ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5347G>A (p.Glu1783Lys)

gnomAD frequency: 0.00002  dbSNP: rs777166275
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000190045 SCV000243719 uncertain significance not provided 2018-01-25 criteria provided, single submitter clinical testing This variant is denoted TSC2 c.5347G>A at the cDNA level, p.Glu1783Lys (E1783K) at the protein level, and results in the change of a Glutamic Acid to a Lysine (GAG>AAG). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. TSC2 Glu1783Lys was observed at an allele frequency of 0.001% (3/244926 alleles) in large population cohorts (Lek 2016). TSC2 Glu1783Lys is not located in a known functional domain. In-silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function. Based on currently available evidence, it is unclear whether TSC2 Glu1783Lys is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Invitae RCV001084324 SCV000285460 benign Tuberous sclerosis 2 2023-12-13 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001084324 SCV002040290 benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV002345684 SCV002646277 likely benign Hereditary cancer-predisposing syndrome 2023-01-03 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000190045 SCV004564378 uncertain significance not provided 2023-02-28 criteria provided, single submitter clinical testing The TSC2 c.5347G>A; p.Glu1783Lys variant (rs777166275), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 207763). This variant is observed in the general population with an overall allele frequency of 0.001% (4/280670 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.493). Due to limited information, the clinical significance of this variant is uncertain at this time.

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