ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.853-1G>A

dbSNP: rs1555564588
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673974 SCV000799238 likely pathogenic Nephropathic cystinosis 2018-05-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003768007 SCV004573523 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2023-04-09 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. Studies have shown that disruption of this splice site is associated with altered splicing resulting in multiple RNA products (PMID: 12442267). ClinVar contains an entry for this variant (Variation ID: 557791). A splice variant(s) at this position has also been reported as 1192-2A>G. Disruption of this splice site has been observed in individual(s) with cystinosis (PMID: 12442267, 28793998, 29421779). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 10 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).

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