The highest population minor allele frequency in gnomAD is 0.00006437 (African). The Ala259 residue is located in the dimerization interface of the protein and is predicted to act in a dominant negative fashion by interfering with the dimerization (MAT III) or tetramerization (MAT I) of the enzyme.

Case765: Female, 9 years report, Spain

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

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

CaseNotHPOs: HP:0003345 (Glutathione synthetase deficiency)

NotHPOsFreeText: N/A

CaseAddInfo: Patient is homozygous for this variant

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

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

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

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

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

Case# P2, M, 1mo onset, Indian

CasePresentingHPOs HP:0001263, HP:0001250, HP:0001298, HP:0008344

CasePreviousTesting Biochemical testing (Leu + Ile- 1235 Val- 591) on Tandem Mass Spectrometry (TMS) and/or abnormal metabolites (elevated BCKAs, 2-keto isocaproate, 3-hydroxy butyrate, 2-hydroxy isovalerate, 2-hydroxy caproate, 2-keto 3-methyl valerate) on a urinary organic acid profile using Gas Chromatography Mass Spectrometry (GC–MS) was performed to make the diagnosis.

CaseMethod1 PCR

CaseMethod2 Direct

CaseGenotypingMethod Coding regions as well as flanking exon–intron boundaries of genes (BCKDHA- 9 exons, BCKDHB- 10 exons, and DBT- 11 exons) were amplified by PCR. Bidirectional Sequencing on products

Variant NM_000709.3(BCKDHA):c.844G>C (p.Asp282His)

ClinVar 204377

VariantEvidence none

CaseAddInfo consanguineous

Case#: P4, F, 13 days (onset)

CasePresentingHPOs: HP:0001250, HP:0007105

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 1810, Val- 275. Diagnosed with classic form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case#: P15, F, 2 months (onset)

CasePresentingHPOs: HP:0001263, HP:0200134

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 517, Val- 315. Diagnosed with intermediate form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case10 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Probable PDE: either pyridoxine-responsive seizures and an affected sibling or neonatal seizures responsive to a single dose of pyridoxine with later recurrence of seizures again responsive to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 7.5(nv 0.4-4.9µmol/liter), AASA in plasma 5.5(nv<0.2µmol/liter), urine AASA 26(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

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

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case6 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 23(nv 0.8-5.5µmol/liter), AASA in plasma 4.6(nv<0.2µmol/liter). Normal urine PA after pyridoxine treatment.

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

ClinVar 1. 17995 2. 17994

gnomAD 1. MAF=0.0001385(Other), no homozygotes 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case5 age/gender unknown, Caucasian, Italy

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 7.8(nv 0.4-4.9µmol/liter), AASA in plasma 5.8(nv<0.2µmol/liter), urine AASA 28(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

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

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

FamilyLabel Family R

FamilyRPresentingHPOs HP:0000750

(Speech delay)

HPOsFreeText born at 40wks gestational age. (infancy/childhood:) motor problems, speech delay/difficulties

FamilyNotHPOs HP:0025116

(Fetal distress)

CountryOrigin n/a

Ethnicity Asian

Race n/a

FamilyRPreviousTesting n/a

ProbandLabel R1

Variant NM_001182.4(ALDH7A1):c.1224T>G (p.Tyr408Ter), homozygous

ClinVar 18000

gnomAD MAF=0.00006535(South Asian), no homozygotes

FamilyAddInfo first cousin parents

FamilyPMIDs n/a

CaseG1 Female, 17mo report, Turkish

CasePresentingHPOs HP:0003270, HP:0002013, HP:0000737, HP:0011169, HP:0010818, HP:0001336, HP:0011182

(Abdominal distension, Vomiting, Irritability, Clonic seizures, Generalized tonic seizures, Myoclonic jerks, Epileptiform EEG discharges)

HPOsFreeText born at 40wks gestation. (neonatal, pre-treatment:) abdominal distension, vomiting, irritability, 3wks onset of clonic and generalized tonic fits as well as myoclonic jerks, epileptiform discharges with normal background activity, resistance to ACD's. Pyridoxine trial introduced at 9wks, trial dose/route of 10mg/kg/d p.o., complete cessation of seizures, but experienced hypotonia/sleepiness, no apnoea or hypotension, initial maintenance daily dose=10mg/kg. Withdrew form trial at 7mo, seizures recurred after 17 days.

CaseNotHPOs HP:0001557, HP:0025116, HP:0001941, HP:0002098, HP:0001290, HP:0010851, HP:0002521, HP:0000486, HP:0000750

(Abnormal intrauterine movements, Fetal distress, Acidosis, Respiratory distress, Hypotonia, EEG with burst suppression, Hypsarrhythmia, Squint, Speech delay)

NotHPOsFreeText (neonatal, pre-treatment:) acidosis, respiratory distress, hypotonia, burst suppression on EEG, hypsarrythmia. (infancy/childhood:) recurrence of seizures with febrile illness, squint, motor problems, speech delay/difficulties, MRI changes

CasePreviousTesting Administration of pyridoxine relieved patient's seizures. CSF pipecolic acid: 0.6(nv<0.15μM), plasma pipecolic acid: 5.5, 4.9(nv<2.5μM), plasma AASA: 4.1(nv<0.2μM), urine AASA: 53(nv<1 mmol/mol creatinine).

