PatientID: III-A

KindredID: 1

Case: M, 45Y0M, EthnicityUnknown

DiseaseAssertion: VHL

FamilyInfo: Multiple first- and second-degree relatives affected with similar phenotypes. Of these, he is genetically tested and found to share VHL mutations with his uncle (proband).

CasePresentingHPOs: N/A

CaseHPOFreeText: Paper asserts that this individual presented with VHL phenotypes but does not specify which.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: Information obtained from Figure 1

Variant: c.340+5G>C

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 36901, https://www.ncbi.nlm.nih.gov/clinvar/variation/36901/

CAID: N/A

gnomAD: 0.01119 https://gnomad.broadinstitute.org/variant/3-10183876-G-C

VariantEvidence: This variant’s large allele frequency means this is likely non disease causing (not deleterious).

MutationType: splice_site_variant

CivicName: P86S (c.256C>T) and Splice Region (c.340+5G>C)

MultipleGeneVariants: Germline, VHL, L158Q (c.473T>A)

Family 6 - Patients 6a and 6b

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0000467, HP:0003327, HP:0200136, HP:0003691, HP:0003306, HP:0002650, HP:0040081, HP:0002111, HP:0100284

HPOsFreeText: myopathic muscle unit action potentials, 6a muscle pathology with vacuolar myopathy with glycogen excess

FamilyNotHPOs: HP:0010628

Ethnicity: Iranian

ProbandLabel: 6a, male, 12yo at onset, 25yo at diagnosis

FamilyAddInfo: 6b (male) dx at 33yo, 6a MRC sum score = 78, 6b MRC sum score = 79, both patients required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: 6a FVC = 19%, 6b FVC = 38%, 6a CK = 820 U/L, 6b CK = 503 U/L, muscle pathology (examined only in 6a), DBS enzyme activity (with inhibition) for 6a = 0 μmol/L/h, for 6b = 0.21 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

Variant: NM_000152.4(GAA):c.1979G>A (p.Arg660His)

ClinVar: 189172, https://www.ncbi.nlm.nih.gov/clinvar/variation/189172/

gnomAD: 3.279e-05, http://exac.broadinstitute.org/variant/17-78086765-G-A

Family 7 - Patient 7

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0003306, HP:0002111, HP:0040081

HPOsFreeText: muscle pathology with vacuolar myopathy with glycogen excess, myopathic muscle unit action potentials

FamilyNotHPOs: HP:0010628, HP:0002015, HP:0003691, HP:0002650

Ethnicity: Iranian

ProbandLabel:

FamilyAddInfo: male, 20yo at onset, 23yo at diagnosis, MRC sum score = 96, patient required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: FVC = 20%, CK = 2,550 U/L, muscle pathology examined, DBS enzyme activity (with inhibition) = 0.1 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.4(GAA):c.2662G>T (p.Glu888Ter)

ClinVar: 578595, https://www.ncbi.nlm.nih.gov/clinvar/variation/578595/

gnomAD: 1.65e-05, http://exac.broadinstitute.org/variant/17-78092467-G-T

Family 1 - Patient 1

FamilyPresentingHPOs: HP:0002355, HP:0003701, HP:0040081, HP:0100284

HPOsFreeText: myopathic muscle unit action potentials

FamilyNotHPOs HP:0010628, HP:0002015, HP:0003691, HP:0003306, HP:0002650

NotHPOsFreeText:

Ethnicity: Iranian

ProbandLabel: Patient 1, male

FamilyAddInfo: 2yo at onset, 4yo at diagnosis, MRC sum score not available, consanguineous family

FamilyPreviousTesting: Respiratory evaluation: FVC = 90%, CK = 2,960 U/L,DBS enzyme activity (with inhibition) = 0.3 μmol/L/h, no muscle pathology performed, cardiac evaluations, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

Variant: NM_000152.4(GAA):c.854C>G (p.Pro285Arg)

ClinVar: 225114, https://www.ncbi.nlm.nih.gov/clinvar/variation/225114/

gnomAD: n/a

Family 8 - Patients 8a and 8b

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0000467, HP:0003327, HP:0010628, HP:0002015, HP:0003691, HP:0002650, HP:0040081

HPOsFreeText: 8b muscle pathology with mild lysosomal vacuolar myopathy with slight glycogen excess, no metachromatic debris, myopathic muscle unit action potentials

FamilyNotHPOs: HP:0003306

Ethnicity: Iranian

ProbandLabel: 8a, female, 27yo at onset, 32yo at diagnosis

FamilyAddInfo: 8b (male) dx at 40yo, 8a MRC sum score = 82, 8b MRC sum score = 60, 8b is wheelchair bound, both patients required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: 8a FVC = 102%, 8b FVC = 17%, 8a CK = 268 U/L, 8b CK = 199 U/L, muscle pathology (examined only in 8b), DBS enzyme activity (with inhibition) for 8a = 0.11 μmol/L/h, for 8b = 0.15 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.4(GAA):c.2078dupA (p.Ala694Glyfs)

ClinVar: 180143, https://www.ncbi.nlm.nih.gov/clinvar/variation/180143/

gnomAD: n/a

Family 3 - Patient 3

FamilyPresentingHPOs: HP:0002355, HP:0003701, HP:0000467, HP:0003327, HP:0002111, HP:0040081, HP:0100284

HPOsFreeText: Vacuolar myopathy, myopathic muscle unit action potentials

FamilyNotHPOs: HP:0010628, HP:0002015, HP:0003691, HP:0003306, HP:0002650

NotHPOsFreeText:

Ethnicity: Iranian

ProbandLabel:

FamilyAddInfo: female, 2yo at onset, 26yo at diagnosis, MRC sum score = 76, NIV used beginning at 22yo

FamilyPreviousTesting: Respiratory Evaluation: FVC = 31%, CK = 1,551 U/L, Vacuolar myopathy present in muscle pathology exam, DBS enzyme activity (with inhibition) = 5.1 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.4(GAA):c.1004G>A (p.Gly335Glu)

ClinVar: 180142, https://www.ncbi.nlm.nih.gov/clinvar/variation/180142/

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

Family 9 - Patient 9

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0000467, HP:0003327, HP:0010628, HP:0003306, HP:0002111, HP:0040081

HPOsFreeText: muscle pathology with slight vacuolar myopathy with mild glycogen excess

FamilyNotHPOs: HP:0002015, HP:0003691, HP:0002650

Ethnicity: Iranian

ProbandLabel:

