ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.3192C>A (p.Asn1064Lys)

gnomAD frequency: 0.00004  dbSNP: rs201670791
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001083071 SCV000285335 likely benign Tuberous sclerosis 2 2025-02-02 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000734482 SCV000862628 uncertain significance not provided 2018-08-13 criteria provided, single submitter clinical testing
GeneDx RCV000734482 SCV002038852 uncertain significance not provided 2021-12-08 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV001083071 SCV002039717 likely benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV002258838 SCV002533372 uncertain significance Hereditary cancer-predisposing syndrome 2021-09-25 criteria provided, single submitter curation
Ambry Genetics RCV002258838 SCV002612161 uncertain significance Hereditary cancer-predisposing syndrome 2024-03-30 criteria provided, single submitter clinical testing The p.N1064K variant (also known as c.3192C>A), located in coding exon 27 of the TSC2 gene, results from a C to A substitution at nucleotide position 3192. The asparagine at codon 1064 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
All of Us Research Program, National Institutes of Health RCV003998821 SCV004828912 uncertain significance Tuberous sclerosis syndrome 2024-09-23 criteria provided, single submitter clinical testing This missense variant replaces asparagine with lysine at codon 1064 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 TSC2-related disorders in the literature. This variant has been identified in 5/281718 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.
Myriad Genetics, Inc. RCV001083071 SCV005406190 likely benign Tuberous sclerosis 2 2024-08-16 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.

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