Variant NM_001182.4(ALDH7A1):c.596C>T (p.Ala199Val), homozygous

ClinVar 17998

gnomAD not in gnomAD

CaseAddInfo 1st cousin parents

CasePMIDs n/a

CasePA007 4do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0011968, HP:0002098, HP:0001290, HP:0002240, HP:0002789, HP:0004372, HP:0001987, HP:0003811

(propionicacidemia, poor feeding, respiratory distress, hypotonia, hepatomegaly, tachypnea, disturbed consciousness, hyperammonemia, neonatal death)

HPOsFreeText poor activity and other phenotypes presented at 4 days old. Died at 6 days old

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val),2. NM_000532.4(PCCB):c.838dup (p.Leu280Profs)

ClinVar 1. 554490, 2. 552435

gnomAD 1. MAF= 0.0003510(East Asian), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

CasePA006 2yo report, Taiwan

CasePresentingHPOs HP:0011343, HP:0003571

(moderate global developmental delay, propionicacidemia)

HPOsFreeText did not experience other classical PA phenotype after liver transplant(10mo) during 12-month follow up. Urine methylcitrate levels and serum propionylcarnitine levels have not markedly decreased

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4(PCCB):c.1534C>T (p.Arg512Cys)

ClinVar 1. 554490, 2. 38879

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. MAF=0.00005440(East Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

CasePA005-2 8yo report, Taiwan

CasePresentingHPOs HP:0003571, HP:0011968, HP:0002013, HP:0001987, HP:0011343

(propionicacidemia, poor feeding, vomiting, hyperammonemia, moderate developmental delay)

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4:c.-4156_183+3713del

ClinVar 1. 554490, 2. n/a

CAID 2. n/a

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. n/a

CaseAddInfo Older sister presented at two weeks old with poor feeding, vomiting, hyperammonemia, metabolic acidosis, recurrent infection, and elevated urine 3-hydroxypropionic and 2-methyl-3-hydroxybutyric acids suggestive of PA. Died of severe infection at 1yr 6mo without genetic testing

CasePMIDs n/a

CasePA004 40do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0001987, HP:0011968, HP:0001263, HP:0000952, HP:0001942, HP:0001522

(propionicacidemia, hyperammonemia, poor feeding, developmental delay, jaundice, metabolic acidosis, death in infancy)

HPOsFreeText severe jaundice and other symptoms at 40days old. Death at 1yr 6mo

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), homozygous

ClinVar 554490

gnomAD MAF= 0.0003510(East Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

CasePA002-2 prenatal diagnosis, Taiwan

CasePresentingHPOs HP:0003571

(propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1316A>G (p.Tyr439Cys), 2. NM_000532.4:c.-4156_183+3713del

ClinVar 1. 225429, 2. n/a

CAID 2. n/a

gnomAD 1. MAF=0.0001631(South Asian), no homozygotes, 2. n/a

CaseAddInfo aborted after prenatal diagnosis. Older sibling presented with recurrent vomiting, conscious disturbance, hyperventilation, metabolic acidosis, and elevated urine 3-hydroxypropionate, 3-hydroxybutyrate, and 3-hydroxyvalerate suggestive of PA. Died at 2yr 8mo without genetic testing.

CasePMIDs n/a

Thinking this needs to be written differently to get into Allele registry, don't know where to start.

"position is located before the beginning of the transcript" error in Allele registry

Is this a variant that only ClinVar would be able to register at this time?

CaseGM01566: Female, 16 years report, Caucasian, Europe

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a compound heterozygote for this variant, Variants were confirmed in trans by parental testing

CasePreviousTesting: N/A

CaseGenotypingMethod: Primers were developed and the CTH exons 1-12 and exon-intron boundaries were PCR amplified and sequenced. All sequence variations were verified by restriction enzyme analysis and/or repeat sequencing.

Variant1: NM_001902.5:c.200C>T (p.Thr67Ile)

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

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

Variant2: CTH, 1-BP DEL, 1220C AKA: NM_001902.5:c.1064del (p.Thr355Ilefs*19)

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

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

Case#:BV (per Bianchi et al)

CaseHPOs:

CaseHPOsFreeText: Febrile seizure at 18 months.

Variant: NM_001482.2:c.446G>A (p.Trp149Ter)

ClinVar: 7302

gnomAD: No listed (note Trp missense at 149)

VariantEvidence:

FamilyLabel: Bianchi family

FamilyPresentingHPOs:HP:0100543, HP:0025051, HP:0000750

(cognitive impairment, reduced brain creatine level by MRS, speech delay)

FamilyHPOsFreeText: Routine blood and urine analysis and extensive investigation for neurometabolic disorders was normal. increase in brain creatine when given oral creatine supplementation, low urine guanidinoacetate

FamilyNotHPOs: Normal brain MRI

CountryOrigin: Italy

ProbandLabel: Patient 1

FamilyPreviousTesting: 1H MRS revealed the total absenceof the Cr/PCr peak in the paraventricular white matter, inthe cerebellum, and in the parieto-occipital cortex. Blood concentrations of creatine and guanidinoacetate were normal, but urine guanidinoacetate and creatinine were low. Normal GAMT enzyme activity. Deficient AGAT activity (<0.3 nmol/hr/mg protein; normal 12.6-23.4), no GATM cDNA detected by RT-PCR.

FamilyMethod1: DGGE

FamilyMethod2: Sequencing

FamilyGenotypingMethod: Direct sequencing of exon 1; exons 2–9 and exon/intron boundaries screened by denaturing gradient gel electrophoresis (DGGE), followed by sequencing of exon 3 (with abnormal DGGE pattern).

Variant: NM_001482.2:c.446G>A (p.Trp149Ter)

ClinVar: 7302

FamilyAddInfo: Sequence analysis showed that parents are heterozygous.

FamilyPMIDs: 10762163 (Bianchi et al)

CaseBI2K: N/A

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

CaseAddInfo: N/A

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

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

gnomAD: Not in gnomAD

Case2: female, Turkish, neonatal screening

CasePresentingHPOs: HP:0000403

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Normal free carnitine. No treatment, but normal at 6 years. Adenotomy and bilateral paracentesis at 5.5 years.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.75 umol/l, ref <0.31). Urinary organic acids showed increased N-methylbutyrylglycine.

