ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.1915C>T (p.Arg639Ter)

gnomAD frequency: 0.00002  dbSNP: rs764776104
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000255734 SCV000322116 pathogenic not provided 2024-12-06 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); This variant is associated with the following publications: (PMID: 31589614, Beene_2015_Paper, 28559085)
Eurofins Ntd Llc (ga) RCV000255734 SCV000703985 pathogenic not provided 2016-12-12 criteria provided, single submitter clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000824874 SCV000965781 likely pathogenic Cohen syndrome 2016-01-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000824874 SCV002231527 pathogenic Cohen syndrome 2025-01-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg639*) 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 (rs764776104, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with clinical features of Cohen syndrome (PMID: 28559085). ClinVar contains an entry for this variant (Variation ID: 265334). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000824874 SCV005672009 pathogenic Cohen syndrome 2024-05-07 criteria provided, single submitter clinical testing
Counsyl RCV000824874 SCV001132510 likely pathogenic Cohen syndrome 2015-08-20 no assertion criteria provided clinical testing
Natera, Inc. RCV000824874 SCV001454810 pathogenic Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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