The ARL6 gene encodes a GTP binding protein involved in intracellular traffic regulation and protein localization to non-motile primary cilium.  GTP binding by ARL6 is essential for the localization of the ciliary membrane BBSome complex consisting of 7 BBS proteins and BBIP10.  ARL6 is also thought to be involved in the key biological processes of GTPase mediated signal transduction, Smoothened signaling pathway regulation, determination of left/right symmetry and fat cell differentiation.

Due to its cellular roles, ARL6 is believed to affect retinal layer formation, visual perception and brain development.  Hence, mutations in this gene can have strong pathological consequences.  Gene defects are associated with Bardet-Biedl syndrome 3 (BBS3), a multi-system ciliopathy characterized by pigmentary retinopathy, polydactyly, polycystic kidneys, hypogenitalism, obesity, and learning disabilities.  The gene has also been implicated in non-syndromic Retinitis Pigmentosa 55 (RP55), a retinal dystrophy characterized by the loss of photoreceptor cells.