Case4: Patient LW (found in GT database)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000421, HP:0006298

(Bruising, Epistaxis, Prolonged bleeding after tooth extraction)

CaseHPOFreeText: Blood transfusions were needed

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: 12% of normal GPIIIa and GPIIb surface expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

Variant: NM_000419.3:c.641T>C (p.Lue214Pro)

LegacyVariant: (p.Leu183Pro)

ClinVar: 2901

CAiD: CA115848

gnomAD: N/A

PreviouslyPublished: References 14 and 15

Case#: Male, 48

Disease: Glazmann's Thrombasthenia Like Syndrome

CasePresentingHPOs: HP:0001873, HP:0000421, HP:0031364, HP:0000225

Thrombocytopenia, Epistaxis, Ecchymosis, Gingival bleeding

CaseNotHPOs: NA

FamilyInfo: Pedigree figure 1. Family history of thrombocytopenia.

PlateletAgreggation: Decreased PLT aggregation and diminished ATP release with the agonists ADP, collagen, and AA, with normal ristocetin agglutination

GenotypingMethod: Genetic analysis of ITGA2B and ITGB3 genes was performed by next-generation sequencing (NGS). Sanger sequencing used to confirm variants.

ClinVar: 50232

CAID: CA10575572

Variant: NM_000419.5:c.3077G>A

GnomAD: European non-Finnish 0.000008801 (1/113618)

ExpressionEvidence: Level of expression on PLT surface determined by FCM: CD41a (GPIIb/IIIa) 49%, CD61 (GPIIIa) 44%, and CD42b (GPIb) 105%. Healthy control value range: CD41a (GPIIb/IIIa) (85-115%); CD61 (GPIIIa) (80-120%); CD42b (GPIb) (70-130%).

Case12: (Proband CabGT-12), Female, age not specified, Caucasian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

ProteinExpression: Flow cytometry showed 19% GPIIb and 40% GPIIIa surface expression

Platelet Aggregation: N/A

CasePreviousTesting: Promoter and exon sequences of aIIb and b3 genes were amplified and directly sequence

Gene: ITGA2B

Variant: NM_000419.3:c.2113T>C (p.Cys705Arg) and NM_000419.3:c.3060+2T>C (p.Val982_Lys1020del)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8602816 and CA290944108

gnomAD MAF in the European (non-Finnish) population is 0.000008792 https://gnomad.broadinstitute.org/variant/17-42455140-A-G and MAF in the European non Finnish population for (p.Val982_Lys1020del) is 0.00003876 https://gnomad.broadinstitute.org/variant/17-42451720-A-G

Case1: Female, 22 years old, Portugese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Also studied were the patient’s mother (I.2),her father (1.1), and her sister (II.2). Of these family members, only her sister has reported excessive bleeding although platelet aggregation tests were normal for all of them. Consanguinity was present as her parents were cousins.

ParentalGenotype: Parents heterozygous for mutation

CasePresentingHPOs: HP:0000967

(Petechia)

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: <5% surface expression of aIIbb3

PlateletAggregation: Absent with physiologic agonists but agglutination with ristocetin was normal

CasePreviousTesting: We examined each of the 30 exons of the b3 gene and each of the 15 exons of the aIIb gene for migration changes in PCR-SSCP analysis

Gene: ITGB3

Variant:

LegacyVariant:

ClinVar:

CAiD:

gnomAD: N/A

Case9: Patient MR, gender and age are not specified, all of these patients are Caucasian (either Italian or European)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: All patients presented with a current or past history of bleeding and a bleeding time >15 min. Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who bled only after trauma or surgery or had minor symptoms, such as epistaxis. Moderate/severe bleeders were defined as those with a history of spontaneous or life threatening hemorrhages, such as gastrointestinal bleeding, or who had repeated episodes requiring platelet transfusions

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: See Table 1

PlateletAggregation: See Table 1

CasePreviousTesting: To identify point mutations responsible for GT, we have sequenced all coding regions of Ib and 3 genes and intron/exon boundaries.

