ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.7429+1G>A

gnomAD frequency: 0.00001  dbSNP: rs386834106
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000050100 SCV000795738 likely pathogenic Cohen syndrome 2017-11-16 criteria provided, single submitter clinical testing
Invitae RCV000050100 SCV001586269 pathogenic Cohen syndrome 2022-03-22 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. ClinVar contains an entry for this variant (Variation ID: 56687). Disruption of this splice site has been observed in individual(s) with Cohen syndrome (PMID: 17990063). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs386834106, gnomAD 0.003%). This sequence change affects a donor splice site in intron 41 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).
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000050100 SCV000082509 probable-pathogenic Cohen syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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