ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.138+5G>A

dbSNP: rs45481400
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001380069 SCV001578011 pathogenic Tuberous sclerosis 2 2021-11-10 criteria provided, single submitter clinical testing This variant has been observed in individual(s) with clinical features of tuberous sclerosis (PMID: 10735580, 11112665). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 50192). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. This sequence change falls in intron 2 of the TSC2 gene. It does not directly change the encoded amino acid sequence of the TSC2 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency).
GeneDx RCV001843466 SCV002102758 pathogenic not provided 2022-02-28 criteria provided, single submitter clinical testing Intronic +5 splice site variant in a gene for which loss-of-function is a known mechanism of disease, and both splice predictors and evolutionary conservation support a deleterious effect, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 11112665, 10735580)
Fulgent Genetics, Fulgent Genetics RCV002496685 SCV002813856 likely pathogenic Lymphangiomyomatosis; Isolated focal cortical dysplasia type II; Tuberous sclerosis 2 2022-01-09 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000043461 SCV000067271 not provided Tuberous sclerosis syndrome no assertion provided curation

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