ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1987_1988del (p.Leu663fs)

dbSNP: rs1596344279
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008500 SCV001168271 pathogenic not provided 2018-12-27 criteria provided, single submitter clinical testing The c.1987_1988delCT pathogenic variant in the TSC2 gene causes a frameshift starting with codon Leucine 663, changes this amino acid to a Phenylalanine residue and creates a premature Stop codon at position 39 of the new reading frame, denoted p.Leu663PhefsX39. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. This variant is not observed in large population cohorts (Lek et al., 2016). Although this pathogenic variant has not been previously reported to our knowledge, its presence is consistent with the diagnosis of TSC in this individual.
Labcorp Genetics (formerly Invitae), Labcorp RCV005093050 SCV005844750 pathogenic Tuberous sclerosis 2 2025-01-01 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu663Phefs*39) in the TSC2 gene. It is expected to result in an absent or disrupted protein product. 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: 817377). For these reasons, this variant has been classified as Pathogenic.

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