ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.546+2_546+5del

dbSNP: rs1181354869
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital RCV001261922 SCV001438055 pathogenic Glycogen storage disease, type II 2020-10-15 criteria provided, single submitter clinical testing The c. 546+2_ 546+5del splice site variant in intron 2 has been reported by Bali et al 2012 PMID: 22252923
Invitae RCV001261922 SCV003288493 likely pathogenic Glycogen storage disease, type II 2024-01-04 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 2 of the GAA gene. RNA analysis indicates that disruption of this splice site induces altered splicing and is likely to result in the loss of the initiator methionine. This variant is present in population databases (no rsID available, gnomAD 0.001%). Disruption of this splice site has been observed in individual(s) with Pompe disease (PMID: 22252923, 33741225). ClinVar contains an entry for this variant (Variation ID: 982296). Studies have shown that disruption of this splice site results in skipping of exon 2, and is expected to result in the loss of the initiator methionine (PMID: 31301153). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic RCV003482356 SCV004228181 pathogenic not provided 2023-05-22 criteria provided, single submitter clinical testing PP4, PM2, PM3, PS3, PVS1

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