ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.345+2T>A

gnomAD frequency: 0.00002  dbSNP: rs1219299972
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001051949 SCV001216134 likely pathogenic Glycogen storage disease, type V 2023-10-13 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the PYGM gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site 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). This variant is present in population databases (no rsID available, gnomAD 0.0009%). Disruption of this splice site has been observed in individual(s) with clinical features of glycogen storage disease type V (GSD V), also known as McArdle disease (PMID: 34534370). ClinVar contains an entry for this variant (Variation ID: 848237). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Baylor Genetics RCV001051949 SCV005052598 pathogenic Glycogen storage disease, type V 2024-03-06 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001051949 SCV005684416 likely pathogenic Glycogen storage disease, type V 2024-03-27 criteria provided, single submitter clinical testing
Natera, Inc. RCV001051949 SCV002092347 likely pathogenic Glycogen storage disease, type V 2020-08-05 no assertion criteria provided clinical testing

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