ClinVar Genomic variation as it relates to human health

This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 219 of the RAD51C protein (p.Leu219Ser). This variant is present in population databases (rs201529791, gnomAD 0.003%). This missense change has been observed in individual(s) with clinical features of RAD51C-related conditions (PMID: 22451500, 25086635). ClinVar contains an entry for this variant (Variation ID: 232604). 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 RAD51C protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects RAD51C function (PMID: 22451500, 25292178). 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.L219S variant (also known as c.656T>C), located in coding exon 4 of the RAD51C gene, results from a T to C substitution at nucleotide position 656. The leucine at codon 219 is replaced by serine, an amino acid with dissimilar properties. In one study, this variant was identified in a Spanish breast and ovarian cancer family and was absent in 550 general population controls (Osorio A et al. Hum. Mol. Genet. 2012 Jul;21:2889-98). When expressed in RAD51C-deficient cells, this variant was not able to restore normal function. This alteration was also reported in a Spanish female diagnosed with ovarian cancer at age 44 and having a family history of breast cancer and prostate cancer (Blanco A et al. Breast Cancer Res. Treat. 2014 Aug;147:133-43). The p.L219S variant was analyzed for homologous recombination (HR) efficiency using a GFP reporter and exhibited significantly reduced HR frequency (Somyajit K et al. Carcinogenesis. 2015 Jan;36:13-24). Authors also demonstrated that this variant displayed 3-fold sensitivity toward PARP inhibitors using CL-V4B cells incubated with 4-ANI. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The RAD51C c.656T>C (p.Leu219Ser) missense change has a maximum subpopulation frequency of 0.0029% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and functional studies suggest that this variant affects RAD51C function (PMID: 22451500, 25292178). This variant has been reported in individuals with a personal and/or family history of breast and ovarian cancer (PMID: 22451500, 25086635). This variant is absent in a database of women older than 70 years of age who have never had cancer (FLOSSIES database, https://whi.color.com/). To our knowledge, this variant has not been reported in individuals with Fanconi anemia. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with a personal and/or family history of breast, ovarian, or colorectal cancer (Osorio et al., 2012; Blanco et al., 2014; Guindalini et al., 2022; Mikaeel et al., 2022; Anwaar et al., 2023); Published functional studies are inconclusive: variant unable to restore wild-type levels of RAD51 foci formation in RAD51C-deficient fibroblasts, but RAD51C protein levels were not evaluated in this study; increased sensitivity to Poly (ADP-ribose) polymerase 1 (PARP1) inhibitors compared to wild-type, failure to suppress G2/M accumulation, but ability to retain stability, and conflicting results on effect on homologous recombination activity (Osorio et al., 2012; Somyajit et al., 2015; Prakash et al., 2022; Hu et al., 2023); This variant is associated with the following publications: (PMID: 25470109, 23117857, 28829762, 22451500, 25086635, 25154786, 25292178, 34761457, 36099300, 37253112, 35264596, 36969410, 14704354)

This missense variant replaces leucine with serine at codon 219 of the RAD51C protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported conflicting results. One study has shown the mutant protein to exhibit reduced homologous recombination activity, reduced ability to form RAD51C foci, and resulted in abnormal cell cycle progression (PMID:22451500, 25292178). Another study has shown that the mutant protein retains near normal homologous recombination activity, with reduced binding to RAD51D (13% of normal levels) and to RAD51B and XRCC3 (over 60% of normal levels) (PMID: 36099300). This variant has been reported in an individual affected with breast cancer with family history of breast cancer and ovarian cancer (PMID: 22451500) and in an individual affected with breast cancer or ovarian cancer (PMID: 23117857). It has also been reported in an individual affected with ovarian cancer, whose sister carries this variant and is unaffected with cancer (PMID: 25086635). This variant has been identified in 2/251286 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 25292178, 22451500].

Variant summary: RAD51C c.656T>C (p.Leu219Ser) results in a non-conservative amino acid change located in the DNA recombination and repair protein Rad51-like, C-terminal domain (IPR013632) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251286 control chromosomes (gnomAD). c.656T>C has been reported in the literature in individuals affected with breast, ovarian, or colorectal cancer without evidence of cosegregation with disease (e.g. Osorio_2012, Blanco_2014, Mikaeel_2022, de Oliveira_2022, Guindalini_2022). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Publications report experimental evidence evaluating an impact on protein function. One study found that the variant resulted in a significant reduction in RAD51 foci-positive cells (Osorio_2012), while another study found that the variant did not result in a deleterious effect on homology-directed repair activity (Hu_2023). The following publications have been ascertained in the context of this evaluation (PMID: 22451500, 25086635, 34761457, 35534704, 35264596, 37253112). ClinVar contains an entry for this variant (Variation ID: 232604). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.