ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.425-2A>G

dbSNP: rs752851284
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410172 SCV000485815 likely pathogenic Glycogen storage disease, type V 2016-02-16 criteria provided, single submitter clinical testing
Invitae RCV000410172 SCV000818344 likely pathogenic Glycogen storage disease, type V 2021-01-05 criteria provided, single submitter clinical testing 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. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PYGM are known to be pathogenic (PMID: 8316268, 16786513). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with PYGM-related disease. ClinVar contains an entry for this variant (Variation ID: 370481). This variant is present in population databases (rs752851284, ExAC 0.002%). This sequence change affects an acceptor splice site in intron 3 of the PYGM gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.
Baylor Genetics RCV000410172 SCV004207268 pathogenic Glycogen storage disease, type V 2023-06-05 criteria provided, single submitter clinical testing
Natera, Inc. RCV000410172 SCV002092346 likely pathogenic Glycogen storage disease, type V 2021-10-19 no assertion criteria provided clinical testing

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