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

Variant: NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile) (homozygous)

ClinVar: 9202

gnomAD: South Asian 0.002678; Overall 0.0008097, no homozygotes

VariantEvidence: Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

CaseAddInfo: Consanguinity. 7 year old brother also found to have enzyme deficiency. No symptoms.

CasePMIDs:

Case4: female, Turkish, neonatal screening

CasePresentingHPOs:

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment of 100 mg L-carnitine/kg body weight and has shown normal development until 3 years.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.68 umol/l and 2.08 umol/l , ref <0.31). Urinary organic acids showed increased N-methylbutyrylglycine.

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

Variant: NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys) (homozygous)

ClinVar: 9203

gnomAD: Latino 0.0004797, Overall 0.0002404, no homozygotes

VariantEvidence: In vitro expression in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stability (PMID: 20547083).

CaseAddInfo:

CasePMIDs:

FamilyLabel Family 1

Family1PresentingHPOs HP:0001250

(Seizures)

HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:)1st seizure at 2days old

FamilyNotHPOs n/a

NotHPOsFreeText intrauterine seizures

CountryOrigin Netherlands

Ethnicity Dutch

Race n/a

Family1PreviousTesting α‐AASA and pipecolic acid tested for in affect patients' plasma and urine.

ProbandLabel Case 1

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

ClinVar 17994

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

FamilyAddInfo n/a

FamilyPMIDs 17088338 , 16159904

FamilyLabel Family 2

Family2PresentingHPOs n/a

HPOsFreeText n/a

FamilyNotHPOs n/a

CountryOrigin Netherlands

Ethnicity Dutch

Race n/a

Family2PreviousTesting α‐AASA and pipecolic acid tested for in affect patients' plasma and urine.

ProbandLabel Case 12

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

ClinVar 17994

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

FamilyAddInfo n/a

FamilyPMIDs 17088338 , 16159904

FamilyLabel Family 3

Family3PresentingHPOs HP:0001250

(Seizures)

HPOsFreeText n/a

FamilyNotHPOs n/a

NotHPOsFreeText intrauterine seizures

CountryOrigin Netherlands

Ethnicity Dutch

Race n/a

Family3PreviousTesting α‐AASA and pipecolic acid tested for in affect patients' plasma and urine.

ProbandLabel 3

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

ClinVar 17994

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

FamilyAddInfo n/a

FamilyPMIDs 17088338 , 16159904

Case9 sex unknown, Netherlands, Dutch

CasePresentingHPOs HP:0001250, HP:0001263, HP:0000750

(Seizures, Psychomotor delay, Speech delay)

HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 3do, first administered pyridoxine(and age at trial) 8mo, initial dose:50mg, maintenance dose:50mg/day, psychomotor delay, poor language skills. (PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"

CaseNotHPOs n/a

NotHPOsFreeText intrauterine seizures

CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 9.6(nv <1mmol/mol cr), α‐AASA plasma 0.8(nv <0.2μmol/l), pipecolic acid urine 2.0(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 22(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)

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 17088338 , 16159904

FamilyRO: N/A

FamilyPresentingHPOs: HP:0001252, HP:0001635, HP:0012664, HP:0001875, HP:0001640, HP:0001324 (Muscular hypotonia, Congestive heart failure, Reduced ejection fraction, Neutropenia, Cardiomegaly, Muscle weakness)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: DNA was extracted from salavia and buccal swabs. DNA sequencing for all 11 exons of the TAZ gene was performed via PCR amplification and direct sequencing. Once the mutation was located, site-specific DNA sequencing was used on four unaffected family members to confirm segregation.

FamilyPreviousTesting: N/A

FamilyAddInfo: N/A

Variant: NM_000116.5(TAZ):c.583G>T (p.Gly195Ter)

ClinVar: 559336, https://www.ncbi.nlm.nih.gov/clinvar/variation/559336/

gnomAD: Not in gnomAD

Affected: 2

Unaffected: 2

Segregations: 4

AddSegregationInfo: Not enough info to count, pedigree in Figure 1

FamilySA1: European

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

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: 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.

FamilyPreviousTesting: Leucine load test showed leucine sensitivity in some patients; Other causes of hypoglycemia were excluded (normal values for plasma cortisol, growth hormone, lactate, ammonia, amino acids, and urine organic acids)

FamilyAddInfo: N/A

Variant: NM_005271.5(GLUD1):c.820C>T (p.Arg274Cys)

ClinVar: 16128, https://www.ncbi.nlm.nih.gov/clinvar/variation/16128/

gnomAD: Not in gnomAD

Affected: 5

Segregations: 4

AddSegregationInfo: Pedigree in Figure 1a

CaseSA4P: Female, 12 months onset, European

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Has mother with confirmed variant and similar phenotypes

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

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

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

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

gnomAD: Not in gnomAD

Case1: Male, 5 years onset, African

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

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

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

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

CasePMIDs: 10767172, 10102904

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

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

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

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

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

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

Variant NM_000532.4(PCCB):c.1228C>T (p.Arg410Trp)

ClinVar 12011

gnomAD MAF=0.00006533(South Asian), no homozygotes

CaseJ 113 Japanese

CasePresentingHPOs HP:0003571 (Propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting none reported

Variant NM_000532.4(PCCB):c.1228C>T (p.Arg410Trp)

ClinVar 12011

gnomAD MAF=0.00006533(South Asian), no homozygotes

CaseAddInfo parents tested heterozygous

CasePMIDs n/a

FamilyLabel Unknown Family

FamilyUnknownPresentingHPOs HP:0003571 (Propionicacidemia)

