ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.565C>T (p.Gln189Ter)

dbSNP: rs1597654770
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002271859 SCV002555985 likely pathogenic Cystinosis 2022-05-20 criteria provided, single submitter clinical testing Variant summary: CTNS c.565C>T (p.Gln189X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251320 control chromosomes (gnomAD). c.565C>T has been reported in the literature in at least one compound heterozygous individual affected with Cystinosis (Bengali_2021). This data does not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV003096120 SCV003217042 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2022-07-02 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CTNS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln189*) in the CTNS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039).
Baylor Genetics RCV003471301 SCV004215219 pathogenic Nephropathic cystinosis 2022-12-22 criteria provided, single submitter clinical testing

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