FamilyAddInfo: onset at 28yo, diagnosed at 35yo, MRC sum score = 81

FamilyPreviousTesting: Respiratory Evaluation: FVC = 71%, CK = 748 U/L, muscle pathology examined, DBS enzyme activity (with inhibition) = 3.5 μmol/L/h

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.4(GAA):c.1799G>A (p.Arg600His)

ClinVar: 370130, https://www.ncbi.nlm.nih.gov/clinvar/variation/370130/

gnomAD: 8.675e-06, http://exac.broadinstitute.org/variant/17-78086421-G-A

GroupPresentingHPOs: HP:0001324, HP:0001270, HP:0002205, HP:0002098, HP:0001635, HP:0001640, HP:0011968

HPOsFreeText: IOPD, reduced GAA activity, paucity of movements

GroupNotHPOs:

NumberMales: 14

NumberFemales: 11

CountryOrigin: mainland China; 12 patients from southern China, 13 from northern China

Ethnicity: Chinese

Race: Chinese

AgeRange: median age at symptom onset = 3.4mo, median age at diagnosis = 4.9mo

*TotalNumber: 25

FamilyInfo: Parents of those individuals with mutations were sequenced

NoFamily: n/a

GroupAddInfo: all patients diagnosed with IOPD between 2013 and 2016 at Shanghai Children's Medical Center. Of the 24 untreated patients, non survived beyond 1.5yrs, only surviving (Patient 25) was 7mo at last follow-up.

GroupPreviousTesting: IOPD diagnosed via reduced GAA enzyme activity in leukocytes or DBS (PMID: 16702880)

GroupGenotypingMethod: DNA isolated from blood samples, coding exons (2-20) and intron/exon boundaries of GAA gene amplified via PCR (primers: PMID: 10338092), resulting DNA was sequenced with ABI3730XL sequencer then was analyzed with Mutation Survey or DNA Variant Analysis software, novel mutations were screened in 60 normal individuals (120 alleles) via direct sequencing and no novel variants were found among these suggesting those found in study patients are uncommon polymorphisms.

fragments containing a mutation in the patients were amplified and sequenced for the corresponding parents

Phylogenetic conservation of missense mutations analyzed with ClustalX program, and pathogenicity of novel variants predicited with MutationTaster, sorting intolerant from tolerant (SIFT), and PolyPhen-2

Variant: NM_000152.4(GAA):c.2662G>T (p.Glu888Ter)

this was identified (by present study) as the most common variant in northern Chinese patients, heterozygous for 5 patients, homozygous for one patient

ClinVar: 578595, https://www.ncbi.nlm.nih.gov/clinvar/variation/578595/

gnomAD: 1.65e-05, http://exac.broadinstitute.org/variant/17-78092467-G-T

GroupPresentingHPOs: HP:0005952, HP:0030197

HPOsFreeText: LOPD confirmed by enzyme analysis in leukocytes or fibroblasts and mutation analysis, median GAA activity in leukocytes = 1.0 nmol glucose/mg hour, median GAA activity in fibroblasts = 12.9 nmol 4MU/mg hour, median MRC sum score = 80.8, 7 patients had total wheelchair dependence, 17 patients had partial wheelchair dependence, median upright FVC = 71.9%, median supine FVC = 54.0%, 4 patients required invasive ventilation, 18 required NIV, 13 patients experienced infusion associated reactions

GroupNotHPOs:

NotHPOsFreeText: no ERT treatments prior to study, no pregnant patients

NumberMales: 37

NumberFemales: 36

CountryOrigin: n/a

Ethnicity: n/a

Race: n/a

AgeRange: at symtom onset = 1.4-62.6yrs, at diagnosis = 1.4-72.7yrs, at ERT start = 26.2-74.0yrs

TotalNumber: 73

FamilyInfo: n/a

NoFamily: n/a

GroupAddInfo: all patients received ERT of 20mg/kg/2wk alglucosidase alfa intravenoulsy, minimum 5 months of treatment. Median duration of disease = 8.2yrs

GroupPreviousTesting: anti-rhGAA antibody titers determined in plasma or serum using ELISA, neutralizing effects of antibodies determined by addition of alglucosidase alfa and patient serum to medium of GAA-deficient fibroblasts then by measurement of GAA activity in cells and medium, manual muscle testing to assess skeletal muscle strength, FVC in upright and supine positions, 46 patients developed anti-rhGAA titers about background of 1:250 (16 high, 29 intermediate, 28 low to no)

GroupGenotypingMethod: mutation analysis (PMID: 18425781)

Variant1: NM_000152.4(GAA):c.-32-13T>G this was carried by all but 1 patient

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

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

The following are the four most common variants on the second allele

Variant2: NM_000152.4(GAA):c.525delT (p.Glu176Argfs)

ClinVar: 4033, https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: 7.041e-05, http://exac.broadinstitute.org/variant/17-78078909-CT-C

Variant3: NC_000017.11:g.(?80118193)(80118357_?)del

ClinVar: 456368, https://www.ncbi.nlm.nih.gov/clinvar/variation/456368/

gnomAD: n/a

Variant4: NM_000152.4(GAA):c.1548G>A (p.Trp516Ter)

ClinVar: 189025, https://www.ncbi.nlm.nih.gov/clinvar/variation/189025/

gnomAD: n/a

Variant5: NM_000152.4(GAA):c.925G>A (p.Gly309Arg)

ClinVar: 188797, https://www.ncbi.nlm.nih.gov/clinvar/variation/188797/

gnomAD: 4.609e-05, http://exac.broadinstitute.org/variant/17-78081665-G-A

Case44: Male, 10yo at onset, 15yo at enrollment

CasePresentingHPOs: HP:0007340, HP:0003701, HP:0003327, HP:0003236, HP:0002111, HP:0100748, HP:0003458

HPOsFreeText: symmetric muscle weakness of extremities, CK = 3313 IU/L, FVC = 23%, Unspecific myopathic change, DBS GAA activity = 0.1, mixed leukocyte GAA activity = 1.80

CaseNotHPOs: HP:0001627, HP:0002086

NotHPOsFreeText:

CaseAddInfo: 5 years between onset and diagnosis

CasePreviousTesting: clinical history, laboratory data, DBS and ML assays to measure GAA activity, electromyography, muscle pathology analysis

CaseGenotypingMethod: full sequencing of GAA gene

VariantAllele1: NM_000152.4(GAA):c.546G>T (p.Thr182=)

ClinVar: 370637, https://www.ncbi.nlm.nih.gov/clinvar/variation/370637/

gnomAD: n/a

VariantAllele2: NM_000152.4(GAA):c.1316T>A (p.Met439Lys)

ClinVar: 371305, https://www.ncbi.nlm.nih.gov/clinvar/variation/371305/

gnomAD: 3.988e-05, http://exac.broadinstitute.org/variant/17-78082617-T-A

CaseP2-GAA: female, ethnicity = North African, country origin = Morocco

CasePresentingHPOs: HP:0010899, HP:0010916, HP:0003236

HPOsFreeText: enzyme activity = 1.41, CPK = 682 U/L, ALT = 68 U/L, AST = 130 U/L, CRIM positive

CaseNotHPOs:

CaseAddInfo: heterozygote, variants in trans. Patient underwent ERT.