FamilyNotHPOs n/a

CountryOrigin Japan

Ethnicity n/a

Race n/a

FamilyUnknownPreviousTesting none reported

ProbandLabel J 146

Variant NM_000532.4(PCCB):c.1228C>T (p.Arg410Trp)

ClinVar 12011

gnomAD MAF=0.00006533(South Asian), no homozygotes

FamilyAddInfo sibling J 171 genotyped, no further info for either case

FamilyLabel pccC Family

FamilypccCPresentingHPOs HP:0003571 (Propionicacidemia)

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity n/a

Race Caucasian

FamilypccCPreviousTesting none reported

ProbandLabel 572

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

ClinVar 38875

gnomAD not in gnomAD

FamilyAddInfo sibling 756 also genotyped, no further info for either case

based on the numbering from the C>T change that was in ClinVar and looking at Figure 4, this deletion takes place at c.12222.

Variant NM_000532.4:c.1222del (p.Ile408SerfsTer?)

ClinVar n/a

CAID unregistered

Going off of the numbering from the C>T variant in ClinVar and Figure 4, this other ClinVar entry matches exactly.

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

ClinVar 38875

gnomAD not in gnomAD

CaseEPI4Kn2: Female, 1 month onset

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263 (Global developmental delay)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

gnomAD: Not in gnomAD

CaseFZ2: Male, Finland, 2.9 yrs deceased

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

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

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

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed de novo in this and two other cases with the same variant and similar presentation, No family history,

CasePreviousTesting: N/A

CaseGenotypingMethod: ALDH18A1 and PYRC1 were investigated by Sanger sequencing, with the latter revealing no abnormalities and the former showing a heterozygous change at the Arg138 residue. qPCR was used to exclude the presence of a exonic deletion and investigation revealed no further variants in the coding regions. Familial sequencing revealed the inheritance was de novo with no variants in the parents.

Variant: NM_002860.4(ALDH18A1):c.412C>T (p.Arg138Trp)

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

gnomAD: Not in gnomAD

CaseFZ5: Male, Mexico, 4 yrs report

CasePresentingHPOs: HP:0001511, HP:0008897, HP:0001999, HP:0000973, HP:0100678, HP:0000963, HP:0010648, HP:0001388, HP:0001374, HP:0001181, HP:0001762, HP:0002650, HP:0000938, HP:0000270, HP:0025356, HP:0001252, HP:0001348, HP:0000518, HP:0000325, HP:0011220, HP:0000337, HP:0000411, HP:0000369, HP:0000252 (Intrauterine growth retardation, Postnatal growth retardation, Abnormal facial shape, Cutis laxa, Premature skin wrinkling, Thin skin, Dermal translucency, Joint laxity, Congenital hip dislocation, Adducted thumb, Talipes equinovarus, Scoliosis, Osteopenia, Delayed cranial suture closure, Psychomotor retardation, Muscular hypotonia, Brisk reflexes, Cataract, Triangular face, Prominent forehead, Broad forehead, Protruding ear, Low-set ears, Microcephaly)

HPOsFreeText: Typical facial gestalt

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

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

CaseGenotypingMethod: ALDH18A1 and PYRC1 were investigated by Sanger sequencing, with the latter revealing no abnormalities and the former showing a heterozygous change at the Arg138 residue. qPCR was used to exclude the presence of a exonic deletion and investigation revealed no further variants in the coding regions. Familial sequencing revealed the inheritance was de novo with no variants in the parents.

Variant: NM_002860.4(ALDH18A1):c.413G>T (p.Arg138Leu)

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

gnomAD: Not in gnomAD

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

VariantEvidence: The above variant was expressed in E coli through an expression vector and DMGDH activity was measured and purified for both the mutant and the wild-type. The flavination in the mutant protein showed a 2-fold decrease compared to the wild-type and the under-flavinated mutant revealed a 27-fold decrease in enzyme activity compared to the flavinated wild-type. Experiments with trypsin digestion also confirmed that the under-flavinated variants may be less stable than the wild-type enzyme.

CaseE: Male, French, Germany

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Phase of the variants are unknown

CasePreviousTesting: N/A

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

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

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

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

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

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

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

CaseD: Male, French, Quebec

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

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

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

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

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

CaseF-3 Male, 5do onset, Ethnicity: North Indian, Hindu

CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0001250, HP:0002098, HP:0001942, HP:0001987, HP:0003571, HP:0002154, HP:0010910, HP:0012026

(Acute encephalopathy, Lethargy, Poor feeding, Seizures, Respiratory distress, Metabolic acidosis, Hyperammonemia, Propionicacidemia, Elevated blood glycine, Elevated blood valine, Elevated blood ornithine)

HPOsFreeText Serum ammonia 143micromolar, acycarnitines 31.7(normal <3.6nmol/mL)

CaseNotHPOs n/a

CasePreviousTesting Also screened for variants in PCCA

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

ClinVar 217896

gnomAD MAF= 0.00003328(South Asian), no homozygotes

CaseAddInfo nonconsanguineous, abnormality in family history noted

CasePMIDs n/a

FamilyDEVR: Europe

FamilyPresentingHPOs: HP:0002078, HP:0002066, HP:0002321, HP:0002017, HP:0000613, HP:0002183, HP:0000639 (Truncal ataxia, Gait ataxia, Vertigo, Nausea and vomiting, Photophobia, Phonophobia, Nystagmus)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0002411 (Myokymia)

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Genomic DNA was isolated from peripheral leukocytes. All exons and flanking introns of the SLC1A3 gene were amplified and sequenced. Restriction digest verified the results.

