ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2040+20_2190-274del

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005407645 SCV006071730 pathogenic Glycogen storage disease, type II 2025-03-12 criteria provided, single submitter clinical testing Variant summary: The variant involves the deletion of exon 15 in the GAA gene. A presumed nomenclature of c.2040+20_2190-274del3648 has been designated for the purposes of this classification. This Copy Number Variant (CNV) is expected to alter the reading frame and predicted to result in a truncation or absence of the encoded protein due to nonsense mediated decay (NMD). The variant was absent in 21694 control chromosomes (gnomAD, structural variants dataset). A similar variant, reported as c.2040+29_2190-270del, which is also expected to result in the deletion of exon 15, has been reported in the literature in at least one individual affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (e.g. Gupta_2019). These data indicate that the variant is likely associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 31606152). ClinVar contains an entry for this variant (Variation ID: 3242829). Based on the evidence outlined above, the variant was classified as pathogenic.

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