ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4006-1G>C

dbSNP: rs1085307853
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000993371 SCV001146283 likely pathogenic not provided 2019-07-17 criteria provided, single submitter clinical testing The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. Not found in the total gnomAD dataset, and the data is high quality (0/220866 chr).
Labcorp Genetics (formerly Invitae), Labcorp RCV003512094 SCV004330569 likely pathogenic Tuberous sclerosis 2 2023-10-18 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 33 of the TSC2 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 TSC2 are known to be pathogenic (PMID: 10205261, 17304050). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 805698). 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.

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