ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1553_1555dup (p.Asp518_Met519insAsn)

dbSNP: rs2039221468
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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 RCV001200869 SCV001371757 uncertain significance Glycogen storage disease, type II 2023-05-29 reviewed by expert panel curation The NM_000152.5:c.1553_1555dup variant in GAA is predicted to cause a change in the length of the protein (p.Asp518_Met519insAsn) due to an in-frame insertion of one amino acid in a non-repeat region (PM4_Supporting). The variant is absent in gnomAD v2.1.1 (PM2_Supporting). To our knowledge, this variant has not been reported in the literature in individuals with Pompe disease, and results of experimental studies are not available. PROVEAN and Mutation Taster predict that this variant will impact the function of GAA (PP3). The is a ClinVar entry for this variant (Variation ID: 932901). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease. ACMG/AMP GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel: PM2_Supporting, PM4_Supporting, PP3. (Classification approved by the ClinGen LD VCEP on May 29, 2023)
Labcorp Genetics (formerly Invitae), Labcorp RCV001200869 SCV002270409 uncertain significance Glycogen storage disease, type II 2021-10-06 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 932901). This variant has not been reported in the literature in individuals affected with GAA-related conditions. This variant is not present in population databases (ExAC no frequency). This variant, c.1553_1555dup, results in the insertion of 1 amino acid(s) to the GAA protein (p.Asp518_Met519insAsn), but otherwise preserves the integrity of the reading frame.

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