ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.4848G>A (p.Trp1616Ter)

dbSNP: rs180177360
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169432 SCV000220845 likely pathogenic Cohen syndrome 2014-10-28 criteria provided, single submitter literature only
Labcorp Genetics (formerly Invitae), Labcorp RCV000169432 SCV002242790 pathogenic Cohen syndrome 2022-11-15 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 68086). This premature translational stop signal has been observed in individual(s) with clinical features of Cohen syndrome (PMID: 16648375). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp1641*) 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).
GeneDx RCV000058896 SCV002526256 pathogenic not provided 2022-06-03 criteria provided, single submitter clinical testing Observed along with a second nonsense variant in the VPS13B gene in multiple patients from one family with Cohen syndrome; however, segregation information was not provided (Seifert et al., 2006); 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: 25525159, 21865173, 20461111, 15141358, 16648375)
SNPedia RCV000058896 SCV000090417 pathogenic not provided no assertion criteria provided not provided Converted during submission to Pathogenic.

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