Gene: ITGA2B

Variant: NM_000419.3:c.1214T>C (p.Ile374Thr)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA290950815

gnomAD: N/A

Case10: Female, 7 years old, Indian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0000790 (Epistaxis, hematuria)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Diagnosis of GT was made on the basis of quantitive determination of receptor count by flow cytometric analysis of GPIIb-IIIa

PlateletAggregation: Diagnosis of GT was made on the basis of impaired platelet aggregation (platelet aggregation was tested against ristocetin, ADP, collagen, epinephrine and arachidonic acid)

CasePreviousTesting: Multiplex PCR by using GPIIb primers and CSGE analysis were performed

Gene: ITGA2B

Variant: NM_000419.3:c.2415del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940581

gnomAD: N/A

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

Case# P4, 4yr onset, Pakistani

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

CasePreviousTesting negative for NAGS and CPS1 genes.

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

Variant NM_001739.1:c.555+4_555+183del180bp

CAID CA658820661

VariantEvidence intronic splice site

CaseAddInfo consanguineous

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

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

NotHPOsFreeText: normal urine isobutyrylgycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3b (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 5358

CAID: CA117441

gnomAD: not in gnomAD

CaseAddInfo: homozygous mutations, no data for SCAD gene variants

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

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

NotHPOsFreeText: normal urine isobutyryglycine

CaseAddInfo: unremarkable clinical condition

Case8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 95589

CAID: CA223125

gnomAD: 0.02252 (European non-Finnish)

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

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

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

Case9 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 5.5(nv 0.7-2.6µmol/liter), AASA in plasma 5.8(nv<0.2µmol/liter). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4:c.696-2A>G (p.=), 2. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), compound heterozygous

ClinVar 1. n/a 2. 17994

CAID 1. CA360730346

gnomAD neither 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

Patient8: Male, 2yo, sibling to patient 9

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 6.4 μmol l−1, Ammonium (μmol l−1) = 30, pH = 7.36, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 108

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 11 days old, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.941C>G

CAID: CA391721562, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391721562

gnomAD: n/a

Patient15: Female, 15yo

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001941

(poor feeding, vomiting, dehydration, acidosis)

HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 7.8 μmol l−1, IVA incorp (%) = 4.9, IVG in urine mmol permol creatinine = 4653, Ammonium (μmol l−1) = 28, pH = 7.18, Protein intake (g kg−1 per day) = 0.8, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 92

CaseNotHPOs: HP:0001254, HP:0001259 (lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed via clinical findings at 6yo, hospitalized outside of detection period

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group, nucleotide changes detected in homozygosity in mRNA

Variant1: NM_002225.3:c.1099T>C

CAID: CA391723803, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391723803

gnomAD: n/a

Variant2: c.1-?_c.295+? (Delexons 1–3) no ClinVar or CAID

Patient9: Female, 3yo, sibling to patient 8

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 3.5 μmol l−1, Ammonium (μmol l−1) = 32, pH = 7.34, Protein intake (g kg−1 per day) = 1.8, PDI/IQ in follow-up = 95

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed via family evaluation at 3yo, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.941C>G

CAID: CA391721562, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391721562

gnomAD: n/a

Patient5: Male, 11mo, sibling to patient 4

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 6.0 μmol l−1, IVA incorp (%) = 64, IVG in urine mmol permol creatinine = 955, Ammonium (μmol l−1) = 65, pH = 7.41, Protein intake (g kg−1 per day) = 1.5, treated with carnitine supplements, PDI/IQ in follow-up = 85

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

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

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 10 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_001159508.1:c.1214T>C

CAID: CA268781818, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268781818

gnomAD: 0.000003977, http://gnomad.broadinstitute.org/variant/15-40710485-T-C

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

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

gnomAD: n/a

CaseREU3: Male, 6 yrs report, United Kingdom

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

HPOsFreeText: Malonic aciduria

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant

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

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

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

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

gnomAD: Not in gnomAD

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

CasePA003 3do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0000952, HP:0011968, HP:0001290, HP:0001942, HP:0002154, HP:0001987, HP:0001522

(propionicacidemia, jaundice, poor feeding, hypotonia, metabolic acidosis, hyperglycinemia, hyperammonemia, death in infancy)

HPOsFreeText died at 5m 15days (also check 2178070 first)

CaseNotHPOs "

NotHPOsFreeText "

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.580T>C (p.Ser194Pro)

ClinVar 1. 554490, 2. n/a

CAID 2. CA354641839

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

CaseAddInfo "

CasePMIDs 2178070

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

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

Case27 Male, 3do onset, Ethnicity: Turkish

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

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

HPOsFreeText feeding difficulties, hypotonia, somnolence, tachypnea (3do)

CaseNotHPOs n/a

CasePreviousTesting Diagnosis by selective metabolic screen.

