Associations at P < 1 × 10−4 were also identified for PTVs in LZTR1, ATR interacting protein (ATRIP) and the known risk gene BARD1. Of the other previously identified breast cancer susceptibility genes, associations with P < 0.01 were observed for CDH1 and RAD51D (Supplementary Table 4). Here, ATRIP is linked to breast cancer.