First, we found a pathogenic missense variant in the SHH gene previously reported to cause holoprosencephaly type 3 (MIM:142945), microphthalmia with coloboma type 5 (MIM:611638), schizencephaly (MIM:269160), or single median maxillary central incisor (MIM:147250) and with no clear mode of inheritance. The gene discussed is SHH; the disease is holoprosencephaly 3.