Saturation genome editing of BRCA1 across cell types improves interpretation of variant pathogenicity

Abstract Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence, over half of reported single-nucleotide variants in BRCA1 lack a definitive clinical interpretation. Furthermore, the consistency of variant effects across cell types remains largely unexplored. Here we performed saturation genome editing (SGE) of BRCA1 in HAP1 cells to score 4,113 previously unassayed variants. Additionally, we developed an SGE assay in human mammary epithelial cells (HMECs), allowing comparison of effects across cell lines, drug treatments and genetic backgrounds. We identified 538 variants impacting gene function through distinct mechanisms. HAP1 function scores discriminate between known pathogenic and benign variants with near-perfect accuracy. Intriguingly, however, nearly half of HAP1 loss-of-function variants scored neutrally in HMECs. We show that discordantly scored variants are hypomorphic and confer intermediate cancer risk. Overall, this work demonstrates how performing SGE across cell models improves the functional interpretation of rare variants.