Analysis of rare missense variants identified evidence of associations of TMEM161A, SIPA1L1, and ERCC2 with overall breast cancer, RNF175 and NCKAP1L with ER-positive disease, and SLC22A10, PHAX, SMARCA2, EML5, NTRK3, and MED23 with ER-negative disease. Here, EML5 is linked to breast cancer.