CasePreviousTesting: initial and confirmatory DBS, biochemical tests, echocardiography

CaseGenotypingMethod: mutation analyses

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

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

gnomAD: n/a

Variant2: NM_000152.4(GAA):c.236_246delCCACACAGTGC (p.Pro79Argfs)

ClinVar: 371302, https://www.ncbi.nlm.nih.gov/clinvar/variation/371302/

gnomAD: n/a

CaseP1-GAA: Male, ethnicity = North African, country origin = Morocco

CasePresentingHPOs: HP:0010899, HP:0010916, HP:0003236

HPOsFreeText: enzyme activity = 0.61, CPK = 448 U/L, ALT = 48 U/L, AST = 98 U/L, CRIM positive

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: heterozygote, variants in trans. Patient underwent ERT.

CasePreviousTesting: initial and confirmatory DBS, biochemical tests, echocardiography

CaseGenotypingMethod: mutation analyses

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

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

gnomAD: n/a

Variant2: NM_000152.4(GAA):c.236_246delCCACACAGTGC (p.Pro79Argfs)

ClinVar: 371302, https://www.ncbi.nlm.nih.gov/clinvar/variation/371302/

gnomAD: n/a

PatientID: III-A

KindredID: 1

Case: M, 30Y0M, EthnicityUnknown

DiseaseAssertion: VHL

FamilyInfo: Multiple first- and second-degree relatives affected with similar phenotypes. Of these, he is genetically tested and found to share VHL mutations with his uncle (proband).

CasePresentingHPOs: N/A

CaseHPOFreeText: Paper asserts that this individual presented with VHL phenotypes but does not specify which.

CaseNotHPOs: NA

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: Information obtained from Figure 1

Variant: p.L158Q (c.473T>A)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 376048, https://www.ncbi.nlm.nih.gov/clinvar/variation/376048/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; transversion

CivicName: P86S (c.256C>T) and Splice Region (c.340+5G>C)

MultipleGeneVariants: Germline, VHL, c.340+5G>C

Family 10 - Patient 10

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0003327, HP:0040081, HP:0002111

HPOsFreeText: muscle pathology with vacuolar myopathy

FamilyNotHPOs: HP:0010628, HP:0002015, HP:0003691, HP:0003306, HP:0002650

Ethnicity: Iranian

ProbandLabel:

FamilyAddInfo: onset at 38yo, diagnosis at 50yo, MRC sum score = 73, patient required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: FVC = 65%, CK = 551 U/L, muscle pathology examined, DBS enzyme activity (with inhibition) = 0.12 μmol/L/h

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.3:c.2596delG

CAID: CA891834514, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA891834514

gnomAD: n/a

Family 4 - Patients 4a and 4b

FamilyPresentingHPOs: HP:0007340, HP:0003701, HP:0000467, HP:0003327, HP:0010628, HP:0002015, HP:0003306, HP:0002111, HP:0011807, HP:0003554, HP:0002111, HP:0100298, HP:0040081

HPOsFreeText: myopathic muscle unit action potentials, 4b muscular pathology with mild atrophy of type 1 and 2 fibers with many moth‐eaten fibers, no vacuoles, no glycogen excess

FamilyNotHPOs: HP:0003691, HP:0002650

NotHPOsFreeText:

Ethnicity: Iranian

ProbandLabel: 4a, female, 7yo at onset, 30yo at diagnosis

FamilyAddInfo: 4b (male) dx at 23yo, 4a MRC sum score = 84, 4b MRC sum score = 86, both patients required use of NIV

FamilyPreviousTesting: Respiratory Evaluation: 4a FVC = 29%, 4b FVC = 66%, 4a CK = 760 U/L, 4b CK = 3,257 U/L, muscle pathology (examined only in 4b), DBS enzyme activity (with inhibition) for 4a = 0.1 μmol/L/h, for 4b = 0.13 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

VariantAllele1: NM_000152.4(GAA):c.-32-13T>G

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

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

VariantAllele2: NM_000152.3:c.1650delG

Clinvar: n/a

CAID: CA627699787, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA627699787

gnomAD: n/a

Family 2 - Patient 2

FamilyPresentingHPOs: HP:0002355, HP:0003701, HP:0000467, HP:0009027, HP:0010628, HP:0002015, HP:0002111

HPOsFreeText:

FamilyNotHPOs: HP:0003691, HP:0003306, HP:0002650

NotHPOsFreeText:

Ethnicity: Iranian

ProbandLabel: Patient 2, male

FamilyAddInfo: 2yo at onset, 9yo at diagnosis MRC sum score = 73, NIV prescribed due to reduced FVC

FamilyPreviousTesting: Respiratory evaluation: FVC = 23%, CK = 83 U/L, Normal muscle pathology exams, DBS enzyme activity (with inhibition) = 0.14 μmol/L/h

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

Variant: NM_000152.3:c.2040+2dup

ClinVar: n/a

CAID: CA891834512, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA891834512

gnomAD: n/a

Family 5 - Patients 5a and 5b

FamilyPresentingHPOs: HP:0009027, HP:0000467, HP:0003327, HP:0003691, HP:0002650, HP:0040081, HP:0100284

HPOsFreeText: Myotonic discharges in paraspinal, tibialis anterior, first dorsal interosseous, and biceps muscles, Myopathic muscle unit action potentials, 5b muscular pathology with Severe lysosomal vacuolar myopathy with prominent glycogen excess

FamilyNotHPOs: HP:0010628, HP:0002015, HP:0003306

Ethnicity: Iranian

ProbandLabel: 5a, male, 10yo at onset, 12yo at diagnosis

FamilyAddInfo: 5b (female) dx at 15 yo, 5a MRC sum score = 94, 5b MRC sum score = 91

FamilyPreviousTesting: Respiratory Evaluation: 5a FVC = 91%, 5b FVC = 106%, 5a CK = 1,202 U/L, 5b CK = 907 U/L, muscle pathology (examined only in 5b), DBS enzyme activity (with inhibition) for 5a = 0.5 μmol/L/h, for 5b = 0.6 μmol/L/h, NCS, EMG

