Associations with P < 1 × 10−4 were also observed for SAMHD1, MRPL27, EXOC4 and PPP1R3B. When instead defining deleterious rare missense variants using Helix and combining with PTVs, 29 genes had a P < 0.001, 25 of which corresponded to an increased risk of breast cancer (Supplementary Table 9). Here, SAMHD1 is linked to breast cancer.