ClinVar Genomic variation as it relates to human health

Variant summary: The RAD51D c.698A>G (p.Glu233Gly) variant locatedin the DNA recombination and repair protein RAD51-like, C-terminal domain (via InterPro) involves the alteration of a conserved nucleotide and 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 2670/277696 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0164 (2034/124022, 20 homozygotes). This frequency is about 131 times the estimated maximal expected allele frequency of a pathogenic RAD51D variant (0.000125), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. Multiple case-control studies also showed that this variant does not confer an increased risk to breast or ovarian cancer (Rodrguez-Lpez 2004, Dowty 2008, Jara 2010, Loveday 2011). Although, the variant was shown to confer a slight increased risk for breast cancer in the BRCA-negative only with BrC cases (p-value = 0.02), this finding was not reproducible in a second study in Chilean BRCA1/2 negative women with a positive family history of breast cancer (Rodrguez-Lpez 2004, Jara 2010). Several in-vitro studies on human cancer cell lines, RAD51D-deficient mouse embryonic fibroblasts, and Yeast two-hybrid analysis have reported increased resistance to DNA-damaging agents, increased cellular proliferation, and decreased interaction with RAD51C (Nadkarni_2009). However, these experimental models are generally considered as weak experimental evidence as it is not clear if the results and conclusions drawn from these studies are applicable to the mechanism and presentation of disease. Two computational studies reporting an effect of this variant on function provide conflicting results (Rodrguez-Lpez 2004 and Zhao_2014). In addition, multiple clinical diagnostic laboratories have classified the variant as likely benign/benign. Furthermore, multiple internal LCA samples report the variant to co-occur with another pathogenic variant: PALB2 - c.196C>T (p.Gln66X), MUTYH - c.1187G>A (p.Gly396Asp), BARD1 - c.1690C>T (p.Gln564X), and likely pathogenic, TP53, c.782+1G>T. Therefore, due to the high occurrence in controls, co-occurrences with another pathogenic variant, and no strong established associated risk, the variant of interest has been classified as benign".

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The RAD51D p.Glu233Gly variant was identified in 252 of 14720 proband chromosomes (frequency: 0.017) from Spanish, Australian, British and Chilean individuals or families with BRCA1/BRCA2 negative breast and ovarian cancers (with or without family history), and was present in 134 of 8936 control chromosomes (frequency: 0.015) from healthy individuals (Song 2015 , Rodriguez-Lopez 2004, Osher 2012, Gutierrez-Enriquez 2013, Dowty 2007, Jara 2010). In multiple case control studies, there was no evidence to support an association between the variant and increased risk of breast cancer, nor any evidence of association between the RAD51D-E233G variant and BC who have a positive family history (Dowty 2007, Jara 2010), but rather a low penetrance susceptibility gene in high risk site specific familial breast cancer with segregation studies finding incomplete segregation with disease (Rodriguez-Lopez 2004). Rolland et al (2014) described a systematic map of human binary protein-protein interactions which showed that the variant affects interactions with a number of proteins, including the known cancer gene product IKZF1. Functional studies also suggest that the variant affects RAD51D functions and protein interactions, by increasing cellular resistance to DNA damaging agents (chemoresistant), contributing to telomere dysfunction by conferring cellular proliferation and decreasing the interaction with RAD51C (Nadkarni 2009). The variant was identified in dbSNP (ID: rs28363284) as “other”, Clinvitae database (classifications benign, likely benign and conflicting interpretations of pathogenicity), Leiden Open Variation Database (LOVD), the ClinVar database (classification benign by GeneDx, Ambry Genetics, Invitae, color Genomics Inc., and likely benign by Illumina and Counsyl). The variant was also identified in control databases in 2567 of 271538 (20 homozygous) chromosomes at a frequency of 0.009 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), identified in the following populations at a frequency greater than 1%: European (Non-Finnish) in 2034 of 124022 chromosomes (freq: 0.02), and Other in 63 of 6354 chromosomes (freq: 0.01). The p.Glu233 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; however, this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.