FamilyGenotypingMethod: GAA analyzed with Sanger Sequencing for entire coding region and conserved exon-intron splice junctions, PCR performed for deletion screening

Variant: NM_000152.3:c.1837T>G

ClinVar: n/a

CAID: CA401369569, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA401369569

gnomAD: n/a

CaseP5-GAA: female, ethnicity = South Asian, country origin = Nepal

CasePresentingHPOs:

HPOsFreeText: enzyme activity = 2.27

CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236

CaseAddInfo: known pseudodeficiency allele (c.1726G>A)

CasePreviousTesting: initial and confirmatory DBS, biochemical tests

CaseGenotypingMethod: mutation analyses

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

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

gnomAD: n/a

CaseP4-GAA: female, ethnicity = European, country origin = Italy

CasePresentingHPOs:

HPOsFreeText: enzyme activity = 2.22

CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236

CaseAddInfo: homozygous

CasePreviousTesting: initial and confirmatory DBS, biochemical tests

CaseGenotypingMethod: mutation analyses

Variant: NM_000152.4(GAA):c.533G>A (p.Arg178His)

ClinVar: 554969; https://www.ncbi.nlm.nih.gov/clinvar/variation/554969/

gnomAD: 2.646e-05, http://exac.broadinstitute.org/variant/17-78078918-G-A

CaseP3-GAA: male, ethnicity = European, country origin = Italy

CasePresentingHPOs:

HPOsFreeText: enzyme activity = 1.97

CaseNotHPOs: HP:0010899, HP:0010916, HP:0003236

CaseAddInfo: known psuedodeficiency alleles (c.1726G>A and c.2065G>A)

CasePreviousTesting: initial and confirmatory DBS, biochemical tests

CaseGenotypingMethod: mutation analyses

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

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

gnomAD: n/a

Case: Male, Spanish, onset at 57yo with pelvic weakness

CasePresentingHPOs: HP:0003236, HP:0002522, HP:0003184, HP:0012515, HP:0003749, HP:0003700, HP:0005144, HP:0002151, HP:0030232, HP:0009058

HPOsFreeText: weakness of hip adduction and shoulder abduction, abolished lower limb reflexes. CK = 500-800 U/L, lactate = 27.0 U/L, GOT = 50 U/L, GPT = 69 U/L, LDH = 449 U/L, aldolase = 8.7 U/L, myopathic motor unit action potentials with early recruitment and spontaneous activity (mainly in quadriceps), asymmetric septal left ventricular hypertrophy with preserved ventricular function, atrophy of both biceps and deltoid muscles, fibrillary deposits in cytoplasm, focal disorganization of sarcomeres, decrease in GAA inhibitory activity (0.64-0.68 μmol/L/h)

CaseNotHPOs: HP:0001283, HP:0002093, HP:0003326, HP:0002487

NotHPOsFreeText:

CaseAddInfo: daughter also underwent genetic testing which showed she was a heterozygous carrier for the same variant. She presented with decreased GAA activity in DBS and isolated lymphocytes.

CasePreviousTesting: blood laboratory exams, electromyography study, echocardiogram, biopsy of biceps and deltoid muscles, histochemical staining which showed no abnormalities, electron microscopy, DBS, enzyme activity analyzed in isolated lymphocytes (confirmed decreased GAA activity)

CaseGenotypingMethod: n/a

Variant: NM_000152.3:c.1249A>C

CAID: CA401365271, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA401365271

gnomAD: n/a

Case31: 2 mo (at biopsy), Indian

Case 31 (Level 2)

CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.257C>T (p.Pro86Leu)

ClinVar: 553773

CAID: CA3847150

gnomAD: 0.00009799 (South Asian)

CaseAddInfo: mut- type, homozygous mutations. documented consanguinity.

Case30: 6 wks (at biopsy), Pakistani

Case 30 (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.55dupG (p.Val19Glyfs)

ClinVar: 222906

CAID: CA10575888

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations. novel variant.

Case28: 1 y 1 mo (at biopsy), European

Case 28 (Level 2)

CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1181dupT (p.Leu394Phefs)

ClinVar: 222930

CAID: CA10575868

gnomAD: n/a

Variant2: NM_000255.3:c.1975C>T (p.Gln659Ter)

ClinVar: 222939

CAID: CA10575859

gnomAD: n/a

CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations, unknown cis or trans.

Case27: no age or ethnicity recorded

Case 27 (Level 2)

CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1061delCinsGGA (p.Ser354TrpfsTer20)

ClinVar: n/a

CAID: CA913187308

gnomAD: n/a

Variant2: NM_000255.3:c.1065_1068dupATGG (p.Ser357MetfsTer5)

ClinVar: 280817

CAID: CA10602989

gnomAD: n/a

CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations. Examination of NGS reads determined mutations are in trans

Case26: 7 y (at biopsy), Hispanic

Case 26 (Level 2)

CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 7.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.970G>A (p.Ala324Thr)

ClinVar: 550893

CAID: CA364400785

gnomAD: 0.0001632 (Other)

Variant2: NM_000255.3:c.1846C>T (p.Arg616Cys)

ClinVar: 551499

CAID: CA3846722

gnomAD: 0.00008688 (Latino)

CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans. Protein change in paper (p.P649L) is different than protein change indicated by clin var and CAID (p.Arg616Cys).

Case29: 3 mo (at biopsy), Chinese

Case 29 (Level 2)

CasePreviousTesting: same as group. found 0.3 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1280G>A (p.Gly427Asp)

ClinVar: 218990

CAID: CA347873

gnomAD: 0.0004011 (East Asian)

Variant2: Exon 13 deletion

ClinVar: n/a

CAID: n/a

gnomAD: n/a

CaseAddInfo: Variant 2 is novel. Heterozygous mutations in MUT, unknown cis or trans. Additional variant found in TCN2 gene (NM_000355.3:c.509G>A, ClinVar: 341197, CAID: CA10184685, gnomAD: 0.007469 (East Asian)). heterozygous Exon 13 deletion confirmed by microarray-based comparative genomic hybridization.

