ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.5678_5679del (p.Leu1893fs)

gnomAD frequency: 0.00001  dbSNP: rs886041586
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000320625 SCV000330274 pathogenic not provided 2019-05-30 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 in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000673370 SCV002243176 pathogenic Cohen syndrome 2023-06-04 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 280368). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. This sequence change creates a premature translational stop signal (p.Leu1918Argfs*12) 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 RCV000673370 SCV000798566 likely pathogenic Cohen syndrome 2018-03-14 no assertion criteria provided clinical testing

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