ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.5955G>A (p.Trp1985Ter)

dbSNP: rs1554892040
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523228 SCV000620343 pathogenic not provided 2017-08-31 criteria provided, single submitter clinical testing The W2010X nonsense variant in the VPS13B gene is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The W2010X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Although this pathogenic variant has not been reported previously to our knowledge, its presence is consistent with the diagnosis of Cohen syndrome.
Labcorp Genetics (formerly Invitae), Labcorp RCV001380881 SCV001579066 pathogenic Cohen syndrome 2020-09-15 criteria provided, single submitter clinical testing This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in VPS13B are known to be pathogenic (PMID: 15141358, 16648375, 20461111). This variant has not been reported in the literature in individuals with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 451620). This sequence change creates a premature translational stop signal (p.Trp2010*) in the VPS13B gene. It is expected to result in an absent or disrupted protein product.

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