Case25: 25 y (at biopsy), White

Case 25 (Level 2)

CasePreviousTesting: same as group. found 1.3 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.935G>T (p.Gly312Val)

ClinVar: 218988

CAID: CA347874

gnomAD: n/a

Variant2: NM_000255.3:c.1909G>A (p.Gly637Arg)

ClinVar: n/a

CAID: CA3846712

gnomAD: [0.000008798] (http://insert-your-link-here.com)(European non-Finnish)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

Case24: no age or ethnicity recorded

Case 24 (Level 2)

CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.795_796insT or NM_000255.3:c.795dupT (p.Met266TyrfsTer7)

ClinVar: n/a

CAID: CA913187322

gnomAD: n/a

Variant2: NM_000255.3:c.1207C>T (p.Arg403Ter)

ClinVar: 167310

CAID: CA234287

gnomAD: 0.0001602 (African)

CaseAddInfo: Variant 1 is novel. Mut0 type, heterozygous mutations, unknown cis or trans.

Case23: 3 mo (at biopsy), French Canadian

Case 23 (Level 2)

CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.753+3A>G

ClinVar: n/a

CAID: CA3847056

gnomAD: 0.000008890 (European non-Finnish)

Variant2: NM_000255.3:c.1332+1delG

ClinVar: 554656

CAID: CA3846920

gnomAD: 0.000008828 (European non-Finnish)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans. Variant 1 is novel.

Case22: 28 mo (at biopsy), Korean

Case 22 (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

Variant2: NM_000255.3:c.1481T>A (p.Leu494Ter)

ClinVar: 551275

CAID: CA3846864

gnomAD: 0.0001088 (East Asian)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

Case21: 2 mo (at biopsy), White

Case 21 (Level 2)

CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

Variant2: NM_000255.3:c.1287C>G (p.Tyr429Ter)

ClinVar: 554278

CAID: CA364398724

gnomAD: 0.00006483 (European non-Finnish)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

Case20: 5 days (at biopsy), White

Case 20 (Level 2)

CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

Case19: 1 mo (at biopsy), White

Case 19 (Level 2)

CasePreviousTesting: same as group. found 1.2 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.655A>T (p.Asn219Tyr)

ClinVar: 1886

CAID: CA249731

gnomAD: 0.0001318 (European non-Finnish)

Variant2: NM_000255.3:c.1332+1delG

ClinVar: 554656

CAID: CA3846920

gnomAD: 0.000008828 (European non-Finnish)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

Case18: 2 mo (at biopsy), French Canadian

Case 18 (Level 2)

CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.655A>T (p.Asn219Tyr)

ClinVar: 1886

CAID: CA249731

gnomAD: 0.0001318 (European non-Finnish)

__

Variant2: NM_000255.3:c.1240delG (p.Glu414LysfsTer17)

ClinVar: n/a

CAID: CA3846936

gnomAD: 0.000008796 (European Non-Finnish)

CaseAddInfo: mut0 type. Variant 2 is novel. heterozygous mutations, unknown cis or trans.

Case17: 6 y (at biopsy), Black

Case 17 (Level 2)

CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.631_633delGAG (p.Glu211del)

ClinVar: n/a

CAID: CA913187321

gnomAD: n/a

Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

CaseAddInfo: mut0 type, heterozygous mutations. Variant 1 is novel. MUT mutations are in trans- demonstrated by RT-PCR of mRNA. Additional variant found in MCEE gene (NM_032601.3:c.428G>A, ClinVar: 336936, CAID: CA1702575, gnomAD: 0.08102 (Latino)) MCEE variant is unlikely to be associated with patient's MMA.

Case16: 5 days (at biopsy), Lao/Thai/Mexican/Portugese

Case 16 (Level 2)

CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.581C>T (p.Pro194Leu)

ClinVar: n/a

CAID: CA364404418

gnomAD: n/a

Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

Case15: 3 wks (at biopsy), white

Case (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

ClinVar: 203854

CAID: CA312777

gnomAD: 0.00006976 (European non-FInnish)

Variant2: NM_000255.3:c.754-2A>G

ClinVar: 552691

CAID: CA364402853

gnomAD: n/a

CaseAddInfo: variant 2 is a novel, splice site mutation. Heterozygous mutations, unknown cis or trans.

Case13: 21 y (at biopsy), English/Irish

Case (Level 2)

CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

ClinVar: 203854

CAID: CA312777

gnomAD: 0.00006976 (European non-FInnish)

Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

Case12: 6y (at biopsy), no ethnicity recorded

Case (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.556A>G (p.Met186Val)

ClinVar: 551460

CAID: CA3847093

gnomAD: 0.00001760 (European Non-Finnish)

Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans

Case11: 6y (at biopsy), White/Hispanic

Case (Level 2)

CasePreviousTesting: same as group. found 2.6 nmol/mg protein/18 h propionate incorporation, 7.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.566A>T (p.Asn189Ille)

ClinVar: 222915

CAID: CA3847091

gnomAD: 0.000008804 (European Non-Finnish)

Variant2: NM_000255.3:c.655A>T (p.Asn219Tyr)

ClinVar: 1886

CAID: CA249731

gnomAD: 0.0001318 (European non-Finnish)

CaseAddInfo: Variant 1 is novel, unknown cis or trans. mut- type.

Case14: 3 mo (at biopsy), White/Australian

Case (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.572C>A (p.Ala191Glu)

ClinVar: 203854

CAID: CA312777

gnomAD: 0.00006976 (European non-FInnish)

Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

CaseAddInfo: mut0 type, heterozygous mutation, unknown cis or trans

Case10: 6 days (at biopsy), Northern European/Filipino

Case (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

Variant2: NM_000255.3:c.682C>T (p.Arg228Ter)

ClinVar: 203855

CAID: CA312778

gnomAD: 0.0002615 (Latino)

CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

Case9: 46 days (at biopsy), Hispanic

Case (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

Variant2: NM_000255.3:c.654A>C (p.Gln218His)

ClinVar: 551243

CAID: CA364404273

gnomAD: 0.000008809 (European non-Finnish)

CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

Case8: 12 days (at biopsy), White/Mexican

Case (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

Variant2: NM_000255.3:c.654A>C (p.Gln218His)

ClinVar: 551243

CAID: CA364404273

gnomAD: 0.000008809 (European non-Finnish)

CaseAddInfo: mut0 class, heterozygous mutations, unknown cis or trans.

Case7: 10 days (at biopsy), White

Case (Level 2)

CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.146_147ins279

ClinVar: n/a

CAID: n/a- could not register

gnomAD: n/a

Variant2: NM_000255.3:c.372_374dupGA (p.Lys124_Asp125insGlu)

ClinVar: 203861

CAID: CA312788

gnomAD: 0.000008799

CaseAddInfo: mut0 class. heterozygous mutations. identified to be in trans through cDNA analysis. variant 1 is novel and consists of a 279 base pair insertion.

