For low-frequency variant burden testing, these studies demonstrated a significant association with PLEC, USH2A, FREM2, DCHS1, GLI3 and POMT1. For common variants, we identified associations of DCHS1 (lead SNP, rs12288387; P = 1.869 × 10− 45) and GBA (lead SNP, rs144123706; P = 1.054 × 10− 33) with severe microtia-atresia. Here, GLI3 is linked to microtia.