Eight significant variants associated with craniofacial malformations such as non-syndromic cleft lip and palate, mandibular prognathism, ocular abnormalities, and tooth defects are found in AXIN2, BMP2, BMP4, NOTCH3, PTCH1, SOX10, and WNT10A (Table 2 and Supplementary Table S6) [44,45,46,47,48,49,50,51]. Here, AXIN2 is linked to cleft lip.