Case6 2 mo (at biopsy), White

Case (Level 2)

CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 3.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.129G>A (p.Trp43Ter)

ClinVar: 222908

CAID: CA10575886

gnomAD: n/a

Variant2: NM_000255.3:c.299A>G (p.Tyr100Cys)

ClinVar: 218991

CAID: CA347866

gnomAD: 0.000008793 (European non-Finnish)

CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. variant 1 is novel.

Case5: 1y 9 mo (at biopsy), Korean

Case (Level 2)

CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

ClinVar: 92688

CAID: CA249743

gnomAD: 0.00008013 (African)

Variant2: NM_000255.3:c.349G>T (p.Glu117Ter)

ClinVar: 1882

CAID: CA115264

gnomAD: n/a

CaseAddInfo: mut0 class. heterozygous mutations. unknown cis or trans.

Case4: 2 y (at biopsy), Black

Case (Level 2)

CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 3.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.91C>T (p.Arg31Ter)

ClinVar: 92688

CAID: CA249743

gnomAD: 0.00008013 (African)

Variant2: NM_000255.3:c.323G>A (p.Arg108His)

ClinVar: 100707

CAID: CA235522

gnomAD: 0.00006152 (African)

CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans. Third variant in TCN2 gene (NM_000355.3:c.89T>G p.Leu30Arg, CAID: CA10184491, ClinVar: 529781, gnomAD: 0.01329 (African))

Case3: 19y (at biopsy), Irish/Scottish/Polish

Case (Level 2)

CasePreviousTesting: same as group. found 1.2 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.29dupT (p.Leu10PhefsTer39)

ClinVar: 553287

CAID: CA567155988

gnomAD: 0.00003269 (South Asian)

Variant2: NM_000255.3:c.1658delT (p.Val553GlyfsTer17)

ClinVar: n/a

CAID: CA450397348

gnomAD: 0.000008808 (European non-Finnish)

CaseAddInfo: mut0 class. heterozygous mutations. variant 1 is novel. unknown cis or trans.

Case2: 1 mo (at biopsy), Palestinian

Case (Level 2)

CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.2T>C (p.Met1Thr)

ClinVar: 222903

CAID: CA10575890

gnomAD: n/a

Variant2: NM_000255.3:c.1630_1631delGGinsTA (p.Gly544Ter)

ClinVar: 203860

CAID: CA312786

gnomAD: 0.0001088 (East Asian)

CaseAddInfo: mut0 class. heterozygous mutations- unknown cis or trans. 3rd mutation in CD320 gene (NM_016579.3:c.658G>A p.Gly220Arg, ClinVar: 136684, CAID: CA289989, gnomAD: 0.3086 (African) )

Case1: 13 mo (at biopsy), no recorded ethnicity

Case (Level 2)

CasePreviousTesting: same as group. found 2.4 nmol/mg protein/18 h propionate incorporation, 4.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1A>G (p.M1?)

ClinVar: n/a

CAID: CA364406084

gnomAD: n/a

Variant2: NM_000255.3:c.2150G>T (p.Gly717Val)

ClinVar: 1881

CAID: CA249729

gnomAD: 0.0006810 (African)

CaseAddInfo: mut- class. heterozygous mutations. unknown cis or trans

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

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

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

Case 53 (Level 2)

CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_005334.2:c.4475C>T (p.Pro1492Leu)

ClinVar: n/a

CAID: CA415114585

gnomAD: n/a

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

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

CasePresentingHPOs: methylmalonic acidemia (HP:0002912)

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

Case 52 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA353555085

gnomAD: n/a

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

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

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

Case 51 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA347515756

gnomAD: 0.00001761 (European non-Finnish)

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

ClinVar: n/a

CAID: CA347515593

gnomAD: n/a

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

Case48: 8 mo (at biopsy), Indian

Case 48 (Level 2)

CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 1.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.2179C>T (p.Arg727Ter)

ClinVar: 218998

CAID: CA347913

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut0 type, homozygous mutations.

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

Case 47 (Level 2)

CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.2150G>T (p.Gly717Val)

ClinVar: 1881

CAID: CA249729

gnomAD: 0.0006810 (African)

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

Case46: 1 y (at biopsy), White

Case 46 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1962_1963delTC (p.Arg655Terfs)

ClinVar: 552144

CAID: CA658821515

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case44: 13y (at biopsy), Arab

Case 44 (Level 2)

CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 1.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1871A>G (p.Gln624Arg)

ClinVar: n/a

CAID: CA3846720

gnomAD: 0.00003266 (South Asian)

CaseAddInfo: mut0 type, homozygous mutations.

Case43: 20 y (at biopsy), Lebanese

Case 43 (Level 2)

CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)

ClinVar: 554675

CAID: CA364395893

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case45: no age or ethnicity recorded

Case 45 (Level 2)

CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1891delG (p.Ala631GlinfsTer17)

ClinVar: n/a

CAID: CA351288

gnomAD: 0.00002896 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

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

Case 42 (Level 2)

CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 9.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1663G>A (p.Ala555Thr)

ClinVar: 203850

CAID: CA312769

gnomAD: 0.0003262 (East Asian)

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

Case41: 6 mo (at biopsy), Pakistani

Case 41 (Level 2)

CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1560G>C (p.Lys520Asn)

ClinVar: n/a

CAID: CA364397073

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations.

Case40: Middle Eastern

Case 40 (Level 2)

CasePreviousTesting: same as group. found 1.8 nmol/mg protein/18 h propionate incorporation, 1.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1420C>T (p.Arg474Ter)

ClinVar: 554873

CAID: CA138795916

gnomAD: 0.00003267 (South Asian)

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case39: 1 y (at biopsy), Asian

Case 39 (Level 2)

CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1280G>A (p.Gly427Asp)

ClinVar: 218990

CAID: CA347873

gnomAD: 0.0004011 (East Asian)

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

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

Case 38 (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.1106G>A (p.Arg369His)

ClinVar: 203846

CAID: CA312764

gnomAD: 0.0001504 (East Asian)

CaseAddInfo: mut0 type, homozygous mutations.

Case37: 18 mo (at biopsy), Moroccan

Case 37 (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.683G>A (p.Arg228Gln)

ClinVar: n/a

CAID: CA3847070

gnomAD: 0.00002905 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case36: 14 mo (at biopsy), Hispanic

Case 36 (Level 2)

CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.406G>T (p.Val136Phe)

ClinVar: n/a

CAID: CA364404792

gnomAD: n/a

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

Case35: 5 y (at biopsy), Hispanic

Case 35 (Level 2)

CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case33: 9 mo (at biopsy), Hispanic

Case 33 (Level 2)

CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Case32: 10 y (at biopsy), Arab

Case 32 (Level 2)

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

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.278G>A (p.Arg93His)

ClinVar: 1880

CAID: CA249728

gnomAD: 0.0004777 (European- Finnish)

CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.

