ClinVar Miner

Submissions for variant NM_000546.6(TP53):c.772G>A (p.Glu258Lys)

dbSNP: rs121912652
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000161071 SCV000211805 pathogenic not provided 2021-11-30 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect: non-functional transactivation, loss of growth suppression activity (Frebourg 1992, Flaman 1998, Waddell 2001, Kato 2003, Malcikova 2010, Monti 2011, Kotler 2018); Not observed at significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15722483, 11593407, 30720243, 21343334, 17606709, 9364015, 7829527, 1458490, 10719737, 21121188, 7732013, 8252037, 10753186, 11429705, 16492679, 9546439, 9635858, 1631137, 21232794, 8570655, 14559903, 12909720, 8313374, 29625052, 29979965, 21552135, 30840781, 30577483, 33309985, 15510160, 1978757, 20128691)
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000161071 SCV000602278 pathogenic not provided 2021-10-06 criteria provided, single submitter clinical testing This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in affected individuals with Li-Fraumeni Syndrome, glioblastoma, gastric, brain, and colon cancers (PMIDs: 29625052 (2018), 26425688 (2015), 21552135 (2011), 17606709 (2007), and 1978757 (1990)). Functional studies showed severe deficiencies in DNA binding and transactivation of transcriptional targets (PMIDs: 21343334 (2011) and 20128691 (2010)). Based on the available information, this variant is classified as pathogenic.
Color Diagnostics, LLC DBA Color Health RCV000772122 SCV000905196 pathogenic Hereditary cancer-predisposing syndrome 2021-01-14 criteria provided, single submitter clinical testing This missense variant replaces glutamic acid with lysine at codon 258 in the DNA binding domain of the TP53 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that the mutant protein to be non-functional and exhibit dominant negative effect in transactivation assays (PMID: 12826609, 16492679, 20128691, 21343334) and in cell growth assays (PMID: 29979965, 30224644). This variant has been reported in individuals affected with Li-Fraumeni syndrome (PMID: 9667734, 10922393, 1978757, 21552135). This variant has been identified in 1/246228 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000792895 SCV000932221 pathogenic Li-Fraumeni syndrome 2024-05-18 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 258 of the TP53 protein (p.Glu258Lys). This variant is present in population databases (rs121912652, gnomAD 0.0009%). This missense change has been observed in individuals with clinical features of Li-Fraumeni syndrome (PMID: 1978757, 9667734, 10922393, 17606709, 21552135, 29625052, 34529667; Invitae). ClinVar contains an entry for this variant (Variation ID: 12348). 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 affects TP53 function (PMID: 12826609, 20128691, 21343334, 29979965, 30224644). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV000772122 SCV001189203 pathogenic Hereditary cancer-predisposing syndrome 2024-11-11 criteria provided, single submitter clinical testing The p.E258K pathogenic mutation (also known as c.772G>A), located in coding exon 6 of the TP53 gene, results from a G to A substitution at nucleotide position 772. The glutamic acid at codon 258 is replaced by lysine, an amino acid with similar properties. The p.E258K variant was first reported in a patient diagnosed with breast cancer at 34 whose tumor demonstrated loss of heterozygosity (LOH), and whose family met classic LFS criteria with a history of early onset sarcomas, and brain tumors (Malkin D et al. Science. 1990 Nov;250:1233-8). This variant has also been reported in a family with a strong history of gastric cancers, and in an individual with glioblastoma multiforme (Masciari S et al. Genet. Med. 2011 Jul;13:651-7; Huang KL et al. Cell, 2018 04;173:355-370.e14). Yeast based functional studies showed this alteration to have loss of transactivation capacity, and dominant negative effect (IARC TP53 database; Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9; Monti P et al. Mol. Cancer Res. 2011 Mar;9:271-9). Studies on this variant conducted in mammalian cells showed inability to suppress growth, and a protein binding profile indicative of a mutant protein conformation (Frebourg T et al. Proc. Natl. Acad. Sci. U.S.A., 1992 Jul;89:6413-7). Additional studies conducted in human cell lines also indicate this alteration is deficient at growth suppression and has a 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). This alteration has been observed numerous times as a somatic mutation in the cancerhotspots.org database (Chang MT et al. Cancer Discov. 2018 02;8:174-183). This variant has been detected in at least one individual at an allele fraction that is suggestive of clonal hematopoiesis, a predictor of TP53 pathogenicity (Ambry internal data; Fortuno C et al. Genet Med. 2022 03;24:673-680). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Genome-Nilou Lab RCV000772122 SCV002582357 likely pathogenic Hereditary cancer-predisposing syndrome 2022-06-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000013141 SCV002583018 likely pathogenic Li-Fraumeni syndrome 1 2022-06-18 criteria provided, single submitter clinical testing
OMIM RCV000013141 SCV000033388 pathogenic Li-Fraumeni syndrome 1 1990-11-30 no assertion criteria provided literature only
Mayo Clinic Laboratories, Mayo Clinic RCV000582699 SCV000692070 uncertain significance not specified no assertion criteria provided clinical testing
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne RCV000785291 SCV000923859 likely pathogenic Ovarian neoplasm 2018-12-01 no assertion criteria provided research

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