TP53 NM_000546.6:c.845G>A, Arg282Gln

Variant summary: TP53 c.845G>A (p.Arg282Gln) results in a conservative amino acid change located in the DNA-binding domain (IPR011615) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251444 control chromosomes (gnomAD). c.845G>A has been reported in the literature in individuals affected with a variety of cancers but not fulfilling the classic criteria of LFS or even the LFI (Li-Fraunemi Incomplete) criteria. In our review of the associated literature, the penetrance of Li-Fraumeni Syndrome (0.67) due to this variant appears to be lower than expected (0.8), therefore no conclusions can be drawn from these data. Specifically, this variant was observed in a patient with neuroblastoma and was reportedly inherited from one of her parents, but the family history (a female patient, diagnosed at age 1 with neuroblastoma, and a maternal aunt with lymphoma diagnosed at 44) was not suggestive of Li-Fraumeni syndrome (Chompret 2000). The variant has been also reported as germline variant in several other cancer patients, including lung-, breast-, prostate and colorectal cancer, but without strong evidence for causality (Meric-Bernstam_2016, Tung_2016, Monti_2007, Giri_2019, Stoltze_2018). In addition, in one of these reports a co-occurrence with another likely pathogenic variant has been reported (PALB2 exon 13 deletion; Giri_2019), providing supporting evidence for limited causality. Additional studies are needed to address the penetrance and cancer risks associated with TP53 pathogenic variation in patients outside LFS spectrum. Several publications reported experimental evidence evaluating an impact on protein function, and multiple yeast assays demonstrated that the variant decreased, but did not abolish the transactivation capacity of TP53 and has been reported as a partially deficient (PD) allele (e.g. Monti_2011, Andreotti_2011 , Resnick_2003, Shi_2002). On the other hand, further studies performed in yeast and in human cells, revealed that the variant could also result in a gain of function activity, by interfering with the function of other p53 family members and increasing the expression of genes involved in cell proliferation- and tumor formation (Monti_2003, Shi_2002, Cordani_2011). These data however do not allow unequivocal conclusions about the variant significance. Six other clinical diagnostic laboratories have submitted conflicting clinical-significance assements for this variant to ClinVar after 2014 (i.e. 4 calling it a VUS, while 2 classifying it as likely pathogenic). At-least two of these submissions reflect a re-evaluation from their original assessment in the pathogenic spectrum. Based on the overall evidence outlined above, the variant was re-classified from its initial assessment as Likely Pathogenic at our laboratory and has since retained its classification as a VUS-possibly pathogenic.

The following ACMG criteria was used: PM2_SUP; PM1; PP3; BS3

This missense variant replaces arginine with glutamine at codon 282 in the DNA binding domain of the TP53 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown no or partially disruptive effect of this variant on transactivation activity in yeast-based assays (PMID: 11429705, 11896595, 11920959, 12826609, 12909720, 12917626, 21343334) and no effect on the anti-proliferative function of TP53 protein in mammalian cell-based assays (PMID: 29979965, 30224644). This variant has been reported in an infant affected with neuroblastoma with history of lymphoma in her maternal aunt (PMID 10864200). This variant has been observed in an individual affected with lung cancer in his seventies, with family history of breast and prostate cancer in his siblings (PMID: 26787237). This variant has also been observed in individuals affected with breast cancer (PMID: 26976419) and glioneuronal tumor (PMID: 29058119), as well as in an individual affected with colorectal cancer with early-onset breast cancer history in her mother and maternal grandmother (PMID: 29324801). This variant has been identified in 1/251444 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same amino acid position (p.Arg282Trp, p.Arg282Pro) are considered to be disease-causing (ClinVar variation ID: 12364, 376659), suggesting that arginine at this position is important for protein function. However, the available clinical and functional evidence is insufficient to determine the role of the p.Arg282Gln variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.R282Q variant (also known as c.845G>A), located in coding exon 7 of the TP53 gene, results from a G to A substitution at nucleotide position 845. The arginine at codon 282 is replaced by glutamine, an amino acid with highly similar properties. This alteration has been reported in a family in which the proband was diagnosed with neuroblastoma at 1 year of age and the proband's maternal aunt was diagnosed with lymphoma at 44 years of age (Chompret A et al. Br. J. Cancer. 2000 Jun;82(12):1932-1937). Functional studies conducted in yeast have demonstrated partially reduced transactivation activity compared to wild type (Campomenosi P et al. Oncogene. 2001 Jun;20:3573-9; Shi XB et al. Prostate. 2002 Apr;51:59-72; IARC TP53 database: Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100(14):8424-9; Monti P et al. Mol. Cancer Res. 2011 Mar;9:271-9). Studies conducted in human cell lines indicate this alteration remains proficient at growth suppression (Kotler E et al. Mol.Cell, 2018 Jul;71:178-190.e8; Giacomelli AO et al. Nat. Genet., 2018 Oct;50:1381-1387). Additional studies in human Saos-2 cell lines showed gain of function properties such as upregulation of several promoters, growth in soft agar, and an increase in DNA synthesis (Shi XB et al. Prostate. 2002 Apr;51:59-72). Crystal structural analysis predict this alteration may cause destabilization of the protein (Tu C et al. Acta Crystallogr. D Biol. Crystallogr. 2008 May;64:471-7). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This alteration has been detected in the literature and numerous times in our laboratory, however, never in a case that meets classic Li-Fraumeni syndorme or Chompret criteria (Ambry internal data). Although this alteration has not been detected in individuals with Li-Fraumeni syndrome, we can not rule out the possibility that it is a low penetrance risk allele. Based on the available evidence, the clinical significance of this variant remains unclear.

This missense variant replaces arginine with glutamine at codon 282 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 no or partially disruptive effect of this variant on transactivation activity in yeast-based assays (PMID: 11429705, 11896595, 11920959, 12826609, 12909720, 12917626, 21343334) and no effect on the anti-proliferative function of TP53 protein in mammalian cell-based assays (PMID: 29979965, 30224644). This variant has been reported in an infant affected with neuroblastoma with history of lymphoma in her maternal aunt (PMID 10864200). This variant has been observed in an individual affected with lung cancer in his seventies, with family history of breast and prostate cancer in his siblings (PMID: 26787237). This variant has also been observed in individuals affected with breast cancer (PMID: 26976419) and glioneuronal tumor (PMID: 29058119), as well as in an individual affected with colorectal cancer with early-onset breast cancer history in her mother and maternal grandmother (PMID: 29324801). This variant has been identified in 1/251444 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same amino acid position (p.Arg282Trp, p.Arg282Pro) are considered to be disease-causing (ClinVar variation ID: 12364, 376659), suggesting that arginine at this position is important for protein function. However, the available clinical and functional evidence is insufficient to determine the role of the p.Arg282Gln variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.