ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.3939G>T (p.Glu1313Asp)

gnomAD frequency: 0.00001  dbSNP: rs149340262
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001705074 SCV000243696 likely benign not provided 2022-02-08 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000535896 SCV000644488 benign Tuberous sclerosis 2 2024-12-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV001021475 SCV001183097 uncertain significance Hereditary cancer-predisposing syndrome 2024-03-19 criteria provided, single submitter clinical testing The c.3939G>T (p.E1313D) alteration is located in exon 33 (coding exon 32) of the TSC2 gene. This alteration results from a G to T substitution at nucleotide position 3939, causing the glutamic acid (E) at amino acid position 1313 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV000535896 SCV002039796 likely benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV003996893 SCV004822324 uncertain significance Tuberous sclerosis syndrome 2023-12-13 criteria provided, single submitter clinical testing This missense variant replaces glutamic acid with aspartic acid at codon 1313 of the TSC2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with tuberous sclerosis complex in the literature. This variant has been identified in 2/239196 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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