One craniorachischisis/exomphalos sample (01F29A) was found to carry a pathogenic missense variant (c.676G>A; p.Ala226Thr; rs104894043) in the Sonic Hedgehog (SHH) gene, which was previously identified in an autosomal‐dominant holoprosencephaly 3 (HPE3) patient (OMIM: 142945).29 HPE3 is characterized by midline brain and craniofacial abnormalities, and it is possible that this variant either contributes to the NTD, whilst other characteristics of HPE are masked by the severity of the midline craniorachischisis/exomphalos phenotype in this individual. Here, SHH is linked to omphalocele.