ClinVar Miner

Submissions for variant NM_000396.4(CTSK):c.400-1G>C

dbSNP: rs1553197262
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665773 SCV000789944 likely pathogenic Pyknodysostosis 2017-02-28 criteria provided, single submitter clinical testing
Invitae RCV002530666 SCV003236273 likely pathogenic not provided 2022-09-22 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 4 of the CTSK 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 CTSK are known to be pathogenic (PMID: 12125807, 21569238). 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. ClinVar contains an entry for this variant (Variation ID: 550892). This variant has not been reported in the literature in individuals affected with CTSK-related conditions. This variant is not present in population databases (gnomAD no frequency).
Genome-Nilou Lab RCV000665773 SCV004049729 likely pathogenic Pyknodysostosis 2023-04-11 criteria provided, single submitter clinical testing

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