ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.901_904del (p.Thr301fs)

dbSNP: rs759536357
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000480446 SCV000564892 likely pathogenic not provided 2021-07-31 criteria provided, single submitter clinical testing Reported as a likely pathogenic variant in a healthy individual enrolled in a preconception carrier screening study (Capalbo A et al., 2019); Frameshift 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 (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31589614)
Labcorp Genetics (formerly Invitae), Labcorp RCV000412175 SCV000959655 pathogenic Cohen syndrome 2023-08-28 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 370733). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. This variant is present in population databases (rs759536357, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Thr301Valfs*7) 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). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV000480446 SCV002497985 pathogenic not provided 2022-04-01 criteria provided, single submitter clinical testing
New York Genome Center RCV000412175 SCV003925152 likely pathogenic Cohen syndrome 2022-06-06 criteria provided, single submitter clinical testing
Counsyl RCV000412175 SCV000486123 likely pathogenic Cohen syndrome 2016-04-01 no assertion criteria provided clinical testing
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals RCV000412175 SCV000803696 pathogenic Cohen syndrome 2017-12-11 no assertion criteria provided clinical testing

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