ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.61+2T>C

gnomAD frequency: 0.00001  dbSNP: rs767289120
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002675467 SCV002289563 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2021-04-02 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, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with CTNS-related conditions. This variant is present in population databases (rs767289120, ExAC 0.02%). This sequence change affects a donor splice site in intron 3 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).
Fulgent Genetics, Fulgent Genetics RCV002052012 SCV002794547 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis 2021-10-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV003475282 SCV004212982 likely pathogenic Nephropathic cystinosis 2023-02-19 criteria provided, single submitter clinical testing

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