ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.562-1G>C

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV003783689 SCV004571048 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2023-11-17 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 8 of the CTNS 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 CTNS are known to be pathogenic (PMID: 9537412, 27102039). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with cystinosis (PMID: 9537412). This variant is also known as c.901-1G>C. 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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