Variant NM_000532.4:c.1309G>A (p.Gly437Ser), homozygous

ClinVar n/a

CAID CA354649286

gnomAD MAF= 0.00008674(Latino), no homozygotes

CaseAddInfo parental consanguinity

CasePMIDs n/a

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

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:

Case3: Female, 1y 5m, Chinese

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

NotHPOsFreeText: normal urine isobutyrylglycine

Case3 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

CaseAddInfo:

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

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

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

Case6 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

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

ClinVar: n/a

CAID: CA6373205

gnomAD: 0.00005790 (Latino)

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

Case41 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 48(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 101(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 0.8. 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 F71S variant creates an MnlI restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved.

Variant 1. NM_000159.3:c.212T>C(p.Phe71Ser), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

ClinVar 1. n/a, 2. 370106

CAID 1. CA404315187

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

CaseAddInfo n/a

CasePMIDs n/a

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

Case25 sex unknown, Spain

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

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

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

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting GC-MS measured glutarate of 6164(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 626(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 A316D variant creates an HgiEII site. This would lead to cleaved patient DNA fragments and uncleaved control fragments.

Variant NM_000159.3:c.947C>A(p.Ala316Asp), homozygous

ClinVar n/a

CAID CA404319620

gnomAD not in gnomAD

CaseAddInfo Sibling (Case 26) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 3556mmol/mol creatinine and 3-OH-glutarate was 420mmol/mol creatinine.

CasePMIDs see note on previous studies

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# Patient 10, Turkish, Male, 1mo diagnosis

CasePresentingHPOs HP:0004923

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

CaseMethod1 PCR

CaseMethod2 DGGE

Variant NM_000320.2:c.350T>A(p.W90Ter)

CAID CA356448578

VariantEvidence null

Case# Patient 2, Male, 17mo diagnosis

Variant NM_000320.2:c.129G>C (p.G17R)

CAID CA438715605

Case# Patient 1, Male, 40do diagnosis

Variant NM_000320.2:c.525A>G (p.G149R)

CAID CA438712209

Case# Patient 16, Female, 2mo diagnosis

Variant NM_000320.2:c.277G>A (p.Gly93Ser)

CAID CA356450231

Case1: Male, 5 years onset, African

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

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

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

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

CasePMIDs: 10767172, 10102904

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

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

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

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

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

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

CaseEPI4Kn2: Female, 1 month onset

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001263 (Global developmental delay)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

gnomAD: Not in gnomAD

CaseFZ2: Male, Finland, 2.9 yrs deceased

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

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

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

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

CaseFZ5: Male, Mexico, 4 yrs report

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

HPOsFreeText: Typical facial gestalt

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

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

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

CaseLE25: Male, 7 yrs report

CasePresentingHPOs: HP:0000639 (Nystagmus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants confirmed in-trans via parental testing

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

CaseGenotypingMethod: See Group

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

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

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

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

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

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

CaseLE17: Male, 7 yrs report

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

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

CaseGenotypingMethod: See Group

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

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

gnomAD: Not in gnomAD

Variant2: NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp)

ClinVar: 31134, https://www.ncbi.nlm.nih.gov/clinvar/variation/31134/

gnomAD: 0.004790, https://gnomad.broadinstitute.org/variant/16-89220556-C-T

CaseE: Male, French, Germany

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Phase of the variants are unknown

