ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.225+1G>A

dbSNP: rs1555561049
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673312 SCV000798499 likely pathogenic Nephropathic cystinosis 2018-03-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002531336 SCV002243001 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2023-05-29 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exons 4 and/or 5 and introduces a premature termination codon (PMID: 12442267). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 557204). Disruption of this splice site has been observed in individual(s) with cystinosis (PMID: 12442267). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 5 of the CTNS gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

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