Saturation mutagenesis enables RAD51D clinical variant interpretation and identifies distinct biochemical functions

The tumor suppressor RAD51D is essential for homologous recombination (HR). Pathogenic variants in RAD51D are associated with breast and ovarian cancers. However, most clinical missense variants are of uncertain significance. Here, we report a multiplex assay of variant effect to test 6,888 RAD51D coding variants for loss-of-function. The resulting variant-to-function map perfectly separates known pathogenic and benign variants and is validated by orthogonal HR and biochemical assays across 70 clinical variants. Our screen shows that variants in the DNA-binding or ATPase core most severely compromise HR, and we identify the RAD51D-RAD51C interface within the BCDX2 complex as essential for regulating its ATPase activity. We hypothesize that, paradoxically, the primary function of RAD51D is to slow the ATPase activity of BCDX2, thereby allowing sufficient time and space for RAD51 filament assembly. Together, we identify hotspots of deleterious RAD51D variants and uncover the mechanisms by which variants compromise its biochemical functions. RAD51D is a tumor suppressor gene where pathogenic variants are associated with increased risk of breast and ovarian cancer. This study reports a high throughput functional screen of 6,888 RAD51D coding variants along with analysis of 70 clinically-identified breast and ovarian cancer variants.