ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.11520del (p.Arg3840fs)

gnomAD frequency: 0.00001  dbSNP: rs747217399
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000409909 SCV000597922 pathogenic Cohen syndrome 2016-01-20 criteria provided, single submitter clinical testing
GeneDx RCV001561612 SCV001784241 likely pathogenic not provided 2019-08-14 criteria provided, single submitter clinical testing 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 a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV000409909 SCV002775340 pathogenic Cohen syndrome 2021-09-01 criteria provided, single submitter clinical testing
Invitae RCV000409909 SCV002989117 pathogenic Cohen syndrome 2023-10-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg3865Serfs*13) 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 (rs747217399, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 371090). For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000409909 SCV000486565 likely pathogenic Cohen syndrome 2016-06-24 no assertion criteria provided clinical testing
Natera, Inc. RCV000409909 SCV002082801 likely pathogenic Cohen syndrome 2020-02-04 no assertion criteria provided clinical testing

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