ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.138+2T>C

dbSNP: rs137854226
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000518195 SCV000615882 pathogenic not provided 2017-02-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001852874 SCV002237804 pathogenic Tuberous sclerosis 2 2024-02-23 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 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). Disruption of this splice site has been observed in individuals with tuberous sclerosis complex (PMID: 18772611; Invitae). ClinVar contains an entry for this variant (Variation ID: 49155). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000518195 SCV005389094 likely pathogenic not provided 2024-04-29 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); This variant is associated with the following publications: (PMID: 25525159, 18772611)
Tuberous sclerosis database (TSC2) RCV000042410 SCV000066201 not provided Tuberous sclerosis syndrome no assertion provided curation

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