FamilyPreviousTesting: Attacks were generally triggered by emotional stress, with some triggered by fatigue; Acetazolamide significantly reduced the frequency of attacks in all 3 affected family members;

FamilyAddInfo: N/A

Variant: NM_004172.5(SLC1A3):c.556T>A (p.Cys186Ser)

ClinVar: 9442, https://www.ncbi.nlm.nih.gov/clinvar/variation/9442/

gnomAD: Not in gnomAD

Affected: 4

Segregations: 2

AddSegregationInfo: Not enough info

CaseDO1: Male, Italy, 3 days onset

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

HPOsFreeText: N/A

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

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

gnomAD: Not in gnomAD

Case2: Male, Belgium

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased 10 months

CasePreviousTesting: N/A

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

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

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

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

Case13a: Male, Pakistan

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

Variant: NM_198271.4:c.1099_1100delAA (p.Asn367Glnfs*11)

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

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

Case1a: Female, Algeria

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

HPOsFreeText: Bilateral femoral fractures, Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

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

Case11b: Male, Sweden

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

Case1b: Female, Algeria

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

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

Case30 Female, 24yo diagnosis (Family 25)

CasePresentingHPOs HP:0001083, HP:0001256, HP:0001263, HP:0002625, HP:0002204

(Lens dislocation, Mild intellectual disability, Developmental delay, Deep vein thrombosis, Pulmonary embolism)

HPOsFreeText Presented with a pulmonary embolus at 23yo after birth of son, presumably secondary to deep vein thrombosis. Patient's plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine.

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Diagnosed by family screen and deep vein thrombosis.

Variant 1. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), 2. NM_000071.2(CBS):c.1105C>T (p.Arg369Cys), comp het

ClinVar 1. 198388, 2. 212860

gnomAD 1. MAF=0.00002683(European(non-Finnish), no homozygotes, 2. MAF= 0.006796(Ashkenazi Jewish), 5 homozygotes

CaseAddInfo mother of patient 29

CasePMIDs n/a

Case12 4yo diagnosis, Anglo-Celtic

CasePresentingHPOs n/a

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

CaseNotHPOs HP:0001249, HP:0001083

(Intellectual disability, Lens dislocation)

NotHPOsFreeText no other sequelae

CasePreviousTesting Diagnosis was based on family screen. 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.146C>T (p.Pro49Leu), compound heterozygous

ClinVar 1. 122, 2. 212872

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. MAF=0.0003116(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case33 41yo diagnosis, South African

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Diagnosis was based on dislocated lens and skeletal deformities. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. 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 HP:0001249

(Intellectual disability)

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.494G>A (p.Cys165Tyr), 2. NM_000071.2:c.1622dup (p.Asn541LysfsTer?), comp het

ClinVar 1. 495531

CAID 2. register

gnomAD 1. MAF=0.00001308(European(non-Finnish)), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case26 2yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0010864, HP:0000939, HP:0001263

(Lens dislocation, Severe intellectual disability, Osteoporosis, Developmental delay)

HPOsFreeText Patient had severe osteoporosis and was diagnosed on the basis of developmental delay and osteogenesis impefecta type IV. 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. (PMID:9156316): Urinary homocysteine was 42μmol/l before and 14μmol/l after treatment with betaine, folic acid, and aspirin.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS. (PMID:9156316): c.992C>A variant was also confirmed with HinfI restriction digest. A G mismatch was introduced to the 3' end of the antisense primer used to amplify the region in order to create the Hinfl restriction site as c.992C>A does not do so on its own. While the father and control sample had only an uncleaved 105bp band, both a 73bp and 32bp fragment were detected on HinfI restriction digestion analysis of the mother and proband.

Variant 1. NM_000071.2(CBS):c.992C>A (p.Ala331Glu), 2. NM_000071.2:c.444dup, comp het

ClinVar 1. 212857

CAID 2. register

gnomAD 1. MAF=0.000008824(European(non-Finnish), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs 9156316

Case20 7yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002650

(Lens dislocation, Scoliosis)

HPOsFreeText Diagnosis based on lens dislocation. 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 HP:0001249

(Intellectual disability)

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.494G>A (p.Cys165Tyr), comp het

ClinVar 1. 117, 2. 495531

gnomAD 1. MAF=0.00041539(Other), no homozygotes, 2. MAF= 0.00001308(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case9 11yo diagnosis, Anglo-Celtic

CasePresentingHPOs n/a

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

CaseNotHPOs HP:0001249, HP:0001083

(Intellectual disability, Lens dislocation)

NotHPOsFreeText no other sequelae

CasePreviousTesting Diagnosis was based on family screen. 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.1221delC (p.Trp408Glyfs), compound heterozygous

ClinVar 1. 120, 2. 495530

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.000008802(European(non-Finnish), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case14 29yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002751, HP:0000939

(Lens dislocation, Kyphoscoliosis, Osteoporosis)

HPOsFreeText Diagnosis was based on dislocated lens and skeletal deformity. Patient has severe kyphoscoliosis. 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 levels did not fall below 20μmol (nv <60μmol) on this treatment alone. (PMID:9156316:): In this study, patient was found to have mild intellectual disability and osteoporosis at 50yo.

CaseNotHPOs HP:0001249

(Intellectual disability)

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. (PMID:9156316): Serum homocysteine was 100μmol/l and methionine was 18μmol/l after five years of treatment. Addition of betaine(3g twice per day) lowered homocysteine to 18μmol/l which remained <50μmol for years.

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.1058C>T (p.Thr353Met), comp het

ClinVar 1. 120, 2. 131

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0002916(African), no homozygotes

CaseAddInfo Patient carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia. (PMID:9156316): Additionally is heterozygous for a c.699C>T(Y233Y) synonymous variant as well as homozygous c.1080T>C(A360A) synonymous variants.

