ClinVar Miner

Submissions for variant NM_001042432.2(CLN3):c.963-1G>A

gnomAD frequency: 0.00001  dbSNP: rs386833742
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410762 SCV000486039 likely pathogenic Neuronal ceroid lipofuscinosis 3 2016-03-18 criteria provided, single submitter clinical testing
Invitae RCV001861373 SCV002286635 likely pathogenic Neuronal ceroid lipofuscinosis 2023-08-24 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 13 of the CLN3 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 CLN3 are known to be pathogenic (PMID: 9311735, 28542676). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CLN3-related conditions. ClinVar contains an entry for this variant (Variation ID: 370667). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Baylor Genetics RCV000410762 SCV004214328 likely pathogenic Neuronal ceroid lipofuscinosis 3 2023-06-30 criteria provided, single submitter clinical testing

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