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

Case 34 (Level 2)

CasePreviousTesting: same as group. found 1.6 nmol/mg protein/18 h propionate incorporation, 1.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)

ClinVar: 1887

CAID: CA249732

gnomAD: 0.0008393 (Latino)

CaseAddInfo: mut0 type, homozygous mutations.

Patient3: Female, 22yo

CasePresentingHPOs: HP:0001249 (intellectual disability)

HPOsFreeText: Blood C5-carnitine (μM) = 14.27, under a protein restricted diet with carnitine and glycine supplementation

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: diagnosed at 3yo after improper treatment

CasePMIDs:

CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

GroupMethod1: PCR (primers in table 2)

GroupMethod2: Direct sequencing

CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

Variant1: NM_002225.4:c.1007G>A (p.Cys309Tyr) listed in paper as (p.Cys307Tyr)

CAID: CA391722967, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391722967

gnomAD: n/a

Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

gnomAD: n/a

Patient5-2 Female, 1yo, sibling to patient 5-1

CasePresentingHPOs:

HPOsFreeText: Blood C5-carnitine (μM) = 13.47, under a protein restricted diet with carnitine and glycine supplementation, normal development

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 2mo and asymptomatic at diagnosis

CasePMIDs:

CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

GroupMethod1: PCR (primers in table 2)

GroupMethod2: Direct sequencing

CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

Variant1: NM_002225.4:c.347C>T (p.Ser89Phe) listed in paper as (p.Ser87Phe)

CAID: CA391716394, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716394

gnomAD: n/a

Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

gnomAD: n/a

Patient1: Male, 6yo

CasePresentingHPOs:

HPOsFreeText: Blood C5-carnitine (μM) = 18.96, under a protein restricted diet with carnitine and glycine supplementation, normal development

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 10days old and asymptomatic at diagnosis

CasePMIDs:

CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

GroupMethod1: PCR (primers in table 2)

GroupMethod2: Direct sequencing

CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

Variant1: NM_002225.3:c.386A>G (p.Tyr99Cys) listed in paper as (p.His100Arg)

CAID: CA391716511, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716511

gnomAD: n/a

Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

gnomAD: n/a

Patient5-1: Female, 2.5yo, sibling to patient 5-2

CasePresentingHPOs:

HPOsFreeText: under a protein restricted diet with carnitine and glycine supplementation, normal development

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 2mo diagnosis

CasePMIDs:

CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

GroupMethod1: PCR (primers in table 2)

GroupMethod2: Direct sequencing

CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

Variant1: NM_002225.4:c.347C>T (p.Ser89Phe) listed in paper as (p.Ser87Phe)

CAID: CA391716394, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716394

gnomAD: n/a

Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

gnomAD: n/a

Case12(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

Variant2: NM_015506.2(MMACHC):c.481C > T (p.Arg161Ter)

ClinVar: 95703

CAID: CA223189

gnomAD: 0.0001241 (African)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) not a carrier

Case 7 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

Variant2: NM_015506.2(MMACHC):c.445_446delTG (p.Cys149Hisfs*32)

ClinVar: 203834

CAID: CA312741

gnomAD: 0.00008509 (Latino)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for both variants

Case 3 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.463_465delGGG

ClinVar: n/a

CAID: n/a

gnomAD: n/a

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) not a carrier

Case 11(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) carrier for p.W203X variant

Case 1 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.80A>G (p.Gln27Arg)

ClinVar: 552467

CAID: CA827620

gnomAD: not in gnomAD

Variant2: NM_015506.2(MMACHC):c.482G>A

ClinVar: 1425

CAID: CA223191

gnomAD: 0.001132 (latino)

CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) carrier of p.Gln27Arg maternal mutation

Case 8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.394C > T (p.Arg132Ter)

ClinVar: 1423

CAID: CA251787

gnomAD: 0.0007190 (South Asian)

__

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.R132X maternal variant

Case 9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

Variant2: NM_015506.2(MMACHC):c.637G>T (p.Glu213Ter)

ClinVar: n/a

CAID: CA340133779

gnomAD: n/a

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

Case 14 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

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

ClinVar: 556708

CAID: CA522810899

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

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

Case 2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.217C > T

ClinVar: 203825

CAID: CA312728

gnomAD: 0.00005560 (East Asian)

Variant2: NM_015506.2(MMACHC):c.658_660delAAG

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, not any phenotypic info given, sibling (fetus) carrier of p.R73X maternal variant

Case 15 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

__

Variant1: NM_015506.2(MMACHC):c.394C > T (p.Arg132Ter)

ClinVar: 1423

CAID: CA251787

gnomAD: 0.0007190 (South Asian)

Variant2: NM_015506.2(MMACHC):c.615C > A (p.Tyr205Ter)

ClinVar: 558292

CAID: CA340133688

gnomAD: 0.0006427 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carries both variants

Case 13 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) carrier for p.W203X variant

Case 16 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.217C > T (p.Arg73Ter)

ClinVar: 203825

CAID: CA312728

gnomAD: 0.00005560 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) is a carrier of variant

Case 5 (Level 2)

**CasePreviousTesting: ** same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.626dupT (p.Thr210Aspfs*35)

ClinVar: not in ClinVar

CAID: Not in ClinGen

gnomAD: not in gnomAD

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for c.626dupT maternal variant

Case 6 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

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

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for both variants

Case 10 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

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

Case 4 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

__

Variant2: NM_015506.2(MMACHC):c.467G>A (p.Gly156Asp)

ClinVar: 554696

CAID: CA340133108

gnomAD: not in gnomAD

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

Case61(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: n/a

CAID: n/a

gnomAD: 0.000008829 (European non-Finnish)

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

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

Case 21 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: n/a

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

CAID: CA340133108

gnomAD: n/a

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

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

Case52(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

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

ClinVar: n/a

CAID: n/a

gnomAD: n/a

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

Case 26 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: n/a

CAID: CA312741

gnomAD: n/a

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

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

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

Case32 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

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

ClinVar: 496436

CAID: CA827827

gnomAD: 0.00006537 (South Asian)

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

ClinVar: 552467

CAID: CA827620

gnomAD: not in gnomAD

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

Case 17 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

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

ClinVar: n/a

CAID: n/a

gnomAD: n/a

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

ClinVar: 556708

CAID: CA522810899

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

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

Case5: Female, 10m, Chinese, part of Family 1

HPOsFreeText: (at 20 days) 1.38 C4 umol/L, 0.19 C4/C2, 1.79 C4/C3, 2.58 (mmol/mol creatinine) urine isobutyrylglycine