CasePMIDs 9156316

Case24 6yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Patient had marfanoid features and 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 HP:0001249

(Intellectual disability)

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.904G>A (p.Glu302Lys), 2. NM_000071.2(CBS):c.430G>A (p.Glu144Lys); 3. NM_000071.2(CBS):c.1316G>A (p.Arg439Gln), comp het, 2&3 in cis

ClinVar 1. 496864, 2. 122; 3. 189088

gnomAD 1. MAF=0.00006153(African), no homozygotes 2. MAF=0.00009799(South Asian), no homozygotes, 3. MAF=0.00005341(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

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

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

NumberMales: 0

NumberFemales: 3

CountryOrigin: Iran

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

TotalNumber: 3

FamilyInfo: 3

NoFamily: 0

GroupAddInfo: All probands are products of consanguineous marriages.

Group (Level 2)

VariantCount: 3

NonVariant: 0

OtherVariant: 0

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

GroupMethod1: PCR

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

Case37 sex unknown, Spain

CasePresentingHPOs HP:0001332

(Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs HP:0002540

(Non-ambulatory)

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 6(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 23(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 7. 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 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. The R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

ClinVar 1. 2083, 2. 2089

gnomAD 1. MAF= 0.0004013(African), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case15 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 n/a

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 Patient died and had no metabolic testing, diangosis based on clinical features and heterozygosity of parents.

CasePMIDs n/a

Case9 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 2982(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 415(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. 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 n/a

CasePMIDs n/a

Case14 sex unknown, Spain

CasePresentingHPOs HP:0001332

(Dystonia)

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

CaseNotHPOs HP:0002540

(Non-ambulatory)

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 2625(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 262(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 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 n/a

Case31 sex unknown, Spain

CasePresentingHPOs HP:0001332, HP:0006846

(Dystonia, Acute encephalopathy)

HPOsFreeText Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs HP:0002540

(Non-ambulatory)

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 12(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 175(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 V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

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

ClinVar 1. 2088, 2. 2085

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

CaseAddInfo n/a

CasePMIDs n/a

Case34 sex unknown, Spain

CasePresentingHPOs HP:0001332

(Dystonia)

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

CaseNotHPOs HP:0002540

(Non-ambulatory)

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 7(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 99(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 30. Patient tested negative in glutarylcarnitine blood spot test, even under carnitine supplementation.

CaseMethod1 SSCP

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. Likewise, the R227P variant creates a NlaIV site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.680G>C (p.Arg227Pro), compound heterozygous

ClinVar 1. 2088, 2. 2089

gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0003566(European(non-Finnish)), no homozygotes

CaseAddInfo Sibling (Case 35) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 6mmol/mol creatinine and 3-OH-glutarate was 36mmol/mol creatinine.

CasePMIDs see note on previous studies

Case28 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 2(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 185(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 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 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

Cas23 sex unknown, Spain

CasePresentingHPOs n/a

HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Patient is otherwise phenotypically asymptomatic. 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 7932(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 1074(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 R383C variant destroys an AciI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved. Likewise, the 387_388del variant destroys an AluI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

Variant 1. NM_000159.3:c.387_388del(p.Glu129AspfsTer?), 2. NM_000159.3(GCDH):c.1147C>T (p.Arg383Cys), compound heterozygous

ClinVar 1. n/a, 2. 188852

CAID 1. register link

gnomAD 1. not in gnomAD, 2. MAF= 0.00008017, no homozygotes

CaseAddInfo n/a

CasePMIDs see note on previous studies

Case: 4 years (Dx), male, Somali

CasePresentingHPOs: HP:0001250, HP:0000750, HP:0000817, HP:0008762

HPOFreeText: 5 months: seizure-like movements, stopped at 8 months with antieplieptic drug. Delayed speech. Protein restricted diet for 5 months with no improvement.

CaseNotHPOs: Normal growth and motor development. 5 years: no dysmorphic features. Normal muscle tone, strength, coordination and deep tendon reflexes. Eye exam, hearing test, EEG, EKG, and MRI normal.

CasePreviousTesting: Blood glucose, urea, creatinine, and liver transaminases normal. Normal chromosome analysis. Southern blot for Angelman syndrome negative. Urine analysis showed large amounts of 2-methylbutyryl glycine. Increased plasma level of C5-acylcarnitine (1.43 micromoles/L, reference range 0.05–0.38) and an increased C5/C3-acylcarnitines ratio of 2.83 (reference range 0.16–0.73).

CaseGenotypingMethod: PCR of all exons and flanking intron sequences of genomic DNA. Mother was also sequenced.

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

ClinVar: 448980

gnomAD:

VariantEvidence: Functional studies demonstrate that the c.303+3A>G variant causes complete exon skipping of exon 3 (Madsen et al., 2006).

CaseAddInfo:

CasePMIDs:

Case22 Male, 13.5yo report, Ethnicity: German

CasePresentingHPOs HP:0003571, HP:0008872, HP:0001531, HP:0002240

(propionicacidemia, feeding difficulties in infancy, failure to thrive in infancy, hepatomegaly)

HPOsFreeText feeding difficulties, failure to thrive, hepatomegaly(4do), 55 IQ on Snijders-Omen Test

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screening. PCC activity was 0.81 in patient fibroblasts vs control.

