Mutations in the gene CEP290 cause an array of debilitating and phenotypically distinct human diseases, ranging in severity from the devastating blinding disease Leber congenital amaurosis (LCA) to Senior Løken Syndrome, Joubert syndrome, and the embryonically lethal Meckel-Grüber syndrome. The pathology observed in these diseases is thought to be due to CEP290's essential role in the development and maintenance of the primary cilium, but despite its critical role in biology and disease we know only little about CEP290's function. Here we identify four novel functional domains of the protein, showing that CEP290 directly binds to cellular membranes through an N-terminal domain that includes a highly conserved amphipathic helix motif, and to microtubules through a domain located within its myosin-tail homology domain. Furthermore, CEP290 activity was found to be regulated by two novel autoinhibitory domains within its N- and C-termini, both of which were also found to play critical roles in regulating ciliogenesis. Disruption of the microtubule-binding domain in the rd16 mouse LCA model was found to be sufficient to induce significant deficits in cilium formation leading to retinal degeneration. Taking these findings into account, we developed a novel model that accurately predicts patient CEP290 protein levels in a mutation-specific fashion. Predicted CEP290 protein levels were found to robustly correlate with disease severity for all reported CEP290 patients. All these data implicate CEP290 as an integral structural and regulatory component of the primary cilium and provide insight into the pathological mechanisms of LCA and related ciliopathies. Our findings also suggest novel strategies for therapeutic intervention in the treatment of CEP290-based disease that, if fully realized, would be the first treatment available for the many patients suffering the devastating effects of CEP290 dysfunction.