ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.3598C>T (p.Arg1200Ter)

gnomAD frequency: 0.00002  dbSNP: rs140353201
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081893 SCV000228162 pathogenic not provided 2012-11-14 criteria provided, single submitter clinical testing
GeneDx RCV000081893 SCV000582388 pathogenic not provided 2023-03-24 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000810563 SCV000950776 pathogenic Cohen syndrome 2023-10-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1200*) 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 (rs140353201, gnomAD 0.008%). 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: 95846). 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.
CeGaT Center for Human Genetics Tuebingen RCV000081893 SCV001500518 pathogenic not provided 2021-02-01 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000810563 SCV003816620 likely pathogenic Cohen syndrome 2022-06-03 criteria provided, single submitter clinical testing
New York Genome Center RCV000810563 SCV003925424 pathogenic Cohen syndrome 2022-02-09 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003894940 SCV004716024 likely pathogenic VPS13B-related disorder 2024-03-01 criteria provided, single submitter clinical testing The VPS13B c.3598C>T variant is predicted to result in premature protein termination (p.Arg1200*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD. Nonsense variants in VPS13B are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Natera, Inc. RCV000810563 SCV001454827 pathogenic Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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