Variant NM_000532.4:c.1218_1231delins12 (p.Gly406fs), homozygous

ClinVar n/a

CAID link to register the deletion, but the insertion is not described

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

Case21 Female, 8.8yo report, Ethnicity: Italian

CasePresentingHPOs HP:0003571, HP:0012523, HP:0002013, HP:0008947, HP:0001259, HP:0002789

(propionicacidemia, oral aversion, vomiting, infantile hypotonia, coma, seizures, tachypnea)

HPOsFreeText feeding refusal, vomiting, hypotonia, coma, seizures, tachypnea, exanthema (14do). 55 IQ on Snijders-Omen Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screen. PCC activity in patient fibroblasts was 1.1% of control.

Variant NM_000532.4(PCCB):c.562G>A (p.Gly188Arg), homozygous

ClinVar 558327

gnomAD MAF= 0.00006152(African), no homozygotes

CaseAddInfo no parental consanguinity

CasePMIDs n/a

CaseKLC: Male, 42 yrs death, Japan, Asian

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

HPOsFreeText: Monoamino-monocarboxylic aciduria, Transient stupor

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

NotHPOsFreeText: N/A

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

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

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

CasePMIDs: 2582682, 11394870

Variant: NM_001003841.3(SLC6A19):c.882_883TG[1] (p.Val295fs)

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

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

Case#: KM05, F, 2 years (Dx)

CasePresentingHPOs: HP:0005974 (Episodic ketoacidosis)

HPOsFreeText: At 11 years old she was eating a normal diet without restriction and plasma branched-chain amino acids were normal.

CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity (~9% of control) and expression of the protein was moderately reduced (PMID 3417306).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Total RNA was prepared from lymphoblastoid cells or peripheral leukocytes. An additional set of primers were used to distinguish each cDNA fragment from 2 different alleles. Clones were amplified and sequenced then confirmed by amplifying genomic DNA and performing restriction enzyme digestion.

Variant: 1. NM_001918.3(DBT):c.1150G>A (p.Gly384Ser); 2. NM_001918.3(DBT):c.294C>G (p.Ile98Met)

ClinVar: 1. 11949; 2. 11948

gnomAD: 1. East Asian 0.9705 (8883 homozygotes), Overall 0.9139; 2. Not in gnomAD

VariantEvidence: Variant 1 is likely benign

CaseAddInfo: Parents not available for testing.

CasePMIDs: 3417306

Case# F2-2:1, 38wk born, Russian

CasePresentingHPOs HP:0001254, HP:0001824, HP:0001943, HP:0001942, HP:0000952, HP:0002789, HP:0002919

CasePreviousTesting molecular analysis of CPS1 and NAGS did no reveal disease-causing mutations. Metabolic analysis (Table 1)

CaseMethod1 Sanger

CaseGenotypingMethod Sanger of all seven CA5A exons

Variant NM_001739.1(CA5A):c.555G>A (p.Lys185=)

ClinVar 127088

gnomAD 0.0004648 (Other), 0.0001554 (Overall)

VariantEvidence RT-PCR amplifying exons 2-7 of CA5A (in proband and WT) generated different sized products. Sanger of smaller band revealed a deletion in exon 4 (Fig. 3).

CaseAddInfo nonconsanguineous, heterozygous parents

Case# F3-2:5, Male, Pakistan, 13mon diagnosis

CasePresentingHPOs HP:0001987, HP:0001942, HP:0001993, HP:0003128

CasePreviousTesting meningo-encephalitis (cultures were negative). Further metabolic investigations are shown in Table 1.

CaseMethod1 Sanger

CaseGenotypingMethod Sanger of CA5A exons

Variant NM_001739.1(CA5A):c.619-3421_774+502del (p.Asp207_Gln258del)

ClinVar 127089

CaseAddInfo consanguineous, heterozygous parents checked with qtPCR

CaseSK: Male, Pakistan, Birth onset

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: Normal lung parenchyma

CaseAddInfo: Born to consanguineous first-cousin once removed parents

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

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

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

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

gnomAD: Not in gnomAD

Case2: Male, White, 18 yrs report

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

HPOsFreeText: N/A

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

NotHPOsFreeText: N/A

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

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

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

Variant1: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

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

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

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

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

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

Case3: Female, 5 yrs report

CasePresentingHPOs: HP:0012072 (Aciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo:

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

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

Variant1: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

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

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

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

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

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

CaseST: Female, 2 days onset

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

HPOsFreeText: Lack of normal sleep or wake features on EEG

CaseNotHPOs: HP:0002650 (Scoliosis)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is confirmed de novo heterozygous

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

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

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

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

gnomAD: Not in gnomAD

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

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

CasePreviousTesting: Identified by the assessment of urinary organic acids by gas chromatography–mass spectrometry; Accumulation of N-acetylated amino acids was much less pronounced than in previously reported patients

CaseGenotypingMethod: Genomic DNA was extracted either from peripheral blood or EBV-transformed lymphocytes. PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries of ACY1 was performed. Restriction digest analysis was performed to confirm homozygosity.

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

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

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

CaseAC014_II-1: Female, 3 yrs report, Lebanon

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

CasePreviousTesting: Identified by the assessment of urinary organic acids by gas chromatography–mass spectrometry; Accumulation of N-acetylated amino acids was much less pronounced than in previously reported patients

CaseGenotypingMethod: Genomic DNA was extracted either from peripheral blood or EBV-transformed lymphocytes. PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries of ACY1 was performed.

