ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.225+5_225+8del

dbSNP: rs1555561048
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665684 SCV000789843 uncertain significance Nephropathic cystinosis 2017-02-24 criteria provided, single submitter clinical testing
Invitae RCV002532045 SCV003443723 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2022-01-19 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. This variant disrupts the c.225+5 nucleotide in the CTNS gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 11708862). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing, but the impact on the resulting protein product is unknown (PMID: 12442267). ClinVar contains an entry for this variant (Variation ID: 550829). This variant is also known as 564+1del4. This variant has been observed in individual(s) with cystinosis (PMID: 12442267). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 5 of the CTNS gene. It does not directly change the encoded amino acid sequence of the CTNS protein. It affects a nucleotide within the consensus splice site.
Baylor Genetics RCV000665684 SCV004212939 likely pathogenic Nephropathic cystinosis 2023-10-11 criteria provided, single submitter clinical testing

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