ClinVar Genomic variation as it relates to human health

RAD50 has been only recently described in association with cancer predisposition and the risks are not well understood. This variant is denoted RAD50 c.1277A>G at the cDNA level, p.Gln426Arg (Q426R) at the protein level, and results in the change of a Glutamine to an Arginine (CAA>CGA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. RAD50 Gln426Arg has not been observed at significant allele frequency in the NHLBI Exome Sequencing Project. This variant is a semi-conservative substitution in which a a neutral polar amino acid is replaced with a positive polar one, altering a position that is well conserved throughout evolution and is not located in a known functional domain. Multiple in silico algorithms predict that this variant may be damaging to protein structure and function. On a molecular level, the impact of this missense variant on protein structure and function is not known and thus we consider this to be a variant of uncertain significance. Furthermore, based on the currently available information, cancer risks associated with this variant, and the RAD50 gene, remain unclear.

Variant summary: RAD50 c.1277A>G (p.Gln426Arg) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 244864 control chromosomes, predominantly within the Non-Finnish European subpopulation at a frequency of 0.00026 in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in RAD50 causing Hereditary Breast and Ovarian Cancer phenotype (6.3e-05), suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. The variant, c.1277A>G, has been reported in the literature as a VUS and/or reporting conflicting interpretations of pathogenicity in settings of multigene panel testing among individuals with a personal- or family history of Breast and/or Ovarian Cancer, and other tumor phenotypes (example, Koczkowska_2018, Scarpitta_2019, Oliver_2019, Tsaousis_2019, Bono_2021), however it was also found in controls (Haiman_2013, Damiola_2014). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. In addition, in a patient who was affected with thyroid cancer, a co-occurrence with another pathogenic variant has been reported (CHEK2 c.444+1G>A; Henn_2019), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and all of them classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

The frequency of this variant in the general population, 0.00028 (35/126948 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals affected with breast and/or ovarian cancer (PMIDs: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/), 34371384 (2021), 32854451 (2020), 31921681 (2019), 31512090 (2019), 31159747 (2019), 30441849 (2018)), and in healthy controls (PMIDs: 24894818 (2014) and 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/)). In one individual affected with medullary thyroid cancer, the individual was also positive for a pathogenic CHEK2 variant (PMID: 30680046 (2019)). 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.

This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 426 of the RAD50 protein (p.Gln426Arg). This variant is present in population databases (rs145428112, gnomAD 0.03%). This missense change has been observed in individual(s) with a personal and/or family history of breast, ovarian, and/or pancreatic cancer (PMID: 30441849, 31512090, 31921681, 32854451, 34371384). ClinVar contains an entry for this variant (Variation ID: 127993). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RAD50 protein function with a positive predictive value of 80%. 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.

This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 426 of the RAD50 protein (p.Gln426Arg). This variant is present in population databases (rs145428112, gnomAD 0.03%). This missense change has been observed in individual(s) with a personal and/or family history of breast, ovarian, and/or pancreatic cancer (PMID: 30441849, 31512090, 31921681, 32854451, 34371384) . Five clinical diagnostic laboratories have submitted clinicalsignificance assessments for this variant to ClinVar (Variation ID:127993) after 2014 without evidence for independent evaluation, and all of them classified the variant as uncertain significance. Multiple in silico algorithms predict that this variant may be damaging to protein structure and function.. 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.Q426R variant (also known as c.1277A>G), located in coding exon 9 of the RAD50 gene, results from an A to G substitution at nucleotide position 1277. The glutamine at codon 426 is replaced by arginine, an amino acid with highly similar properties. This variant has been reported in multiple studies of individuals with suspected hereditary breast and/or ovarian cancer syndrome, including patients with male breast cancer, ovarian cancer, and bilateral breast cancer (Urhammer N and Bignon YJ. "Abstract# 3037: Contribution of the Rad50, Mre11A, and NBN genes to HBOC." Cancer Res.2009;69; Koczkowska M et al. Cancers (Basel), 2018 Nov;10;442; Oliver J et al. Front Oncol., 2019 Dec;9:1429; Scarpitta R et al. Breast Cancer Res. Treat., 2019 Dec;178:557-564; Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535; Fanale D et al. Cancers (Basel), 2020 Aug;12:E2415). However, in another study, this variant was not observed in 1313 cases diagnosed with breast cancer before the age of 45 but was reported in 1/1123 controls (Damiola F et al. Breast Cancer Res. 2014 Jun;16:R58). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The RAD50 c.1277A>G variant is predicted to result in the amino acid substitution p.Gln426Arg. This variant has been reported in an individual undergoing hereditary cancer testing (Tsaousis et al. 2019. PubMed ID: 31159747, Table S5), in an individual with bilateral breast cancer (Fanale et al. 2020. PubMed ID: 32854451), in an individual with hereditary breast and ovarian cancer (Oliver et al. 2019. PubMed ID: 31921681, Table S1), in at least one individual with ovarian cancer (Koczkowska et al. 2018. PubMed ID: 30441849, Table S1), and in an individual with male breast cancer, pancreatic cancer, and bladder cancer (Scarpitta et al. 2019. PubMed ID: 31512090, Table 1). These studies interpreted this variant as uncertain significance. It is reported in 0.028% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/127993/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.