Patient36: Male, 3 year onset

CasePresentingHPOs: HP:0001324, HP:0002098, HP:0003236 (Muscle weakness, Respiratory distress, Increased serum CK)

HPOsFreeText: GAA activity 5.7% from leukocyte, Wheelchair needed, Respiratory Assistance needed

CaseNotHPOs: HP:0001640, HP:0002240 (Cardiomegaly, Hepatomegaly)

NotHPOsFreeText: N/A

CaseAddInfo: LOPD550825

Patient6: Male, 5 years report, 1 month onset

CasePresentingHPOs: HP:0001640, HP:0001324, HP:0002098 (Cardiomegaly, Muscle weakness, Respiratory distress)

HPOsFreeText: GAA activity 6.8% from leukocyte, Wheelchair needed, Respiratory Assistance needed

CaseNotHPOs: HP:0002240 (Hepatomegaly)

NotHPOsFreeText: N/A

CaseAddInfo: IOPD

Patient31: <1 year onset

CasePresentingHPOs: HP:0002240 (Hepatomegaly)

CaseAddInfo: LOPD

Patient9: Male, <1 year onset

CaseAddInfo: LOPD

Patient8: Female, 8 year onset

CasePresentingHPOs: HP:0001324 (Muscle Weakness)

HPOsFreeText: GAA activity 3.2% from dried blood spot

CaseNotHPOs: HP:0002098, HP:0001640, HP:0002240 (Respiratory distress, Cardiomegaly, Hepatomegaly)

NotHPOsFreeText: No wheelchair needed, Respiratory Assistance not needed

CaseAddInfo: LOPD

Patient5: Female, 4 years report, 10 months onset

CasePresentingHPOs: HP:0001640, HP:0002240, HP:0001324 (Cardiomegaly, Hepatomegaly, Muscle weakness)

HPOsFreeText: GAA activity 2.4% from leukocyte

CaseNotHPOs: HP:0002098 (Respiratory distress)

NotHPOsFreeText: No wheelchair needed, Respiratory Assistance not needed

CaseAddInfo: IOPD

Case65

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.1798C>T (p.Arg600Cys)

CAID: CA8815481 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.1798C%3ET

gnomAD: South Asian 3.267e-5, Overall 4.025e-6 http://gnomad.broadinstitute.org/variant/17-78086420-C-T

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

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

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

CaseAddInfo: Adult Late Onset Pompe Disease

Patient11: 4yo

CasePresentingHPOs: HP:0001638

HPOsFreeText: rhGAA dosage = 20 EOW, independent walker

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 2mo at ERT start

CasePMIDs:

CasePreviousTesting: same a group

CaseGenotypingMethod: same as group

Variant1: NM_000152.3:c.872T>C

CAID: CA401363854, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA401363854

gnomAD: n/a

Variant2: NM_000152.3:c.1798C>T

CAID: CA8815481, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8815481

gnomAD: 8.669e-06, http://exac.broadinstitute.org/variant/17-78086420-C-T

Case22: Male, 0.5 yr onset, 1 yr diagnosis, 1.3 yr report

HPOsFreeText: Wheelchair used at 4 yr, Died of respiratory failure at 10 yr, FVC z-score sitting -4.77 (45% pred) at 9 yr, 586 CK U/l, Deficient GAA activity (nmol/h/mg)^h from cultured fibroblasts