B9D1 is a ciliary transition zone protein essential for ciliogenesis and hedgehog signaling. As a component of the B9 domain-containing protein complex (MKS1-B9D2-B9D1), B9D1 localizes to the transition zone between the basal body and axoneme, functioning as a diffusion barrier that prevents inappropriate entry of transmembrane proteins into cilia 1. B9D1 also localizes to centrioles prior to ciliogenesis, where it facilitates the initiation of cilium assembly 2. The protein interacts with TMEM67 and regulates axonemal microtubule posttranslational modifications, critical for proper ciliary function 2. B9D1 dysfunction disrupts sonic hedgehog signaling and ciliary protein localization, leading to severe developmental defects 3. Mutations in B9D1 cause Meckel syndrome 9 (MKS9), a lethal ciliopathy characterized by occipital encephalocele, polycystic kidneys, polydactyly, and liver malformations 43. B9D1 is also associated with Joubert syndrome 27, though variants affecting different B9 complex functions produce distinct phenotypic severity 2. The discovery of B9D1 as an MKS gene revealed substantial genetic heterogeneity in ciliopathies and established the critical importance of transition zone architecture in maintaining cilia as compartmentalized signaling organelles.