ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.681+1G>A

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001241230 SCV001414236 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis 2019-10-25 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 9 of the CTNS gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs749317721, ExAC 0.003%). This variant has been observed in several individuals affected with cystinosis (PMID: 10556299, 12825071). This variant is also known as c.1020+1G>A in the literature. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants 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). For these reasons, this variant has been classified as Pathogenic.

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