ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5391CTC[1] (p.Ser1799del)

dbSNP: rs796053480
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189952 SCV000243620 uncertain significance not provided 2022-08-17 criteria provided, single submitter clinical testing In-frame deletion of 1 amino acid in a non-repeat region; Previously reported as a variant of uncertain significance in a woman with a clinical diagnosis of tuberous sclerosis and lymphangioleiomyomatosis (Liu et al., 2019); In silico analysis supports a deleterious effect on protein structure/function; Published functional studies demonstrate reduced levels of TSC1 and TSC2 protein and elevated levels of phosphorylated AKT (Mrozek et al., 2021); This variant is associated with the following publications: (PMID: 31856217, 33891611)
Invitae RCV001081593 SCV000644644 likely benign Tuberous sclerosis 2 2023-12-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV001024027 SCV001185979 uncertain significance Hereditary cancer-predisposing syndrome 2023-11-01 criteria provided, single submitter clinical testing The c.5394_5396delCTC (p.S1799del) alteration is located in exon 42 (coding exon 41) of the TSC2 gene. This alteration consists of an in-frame deletion of 3 nucleotides between nucleotide positions c.5394 and c.5396, resulting in the deletion of 1 residue. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV001775094 SCV002012384 uncertain significance Tuberous sclerosis syndrome 2021-09-09 criteria provided, single submitter clinical testing The TSC2 c.5394_5396del (p.Ser1799del) change has a maximum subpopulation frequency of 0.0041% in gnomAD v2.1.1 ( The change results in the deletion of a single serine residue in a region without a known function at the c-terminal end of the gene (BP3). To our knowledge, functional studies have not been performed. This variant has been reported in a woman with lymphangioleiomyomatosis (PMID: 31856217). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: BP3.

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