ClinVar Miner

Submissions for variant NM_018668.5(VPS33B):c.1030+1G>A

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV005012223 SCV005643381 likely pathogenic Arthrogryposis, renal dysfunction, and cholestasis 1; Keratoderma-ichthyosis-deafness syndrome, autosomal recessive; Cholestasis, progressive familial intrahepatic, 12 2024-04-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV005112603 SCV005780268 likely pathogenic not provided 2024-09-11 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 13 of the VPS33B 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 VPS33B are known to be pathogenic (PMID: 15052268, 16896922). This variant is present in population databases (rs774653538, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with VPS33B-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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