In this study, we recruited several families with polydactyly and identified three GLI3 variants, including a novel deletion variant (NM_000168.6: c.1372del, p.Thr458GlnfsTer44), a novel insertion-deletion (indel) variant (NM_000168.6: c.1967_1968delinsAA, p.Ser656Ter), and a previously reported nonsense variant (NM_000168.6: c.2374 C > T, p.Arg792Ter). This evidence concerns the gene GLI3 and polydactyly.