Variant: NM_000666.3(ACY1):c.1132C>T (p.Arg378Trp)

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

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

FamilyLabel HCU-220

Family#PresentingHPOs HP:0001249, HP:0001083, HP:0002970, HP:0001010, HP:0000924, HP:0001263

(Intellectual disability, Ectopia lentis, Genu varum, Hypopigmentation, Skeletal abnormality, cognitive delay)

HPOsFreeText CBS deficiency diagnosis, skeletal abnormality/elongated long bones, cognitive delay was apparent as early as 2yo

FamilyNotHPOs HP:0000501

(Glaucoma)

CountryOrigin Iran

Ethnicity Sistani

Race n/a

Family#PreviousTesting no other CBS variants were observed after Sanger sequencing

FamilyMethod1 Linkage analysis or Homozygosity mapping (genome-wide)

FamilyMethod2 Sanger

FamilyGenotypingMethod Genome-wide SNP genotyping and whole genome linkage analysis using MERLIN to analyze DNA of the parents and 7 siblings. Homoygosity mapping of the homozygous regions common to the three affected individuals and absent in unaffected individuals then narrowed the homozygous region to a locus including 296 protein coding genes. CBS, being one of those genes, was considered since intellectual disability accompanies homocysteinuria. The 15 coding exons and flanking intronic sequences of the CBS gene were PCR amplified then Sanger sequenced.

ProbandLabel HCU-220-5

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

ClinVar 188787

gnomAD MAF=0.00002892(Latino), no homozygotes

FamilyAddInfo family from a remote village in the province of Sistan and Baluchestan. consanguinity-first cousin parents, several heterozygous family members (both parents and 2 siblings) had cardiac disorders such as mitral regurgitation or mitral valve prolapse, but were generally negative for the phenotypes of the affected individuals. Heterozygous sibling HCU-220-3 is the only individual who presented in this study with glaucoma and mitral valve prolapse.

FamilyPMIDs n/a

Case25014: Female, 31 yrs onset, United States

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

HPOsFreeText: 5/7 disability score, Chronic microvascular disease

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

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

CaseAddInfo: Case is sporadic

Variant: NM_002860.4(ALDH18A1):c.755G>A (p.Arg252Gln)

ClinVar: 217117 https://www.ncbi.nlm.nih.gov/clinvar/variation/217117/

gnomAD: Not in gnomAD

FamilyFSP856: France

FamilyPresentingHPOs: HP:0001263, HP:0002317, HP:0001324, HP:0007350, HP:0003487, HP:0006938, HP:0002066, HP:0002174, HP:0000252, HP:0001999 (Global developmental delay, Spastic gait, Muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Impaired vibration sensation at ankles, Gait ataxia, Postural tremor, Microcephaly, Abnormal facial shape)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0001260, HP:0000973 (Dysarthria, Cutis laxa)

NotHPOsFreeText: N/A

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

FamilyPreviousTesting: Normal MRI

FamilyAddInfo: Family displays autosomal recessive inheritance, Family is homozygous for this variant

Variant: NM_002860.4(ALDH18A1):c.2143G>C (p.Asp715His)

ClinVar: 217115 https://www.ncbi.nlm.nih.gov/clinvar/variation/217115/

gnomAD: 0.00002641, https://gnomad.broadinstitute.org/variant/10-97370017-C-G

Affected: 2

Unaffected: 2

Segregations: 4

AddSegregationInfo: Whole Exome Sequencing, Figure 1 Pedigree

FamilyFSP429: France

FamilyPresentingHPOs: HP:0002064, HP:0002460, HP:0002395, HP:0007350, HP:0003487, HP:0031993, HP:0003572, HP:0005961 (Spastic gait, Distal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Hoffman sign, Low plasma citrulline, Hypoargininemia)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0000973, HP:0001999, HP:0100543 (Cutis laxa, Abnormal facial shape, Cognitive impairment)

NotHPOsFreeText: N/A

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

FamilyPreviousTesting: Amino acid levels in Table 4

FamilyAddInfo: Family displays autosomal dominant inheritance

Variant: NM_002860.4(ALDH18A1):c.1994G>T (p.Arg665Leu)

ClinVar: 217119 https://www.ncbi.nlm.nih.gov/clinvar/variation/217119/

gnomAD: Not in gnomAD

Affected: 2

Unaffected: 7

Segregations: 1

AddSegregationInfo: Candidate gene sequencing, Figure 1 Pedigree

CaseB1: United States, White

CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;

CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.

Variant: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)

ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/

gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A

FamilyBJG_F1: Malaysia

FamilyPresentingHPOs: N/A

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: See Group

FamilyPreviousTesting: See Group

FamilyAddInfo: Proband is confirmed homozygous for this variant

Variant: NM_006721.4(ADK):c.704A>C (p.Asp235Ala)

ClinVar: 29604, https://www.ncbi.nlm.nih.gov/clinvar/variation/29604/

gnomAD: Not in gnomAD

Affected: 2

Unaffected: 0

Segregations: 1

AddSegregationInfo: Not enough info

Case2928: Female, 2 years diagnosis, Czech

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

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

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

NotHPOsFreeText: N/A

CaseAddInfo: Patient is compound heterozygous for these mutations

CasePreviousTesting: Cystathionine (Cysta), total cysteine (tCys), and total homocysteine (tHcy) panels

CaseGenotypingMethod: PCR amplification of CTH coding regions and exon-intron boundaries was performed. These fragments were sequenced and aligned with a reference to find mutations. Those found were confirmed by restriction digest of 100 controls.

Variant1: NM_001902.5:c.200C>T (p.Thr67Ile)

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

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

Variant Too Long

Variant2: NP_001893.2:p.Gly57_Gln196del

ClinVar:

gnomAD:

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

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

HPOsFreeText: Syringomyelia length of 3.5 cm

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Parents are consanguineous, Older sister are unaffected, This variant results in a splicing alteration in the acceptor site of Exon 6, skipping exon 6 (amino acid residues 121 to 146) and causing a premature stop codon; Proband is confirmed homozygous via parental testing

CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; MRI of the head and spine was performed at age 3 mo

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

Variant: NM_000666.3(ACY1):c.360-1G>A

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

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