The B9D1 gene encodes the B9 Domain-Containing Protein 1.  Similar to other B9 domain containing proteins, B9D1 associates with basal bodies and primary cilia in mammalian cells.  The protein forms a component of the tectonic-like complex, which localizes to the transition zone of primary cilia and plays an important role in preventing the diffusion of transmembrane proteins between the cilia and plasma membranes.  The protein is also involved in cilium assembly and the Sonic hedgehog signaling pathway.  Based on studies of mouse orthologs, human B9D1 protein is predicted to play a role in in-utero embryonic development, vasculature development, digit morphogenesis, eye development and neuro-epithelial cell differentiation.

The gene is associated with Meckel Syndrome, type 9 (MKS9), an often fatal ciliopathy defined by the presence of occipital encephalocele, polydactyly, and renal and biliary ductal dysplasia.  It is also associated with Joubert Syndrome 27 (JBTS27), a phenotypically diverse disorder characterized by hypoplasia of the cerebellar vermis resulting in the neuroradiologic molar tooth sign, along with other neurological, ocular and renal manifestations.

Located on the short arm of chromosome 17, this gene spans a length of 42.9 kb and its coding sequence consists of 13 exons.  The protein encoded by the B9D1 gene is 22 kDa in mass and is made up of 204 amino acids.  An additional isoform of the B9D1 protein, made up of only 153 amino acids, has also been identified.  Both homozygous and compound heterozygous mutations in the B9D1 gene are associated with MKS9 and JBTS27.  These are mainly transitions, insertions and deletions.