ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8827C>T (p.Arg2943Ter)

gnomAD frequency: 0.00001  dbSNP: rs755996065
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000820837 SCV000961567 pathogenic Cohen syndrome 2024-03-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2968*) in the VPS13B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in VPS13B are known to be pathogenic (PMID: 15141358, 16648375, 20461111). This variant is present in population databases (rs755996065, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 663053). 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.
Fulgent Genetics, Fulgent Genetics RCV000820837 SCV005667403 likely pathogenic Cohen syndrome 2024-01-22 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004742652 SCV005365656 likely pathogenic VPS13B-related disorder 2024-09-20 no assertion criteria provided clinical testing The VPS13B c.8827C>T variant is predicted to result in premature protein termination (p.Arg2943*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.010% of alleles in individuals of East Asian descent in gnomAD. Nonsense variants in VPS13B are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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