ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6657+1G>T

dbSNP: rs180177366
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000668268 SCV000792841 likely pathogenic Cohen syndrome 2017-07-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002360695 SCV002666842 pathogenic Inborn genetic diseases 2018-02-20 criteria provided, single submitter clinical testing The c.6732+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 36 of the VPS13B gene. This variant has been detected in trans with another pathogenic mutation in VPS13B by our laboratory. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.
Labcorp Genetics (formerly Invitae), Labcorp RCV000668268 SCV004520744 pathogenic Cohen syndrome 2023-06-04 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 37 of the VPS13B gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with Cohen syndrome (PMID: 15141358, 16648375, 25472526). ClinVar contains an entry for this variant (Variation ID: 552918). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 16648375). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

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