Case28

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

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

Variant1: NM_000152.4:c.1099T>C (p.Trp367Arg)

ClinVar: 555820 https://www.ncbi.nlm.nih.gov/clinvar/variation/555820/

gnomAD: Not in gnomAD

Variant2: NM_000152.4:c.1802C>T (p.Ser601Leu)

ClinVar: 194154 https://www.ncbi.nlm.nih.gov/clinvar/variation/194154/

gnomAD: East Asian 6.418e-4, Overall 3.187e-5 http://gnomad.broadinstitute.org/variant/17-78086424-C-T

CaseAddInfo: Infantile Onset Pompe Disease

Case#: Patient 3, Gender N/A, 5-6 months old when diagnosed.13 months when died, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo:

CasePresentingHPOs: HP:0002094 HP:0001639. HP:0005165 (Hypertrophic Cardiomyopathy, Dyspnea, Shortened PR interval)

CaseHPOFreeText: Generalized Muscle weakness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: GAA enzyme activity in leukocytes was 0% of the normal control value.

PCR of all exons was performed and subsequently subjected to capillary Sanger sequencing in both directions

Variant1: NM_000152.5(GAA):c.1099T>C (p.Trp367Arg)

ClinVar:<br /> 555820

CAID: CA401364951

gnomAD: N/A

Variant2: NM_000152.5(GAA):c.1942G>A (p.Gly648Ser)

ClinVar: 188902

CAID: CA274102

gnomAD: Highest population MAF = 0.0003365 (South Asian)

ParentalGenotype: Father was carrier for Variant1 NM_000152.5(GAA):c.1099T>C (p.Trp367Arg)

Mother was carrier of Variant 2 NM_000152.5(GAA):c.1942G>A (p.Gly648Ser)

PreviouslyPublished: N/A