ClinVar Miner

Submissions for variant NM_000289.6(PFKM):c.1500+1G>A

gnomAD frequency: 0.00001  dbSNP: rs770066278
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001215088 SCV001386809 likely pathogenic Glycogen storage disease, type VII 2024-01-19 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 16 of the PFKM 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 PFKM are known to be pathogenic (PMID: 7825568, 8037209). This variant is present in population databases (rs770066278, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with PFKM-related conditions. ClinVar contains an entry for this variant (Variation ID: 944644). 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.
Revvity Omics, Revvity RCV001215088 SCV003811376 likely pathogenic Glycogen storage disease, type VII 2021-12-03 criteria provided, single submitter clinical testing
Baylor Genetics RCV001215088 SCV004203929 pathogenic Glycogen storage disease, type VII 2023-10-16 criteria provided, single submitter clinical testing
Natera, Inc. RCV001215088 SCV002091088 likely pathogenic Glycogen storage disease, type VII 2020-03-17 no assertion criteria provided clinical testing

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