ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.2178-1G>A

gnomAD frequency: 0.00005  dbSNP: rs143670942
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520606 SCV000617997 likely pathogenic not provided 2019-06-27 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (Stenson et al., 2014); Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity Omics RCV001783020 SCV002019587 pathogenic Glycogen storage disease, type V 2019-03-08 criteria provided, single submitter clinical testing
Invitae RCV001783020 SCV003781396 likely pathogenic Glycogen storage disease, type V 2022-07-23 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with PYGM-related conditions. This variant is present in population databases (rs143670942, gnomAD 0.02%). This sequence change affects an acceptor splice site in intron 17 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). ClinVar contains an entry for this variant (Variation ID: 449668). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.
Baylor Genetics RCV001783020 SCV004207251 likely pathogenic Glycogen storage disease, type V 2023-07-15 criteria provided, single submitter clinical testing
Natera, Inc. RCV001783020 SCV002092309 likely pathogenic Glycogen storage disease, type V 2020-06-29 no assertion criteria provided clinical testing

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