ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.11044+2T>C

dbSNP: rs587777382
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000119264 SCV003440763 pathogenic Cohen syndrome 2022-08-30 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Studies have shown that disruption of this splice site alters VPS13B gene expression (PMID: 24311531). ClinVar contains an entry for this variant (Variation ID: 132795). This variant is also known as IVS57+2T>C. Disruption of this splice site has been observed in individual(s) with clinical features of Cohen syndrome (PMID: 24311531). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 57 of the VPS13B gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VPS13B are known to be pathogenic (PMID: 15141358, 16648375, 20461111).
OMIM RCV000119264 SCV000154699 pathogenic Cohen syndrome 2014-02-01 no assertion criteria provided literature only

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