Case5 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

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

ClinVar: n/a

CAID: CA6373205

gnomAD: 0.00005790 (Latino)

CaseAddInfo: younger sister of patient 6, trans heterozygous, inherited one allele from each parent

Case4: Male, 1y 2m, Chinese

HPOsFreeText: (at 21 days) 0.77 C4 umol/L, 0.07 C4/C2, 0.86 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case4 (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.444G>T (p.Pro148=)

ClinVar: n/a

CAID: CA6372946

gnomAD: 0.0002772 (Other)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

Case1: Female, 1y 7m, Chinese

HPOsFreeText: (at 13 days) C4 1.31 umol/L, C4/C2 0.21, C4/C3 1.96

NotHPOsFreeText: normal urine isobutyrylglycine

Case1 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.235C>G (p.Arg79Gly)

ClinVar: n/a

CAID: CA6372884

gnomAD: 0.0002718 (East Asian)

Variant2: NM_014384.2:c.1000C>T (p.Arg334Cys)

ClinVar: n/a

CAID: CA6373194

gnomAD: 0.0003007 (East Asian)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

Case2: Male, 1y 7m, Chinese

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

NotHPOsFreeText: normal urine isobutyrylglycine

Case2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

CaseAddInfo:

Case7: Male, 6m, Chinese

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

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

NotHPOsFreeText: normal urine isobutyrylglycine

Case7 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372946

gnomAD: 0.0002772 (Other)

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

ClinVar: n/a

CAID: CA6373249

gnomAD: 0.0001088 (East Asian)

CaseAddInfo: trans heterozygous, inherited one allele from each parent

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

Case11: Male, 3 wk at initiation of follow up, African American ancestry

HPOsFreeText: NBS C4-acylcarnitine 1.4 umol/L, lasma C4 acylcarnitine 1.87 umol/L, in vitro probe isoC4-acylcarnitine 0.053 umol/ g protein

NotHPOsFreeText: normal in vitro probe C4-aclycarnitine, normal urine isobutyrylglycine, normal urine C4-acylcarnitine, normal urine C4/C3 ratio

CaseAddInfo: mild biochemical phenotype observed. Suggested to be at minimum a carrier of IBD deficiency- however presence of promoter mutation, large deletion, or splice-site alteration undetectable by direct gene sequencing cannot be ruled out.

Case11 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

ClinVar: 5356

CAID: CA117435

gnomAD: 0.0001551 (European non-Finnish)

CaseAddInfo: heterozygous for mutation

Case6: Female, 16 days at initiation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.0 umol/L, Plasma C4-acylcarnitine 1.36 umol/L, in vitro probe isoC4-acylcarnitine 0.160 umol/g protein, in vitro probe C4-acylcarnitine 0.150 umol/g protein, urine c4 acylcarnitine 19.13 mmol/mol creatinine, urine C4/C3 ratio 101

CaseNotHPOs: normal urine isobutyryglycine

CaseAddInfo: no data for clinical condition or SCAD gene variants

Case6 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2(ACAD8):c.958G>A (p.Ala320Thr)

ClinVar: 372297

CAID: CA6373180

gnomAD: 0.001725 (European Finnish)

Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

ClinVar: 5356

CAID: CA117435

gnomAD: 0.0001551 (European non-Finnish)

CaseAddInfo: compound heterozygote, specified allele 1 and 2 but not maternal and paternal. no potential splice site alteration

Case7a: Male, 7 days at initiation of follow up, Hispanic ancestry

HPOsFreeText: NBS C4-acylcarnitine 2.2 umol/L, plasma C4-acylcarnitine 2.09 umol/L, in vitro probe isoC4-acylcarnitine 0.070 umol/g protein, urine C4-acylcarnitine 3.58 mmol/mol creatinine, Urine C4/C3 ratio 130.

CaseNotHPOs: normal in vitro probe C4-acylcarnitine, normal urine isobutyrylglycine,

CaseAddInfo: younger brother of patient 7b, part of Family2, unremarkable clinical condition

Case7a (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.687T>G (p.Phe229Leu)

ClinVar: n/a

CAID: CA6373030

gnomAD: 0.00008673 (Latino)

Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

ClinVar: 5356

CAID: CA117435

gnomAD: 0.0001551 (European non-Finnish)

CaseAddInfo: no potential splice site alteration, no data for SCAD gene variants

Case1: Female, 9 days at follow up, North African ancestry

CasePresentingHPOs: HP:0002013, HP:0001944,HP:0031123, HP:0000388 (emesis, dehydration, recurrent gastroenteritis, otitis media)

HPOsFreeText: NBS C4-acylcarnitine 2.9 umol/L, plasma C4 acylcarnitine 1.35 umol/L, isoC4-acylcarnitine 0.090 umol/g protein,

CaseNotHPOs:

NotHPOsFreeText: normal urine isobutyrylglycine

CaseAddInfo: repeatedly hospitalized during first 2 years of life.

CasePMIDs:

Case (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.988C>T (p.Arg330Trp)

ClinVar: 5357

CAID: CA117438

gnomAD: 0.00006155 (African)

CaseAddInfo: homozygous mutations

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

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

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case4 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: n/a

CAID: CA6372945

gnomAD: not in gnomAD

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

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

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

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

NotHPOsFreeText: normal urine isobutyrylglycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3a (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 5358

CAID: CA117441

gnomAD: not in gnomAD

CaseAddInfo: homozygous mutations

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

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

NotHPOsFreeText: normal urine isobutyrylglycine

CaseAddInfo: unremarkable clinical condition

Case9 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 430160

CAID: CA6372883

gnomAD: n/a

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

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

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

CaseAddInfo: no data for urine excretion, unremarkable clinical condition

Case2 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

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

ClinVar: 281037

CAID: CA6372897

gnomAD: 0.0002175 (East Asian)

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

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

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

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.

Case43: Male, Chinese, 2.3y (end of study)

HPOsFreeText: 2y onset, poor neurological outcome

NotHPOsFreeText: not responsive to vitamin B12

Case43 (Level 2)

CasePreviousTesting: NBS

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000255.3:c.2107G>A (p.Gly703Arg)

ClinVar: n/a

CAID: CA364394252

gnomAD: 0.00006152 (African)

CaseAddInfo: one variant, not homozygous.

Case42: Female, Chinese, 2.3y (end of study)