ClinVar Genomic variation as it relates to human health

The TP53 c.830G>T variant is predicted to result in the amino acid substitution p.Cys277Phe. To our knowledge, this variant has not been reported in the literature in association with TP53-related disease. Functional studies in vitro indicate that this variant affects protein function (see for example, Kato et al. 2003. PubMed ID: 12826609; Malcikova et al. 2009. PubMed ID: 19850740; Giacomelli AO et al. 2018. PMID: 30224644). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-7577108-C-A). In ClinVar, it is classified as a variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/458567/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive genetic evidence.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 18524770, 27813088, 29979965]. This variant is expected to disrupt protein structure [Myriad internal data].

Each variant was annotated with functional scores from MAVE data which was translated into functional evidence codes. All other evidence codes and combining criteria were adhered to as closely as possible based on the ClinGen VCEP (Variant Curation Expert Panel) gene-specific recommendations. See Supplemental Figure 34 of final paper (Supp Fig. 28 in preprint: doi:10.1101/2024.04.11.24305690) for a table to see which lines of evidence we did not have data for. The ClinGen VCEPs are highly regarded as the gold-standard for gene-specific variant curation and are developed after extensive evaluation of the evidence by clinical and scientific experts for the particular gene to classify genomic variants on a spectrum from pathogenic to benign using the 2015 ACMG/AMP Variant Interpretation Guidelines as a backbone (PMID: 25741868). Reclassification of these VUS variants from gnomAD or All of Us focused only on variants originally prescribed as VUS in ClinVar. To ensure reproducibility, transparency, and increased throughput, all the procedures for annotating variants and assigning evidence codes were codified using Python. All code has been made freely available and is linked in the Code Availability section and all reclassified variants with evidence codes used can be found in Tables S18-19 (preprint: doi:10.1101/2024.04.11.24305690). For the MAVE data, the clinical curation and clinical strength assignment as per the ClinGen recommendations in Brnich et al. (2020) (PMID: 31892348) for or against pathogenicity or benignity of each of these MAVE datasets utilized in this study were previously published in Fayer et al. (2021) (PMID: 34793697).For TP53, we used the output of the Naïve Bayes classifier that synthesized data from four different TP53 MAVEs in Fayer et al. (2021) (PMID: 34793697). If the classifier predicted a variant to be "Functionally abnormal," the variant was assigned PS3 evidence and no BS3 evidence. If a variant was predicted to be "Functionally normal," BS3_moderate evidence was used with no PS3 evidence. This variant GRCh38:17:7673790:C>A was assigned evidence codes ['PS3', 'PP3_Moderate'] and an overall classification of Likely pathogenic

This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 277 of the TP53 protein (p.Cys277Phe). This variant is present in population databases (rs763098116, gnomAD 0.0009%). 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: 458567). 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. Experimental studies have shown that this missense change affects TP53 function (PMID: 9407971, 12826609, 19850740, 26070072, 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.

The p.C277F pathogenic mutation (also known as c.830G>T), located in coding exon 7 of the TP53 gene, results from a G to T substitution at nucleotide position 830. The cysteine at codon 277 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration has been shown to have a loss of transactivation activity in yeast based functional studies (IARC TP53 database: Kato S et al. Proc. Natl. Acad. Sci. U.S.A., 2003 Jul;100:8424-9; Kucab JE et al. DNA Repair (Amst.), 2016 Mar;39:21-33; Paget V et al. PLoS ONE, 2012 Feb;7:e30921). 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). Another alteration at the same codon, p.C277R (c.829T>C), has been detected an individual with a personal history of adrenocortical carcinoma and shown to segregate with disease in three affected family members in one family with early-onset breast cancer tested by our laboratory (Ambry internal data). This amino acid position is well conserved in available vertebrate species. The p.C277F 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) non-cancer dataset. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this variant is interpreted as a disease-causing mutation.