After correction for multiple testing (P = 7.81 × 10− 4), PLEC (plectin), USH2A (usherin), FREM2 (Fras1-related extracellular matrix protein 2), DCHS1, GLI3 (GLI family zinc finger 3) and POMT1 (protein O-mannosyltransferase 1) were identified as significantly associated with severe microtia-atresia (Table 3, Additional file 5). Here, GLI3 is linked to microtia.