ClinVar Miner

Submissions for variant NM_033305.3(VPS13A):c.2513-2A>T

dbSNP: rs1037030970
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521085 SCV000621275 likely pathogenic not provided 2019-10-18 criteria provided, single submitter clinical testing Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000521085 SCV001386843 likely pathogenic not provided 2024-01-16 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 24 of the VPS13A 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 VPS13A are known to be pathogenic (PMID: 12404112, 21598378). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with VPS13A-related conditions. ClinVar contains an entry for this variant (Variation ID: 452465). 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.
Natera, Inc. RCV001835838 SCV002078240 likely pathogenic Chorea-acanthocytosis 2021-08-23 no assertion criteria provided clinical testing

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