Of these, six met exome-wide significance (P < 2.5 × 10−6), of which five are known breast cancer risk genes— ATM, BRCA1, BRCA2, CHEK2 and PALB2. Associations were also identified for PTVs in MAP3K1 (P = 1.2 × 10−9). Here, MAP3K1 is linked to breast cancer.