ClinVar Miner

Submissions for variant NM_000546.6(TP53):c.716A>C (p.Asn239Thr)

gnomAD frequency: 0.00001  dbSNP: rs1057519999
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000633336 SCV000754558 uncertain significance Li-Fraumeni syndrome 2023-03-09 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with threonine, which is neutral and polar, at codon 239 of the TP53 protein (p.Asn239Thr). This variant is not present in population databases (gnomAD no frequency). 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. Experimental studies have shown that this missense change affects TP53 function (PMID: 12826609, 20407015). 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. ClinVar contains an entry for this variant (Variation ID: 376638). This variant has not been reported in the literature in individuals affected with TP53-related conditions.
Ambry Genetics RCV002374626 SCV002665599 pathogenic Hereditary cancer-predisposing syndrome 2021-06-24 criteria provided, single submitter clinical testing The p.N239T pathogenic mutation (also known as c.716A>C), located in coding exon 6 of the TP53 gene, results from an A to C substitution at nucleotide position 716. The asparagine at codon 239 is replaced by threonine, an amino acid with similar properties. This variant is in the DNA binding domain of the TP53 protein and is reported to have non-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 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 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.

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