ClinVar Miner

Submissions for variant NM_000546.6(TP53):c.393C>A (p.Asn131Lys)

gnomAD frequency: 0.00001  dbSNP: rs769270327
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen TP53 Variant Curation Expert Panel, ClinGen RCV000465360 SCV001429627 uncertain significance Li-Fraumeni syndrome 2020-08-11 reviewed by expert panel curation This variant has been reported in 4 probands meeting Chompret criteria (PS4_Moderate; PMID: Internal laboratory contributors, SCV000293984.11, SCV000581099.3, National Cancer Institute). This variant has been observed in 2-7 60+ year old females without a cancer diagnosis (BS2_Supporting; Internal laboratory contributor, SCV000545263.5). Transactivation assays show a partially functional variant according to Kato, et al. and there is no evidence of a dominant negative effect or loss of function according to Giacomelli, et al. (BS3_Supporting; PMID: 12826609, 30224644). In summary, the clinical significance of TP53 c.393C>A (p.Asn131Lys) is uncertain for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PS4_Moderate, BS3_Supporting, BS2_Supporting.
GeneDx RCV000236166 SCV000293984 uncertain significance not provided 2024-09-16 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16546179, 12826609, 25412846, 28222664, 29979965, 28861920, 30840781, 30224644, 23117049, 35514255, 34273903, 36353970, 15510160)
Labcorp Genetics (formerly Invitae), Labcorp RCV000465360 SCV000545263 uncertain significance Li-Fraumeni syndrome 2024-01-04 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 131 of the TP53 protein (p.Asn131Lys). This variant is present in population databases (rs769270327, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with TP53-related conditions. ClinVar contains an entry for this variant (Variation ID: 246429). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is expected to disrupt TP53 function with a positive predictive value of 97.5%. Experimental studies have shown that this missense change does not substantially affect TP53 function (PMID: 12826609, 29979965, 30224644). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000492741 SCV000581099 uncertain significance Hereditary cancer-predisposing syndrome 2024-03-21 criteria provided, single submitter clinical testing The p.N131K variant (also known as c.393C>A), located in coding exon 4 of the TP53 gene, results from a C to A substitution at nucleotide position 393. The asparagine at codon 131 is replaced by lysine, an amino acid with similar properties. This variant is in the DNA binding domain of the TP53 protein and is reported to have partially functional transactivation in yeast based assays (Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9). Studies conducted in human cell lines indicate this alteration is proficient at growth suppression and has no dominant negative effect (Kotler E et al. Mol.Cell. 2018 Jul;71:178-190.e8; Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). While there are no reports of p.N131K as a germline alteration in the literature, another alteration at this same position, p.N131I, was reported in a Li-Fraumeni syndrome family (Agarwalla PK et al. Pediatr Neurosurg. 2008;44(6):501-8). This amino acid position is highly conserved through mammals but not in all 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.
Color Diagnostics, LLC DBA Color Health RCV000492741 SCV000903736 uncertain significance Hereditary cancer-predisposing syndrome 2021-07-08 criteria provided, single submitter clinical testing This missense variant replaces asparagine with lysine at codon 131 of the TP53 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). An experimental functional studies in yeast demonstrated a partial impact of this variant on TP53 transactivation activity (PMID 12826609), but the variant behaved like wild-type in human cell growth suppression and proliferation assays (PMID: 29979965, 30224644). This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 4/282018 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.
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000236166 SCV002009074 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Baylor Genetics RCV003463702 SCV004206257 uncertain significance Adrenocortical carcinoma, hereditary 2024-03-08 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000236166 SCV004221355 uncertain significance not provided 2022-12-15 criteria provided, single submitter clinical testing The frequency of this variant in the general population, 0.00029 (3/10362 chromosomes in Ashkenazi Jewish subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals with myeloid neoplasm (PMID: 25412846 (2015)) and breast cancer (PMID: 27713152 (2016)) but has not been confirmed to occur in the germline state in the literature. Functional studies have concluded this variant to be partially functional in transactivation (PMID: 12826609 (2003)) and mostly functional in cell proliferation (PMID: 29979965 (2018)). In addition, the variant did not exhibit loss of function (LOF) or dominant negative effect (DNE) (PMID: 30224644 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
All of Us Research Program, National Institutes of Health RCV000465360 SCV004823810 uncertain significance Li-Fraumeni syndrome 2023-05-31 criteria provided, single submitter clinical testing This missense variant replaces asparagine with lysine at codon 131 of the TP53 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). An experimental functional studies in yeast demonstrated a partial impact of this variant on TP53 transactivation activity (PMID 12826609), but the variant behaved like wild-type in human cell growth suppression and proliferation assays (PMID: 29979965, 30224644). This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 4/282018 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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