ClinVar Miner

Submissions for variant NM_001042432.2(CLN3):c.906+2T>A

gnomAD frequency: 0.00001  dbSNP: rs771788391
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726946 SCV000704392 pathogenic not provided 2016-12-05 criteria provided, single submitter clinical testing
Invitae RCV002523852 SCV003228509 likely pathogenic Neuronal ceroid lipofuscinosis 2022-08-19 criteria provided, single submitter clinical testing This variant is present in population databases (rs771788391, gnomAD 0.002%). This sequence change affects a donor splice site in intron 12 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 has not been reported in the literature in individuals affected with CLN3-related conditions. 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: 370455).
Baylor Genetics RCV000410383 SCV005058460 likely pathogenic Neuronal ceroid lipofuscinosis 3 2023-12-06 criteria provided, single submitter clinical testing
Counsyl RCV000410383 SCV000485784 likely pathogenic Neuronal ceroid lipofuscinosis 3 2019-07-12 no assertion criteria provided clinical testing

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