ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1192dup (p.Leu398fs)

dbSNP: rs1057516546
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel RCV000411138 SCV001443332 pathogenic Glycogen storage disease, type II 2020-09-20 reviewed by expert panel curation This variant, c.1192dup (p.Leu398ProfsTer108), is a frameshift variant that is predicted to result in a premature termination codon, nonsense mediated decay, and lack of gene product, meeting PVS1. This variant is not in gnomAD v2.1.1, meeting PM2. One patient has been reported who meets the ClinGen LSD VCEP's specifications for PP4 and who is compound heterozygous with c.-32-13T>G pathogenic variant, phase unknown (PMID 17616415), meeting PM3_Supporting. The variant has been reported in additional publications but GAA activity was not provided and therefore the data was not included (PMIDs 22980766, 27711114). There is a ClinVar entry for this variant (Variation ID: 370510, 1 star review status) with one submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PVS1, PM2, PM3_supporting, PP4.
Counsyl RCV000411138 SCV000485853 likely pathogenic Glycogen storage disease, type II 2016-02-23 criteria provided, single submitter clinical testing

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