ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.3693_3696del (p.Ser1232fs) (rs137853993)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489018 SCV000577131 pathogenic not provided 2018-10-16 criteria provided, single submitter clinical testing The c.3693_3696delGTCT pathogenic variant in the TSC2 gene has been reported previously in multiple unrelated individuals with a clinical diagnosis of TSC (Hung et al., 2006; Au et al., 2007; TSC2 LOVD). The deletion causes a frameshift starting with codon Serine 1232, changes this amino acid to a Threonine residue and creates a premature Stop codon at position 92 of the new reading frame, denoted p.Ser1232ThrfsX92. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3693_3696delGTCT variant is not observed in large population cohorts (Lek et al., 2016; 1000Genomes Consortium et al., 2015; Exome Variant Server).
Athena Diagnostics Inc RCV000489018 SCV001146282 pathogenic not provided 2019-08-12 criteria provided, single submitter clinical testing The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and not found in general population data.
Invitae RCV001194684 SCV001417486 pathogenic Tuberous sclerosis 2 2019-11-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser1232Thrfs*92) in the TSC2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with tuberous sclerosis complex (PMID: 16981987, 29500070). ClinVar contains an entry for this variant (Variation ID: 50013). Loss-of-function variants in TSC2 are known to be pathogenic (PMID: 10205261, 17304050). For these reasons, this variant has been classified as Pathogenic.
Tuberous sclerosis database (TSC2) RCV000043281 SCV000067083 not provided Tuberous sclerosis syndrome no assertion provided curation
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute,Kanazawa Medical University RCV001194684 SCV001364430 pathogenic Tuberous sclerosis 2 2020-06-11 no assertion criteria provided clinical testing

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