Here, we describe the case of an 11-year-old boy with MGDA, mild midfacial defects, digital anomalies, moyamoya vasculopathy, and sphenoid cephalocele, who harbored a new rare missense variant in OFD1. This gene is responsible for the oral-facial-digital syndrome type 1 (OFD1; OMIM 311200), a X-linked-dominant male-lethal ciliopathy characterized by malformation of face, oral cavity and digits, cystic kidney disease, and a wide spectrum of brain malformations [21]. This evidence concerns the gene PAX6 and cystic kidney disease.