ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.5076+1G>C

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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 RCV003606989 SCV004553475 likely pathogenic Cohen syndrome 2023-06-10 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 32 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).
PreventionGenetics, part of Exact Sciences RCV004723459 SCV005336772 likely pathogenic VPS13B-related disorder 2024-08-27 no assertion criteria provided clinical testing The VPS13B c.5076+1G>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Variants that disrupt the consensus splice donor site in VPS13B are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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