ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1085T>C (p.Leu362Pro) (rs137854345)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000413741 SCV000491424 likely pathogenic not provided 2016-02-02 criteria provided, single submitter clinical testing A L362P variant that is likely pathogenic has been identified in the TSC2 gene. The L362P variant has been reported in the TSC2 LOVD database as probably pathogenic because it was identified as a de novo change in an individual with TSC and a fetus with a cardiac rhabdomyoma (TSC2 LOVD). However, additional clinical information was not provided and functional characterization of the variant was not completed. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The L362P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. Additionally, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Furthermore, a missense variant in a nearby residue (L361P) has been reported in the TSC2 LOVD in association with TSC (TSC2 LOVD). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Invitae RCV001065226 SCV001230176 likely pathogenic Tuberous sclerosis 2 2019-03-08 criteria provided, single submitter clinical testing This sequence change replaces leucine with proline at codon 362 of the TSC2 protein (p.Leu362Pro). The leucine residue is highly conserved and there is a moderate physicochemical difference between leucine and proline. This variant is not present in population databases (ExAC no frequency). This variant has been observed to be de novo in an individual affected with tuberous sclerosis complex (Invitae). ClinVar contains an entry for this variant (Variation ID: 49140). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
Tuberous sclerosis database (TSC2) RCV000042395 SCV000066185 not provided Tuberous sclerosis syndrome no assertion provided curation

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