ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6295_6296del (p.Met2099fs)

gnomAD frequency: 0.00001  dbSNP: rs748404277
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409691 SCV000486267 likely pathogenic Cohen syndrome 2016-04-28 criteria provided, single submitter clinical testing
GeneDx RCV000598802 SCV000710030 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing Observed with another VPS13B variant on the opposite allele (in trans) in a patient with microcephaly and malformation of cortical development in published literature (Zillhardt et al., 2016); 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); This variant is associated with the following publications: (PMID: 29149870, 26395554)
Labcorp Genetics (formerly Invitae), Labcorp RCV000409691 SCV002131466 pathogenic Cohen syndrome 2023-12-09 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Met2124Valfs*44) 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 (rs748404277, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with VPS13B-related conditions (PMID: 26395554, 29149870). This variant is also known as c.6295_6296delAT. ClinVar contains an entry for this variant (Variation ID: 242548). For these reasons, this variant has been classified as Pathogenic.
NIHR Bioresource Rare Diseases, University of Cambridge RCV000504997 SCV000598902 uncertain significance Abnormality of the eye 2015-01-01 no assertion criteria provided research

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