CasePreviousTesting: N/A

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

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

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

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

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

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

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

CaseD: Male, French, Quebec

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

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

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

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

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

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

Case# KA, Lebanese

CasePresentingHPOs HP:0004923

CaseMethod1 PCR

CaseGenotypingMethod PCR of entire DHPR coding sequence

Variant NM_000320.2(QDPR):c.390_391insACT

CAID CA658795205

CaseAddInfo consanguineous parents

CaseDO2: Male, Italy, 1 day onset

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001875 (Neutropenia)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

gnomAD: Not in gnomAD

CaseDO1: Male, Italy, 3 days onset

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

HPOsFreeText: N/A

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

NotHPOsFreeText: N/A

CaseAddInfo: N/A

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

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

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

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

gnomAD: Not in gnomAD

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

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

HPOsFreeText: unspecified abnormalities in sitting and speech

Case (Level 2)

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

CaseMethod1: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

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

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

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

Case (Level 2)

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

CaseMethod1: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

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

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

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

HPOsFreeText: congenital malformations

Case (Level 2)

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

CaseMethod1: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA913187295

gnomAD: n/a

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

Case1: Male, 3 months onset, China, Asian

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

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

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

NotHPOsFreeText: N/A

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

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

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

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

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

gnomAD: Not in gnomAD

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

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

gnomAD: Not in gnomAD

Case2: Male, Belgium

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased 10 months

CasePreviousTesting: N/A

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

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

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

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

Case4: Male, Japan, Asian

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

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Alive at 4 months

CasePreviousTesting: N/A

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

Variant: NM_198271.4:c.231G>A (p.Trp77*)

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

gnomAD: Not in gnomAD

Case13a: Male, Pakistan

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

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

Case1a: Female, Algeria

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

HPOsFreeText: Bilateral femoral fractures, Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

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

Case7: Female, Japan, Asian

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

HPOsFreeText: Atrophic myofibers

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

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

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

gnomAD: Not in gnomAD

Case11b: Male, Sweden

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

Case1b: Female, Algeria

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0001627 (Cardiac abnormality)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

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

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

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:

CaseKLC: Male, 42 yrs death, Japan, Asian

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

HPOsFreeText: Monoamino-monocarboxylic aciduria, Transient stupor

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

NotHPOsFreeText: N/A

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

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

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

CasePMIDs: 2582682, 11394870

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

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

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

CaseKLD: Female, 6 yrs report, Japan, Asian

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

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

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

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

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

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

CasePMIDs: 2582682, 11394870

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

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

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

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

Patient7: Female, 1.9yo

CasePresentingHPOs: HP:0001254, HP:0011968, HP:0001298, HP:0001259, HP:0007021 (lethargy, poor feeding, encephalopathy, coma, pain insensitivity)

HPOsFreeText: acute neonatal IVA, convulsions, treated with IVA special formula along with L-carnitine and glycine supplements, elevated isovalerylglycine, C5-carnitine = 2.45 µmol/l, weight = 11kg, height = 90cm, currently meeting normal milestones and has normal neurological examination

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: symptom onset at 3do, diagnosis at 10do via clinical presentation, consanguineous family

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.3:c.1136T>C

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

gnomAD: n/a

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

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

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

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

Patient5: Male, 7yo

CasePresentingHPOs: HP:0002572, HP:0011968, HP:0011675, HP:0001254, HP:0011675, HP:0002616, HP:0001659 (episodic vomiting, poor feeding, lethargy, abnormal EKG, aortic root dilation, aortic regurgitation)

HPOsFreeText: chronic intermittent IVA, recurring hospitalization (every 3mo), abnormal urine odor, treated with vegetarian diet with L-carnitine, elevated isovalerylglycine, C5-carnitine = 4.6 µmol/l, birth weight = 3.5kg, at 7yo had an abnormal EKG and had subsequent abnormal ECHO, sat at 6mo, walked at 1.2yo, spoke first word at 1yo, current height = 128cm, current weight = 18kg

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: symptom onset at 12mo, diagnosis at 60mo via clinical presentation, consanguineous family, older sister had poor sucking at birth and died at 7 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_002225.3:c.749G>C

CAID: CA391718929, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391718929

gnomAD: n/a

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

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

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

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

CaseCA5: Male, 9 months death

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

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

CaseCA3: Male, 6 months diagnosis

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

HPOsFreeText: N/A

CaseNotHPOs: HP:0003107 (Abnormal circulating cholesterol concentration)

NotHPOsFreeText: N/A

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

CasePreviousTesting: N/A

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

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

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

gnomAD: Not in gnomAD

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