ClinVar Miner

Submissions for variant NM_001042432.2(CLN3):c.533+1G>C

dbSNP: rs386833728
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049691 SCV000797822 likely pathogenic Neuronal ceroid lipofuscinosis 3 2018-02-13 criteria provided, single submitter clinical testing
Invitae RCV001853043 SCV002229395 pathogenic Neuronal ceroid lipofuscinosis 2023-04-09 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as 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: 56279). Disruption of this splice site has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 7553855). 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 8 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).
OMIM RCV000049691 SCV000023897 pathogenic Neuronal ceroid lipofuscinosis 3 1995-09-22 no assertion criteria provided literature only
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049691 SCV000082098 probable-pathogenic Neuronal ceroid lipofuscinosis 3 no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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