ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.10735A>T (p.Lys3579Ter)

dbSNP: rs1057520769
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000429941 SCV000517363 likely pathogenic not provided 2024-04-03 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
Labcorp Genetics (formerly Invitae), Labcorp RCV000558120 SCV000630856 pathogenic Cohen syndrome 2023-06-16 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: 379881). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Lys3604*) 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).
Counsyl RCV000558120 SCV001132511 likely pathogenic Cohen syndrome 2015-09-14 no assertion criteria provided clinical testing

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