ClinVar Miner

Submissions for variant NM_033305.3(VPS13A):c.7736_7739del (p.Arg2579fs)

dbSNP: rs748828128
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001220781 SCV001392792 pathogenic not provided 2024-01-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2579Asnfs*26) in the VPS13A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in VPS13A are known to be pathogenic (PMID: 12404112, 21598378). This variant is present in population databases (rs748828128, gnomAD 0.004%). 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: 949342). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003405407 SCV004113494 likely pathogenic VPS13A-related disorder 2023-01-27 criteria provided, single submitter clinical testing The VPS13A c.7736_7739delGAGA variant is predicted to result in a frameshift and premature protein termination (p.Arg2579Asnfs*26). This variant was reported in the compound heterozygous states individuals with choreoacanthocytosis (reported as c.7731_7734delAGAG in Futamura et al 2020. PubMed ID: 32129282; Vaisfeld A et al 2021. PubMed ID: 33652783). This variant is reported in 0.0044% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-79971707-TAGAG-T). Frameshift variants in VPS13A are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Natera, Inc. RCV001828759 SCV002081094 pathogenic Chorea-acanthocytosis 2020-11-13 no assertion criteria provided clinical testing

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