Required for normal ciliary development and function. Inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling that regulates planar cell polarity. Probably acts as a molecular switch between different Wnt signaling pathways. Required for proper convergent extension cell movements. Interacts with NPHP1 and INVS/NPHP2. Interacts (when myristoylated) with UNC119 and UNC119B; interaction is required for localization to cilium (By similarity). Interacts with CEP164 (By similarity). Component of a complex containing at least ANKS6, INVS, NEK8 and NPHP3. ANKS6 may organize complex assembly by linking INVS and NPHP3 to NEK8 and INVS may target the complex to the proximal ciliary axoneme (By similarity). Localization to cilium is mediated via interaction with UNC119 and UNC119B, which bind to the myristoyl moiety of the N-terminus. Additional isoforms seem to exist. In gastrulation-stage embryos, it is confined to the node between 7.5 and 8.25 dpc In sections of 14.5 and 16.5 dpc. embryos, it is strongly expressed in neural tissue (brain and ganglions). Also weakly expressed included in kidney tubules, retina, respiratory epithelium, biliary tract and liver. In the adult kidney, it is weakly but specifically expressed in distal tubules located at the cortico-medullary border, which corresponds to the site of cyst formation in mice lacking Nphp3. Expressed in retina and liver. Defects in Nphp3 may be the cause of polycystic kidney disease (pcy). Pcy is a recessive disorder causing chronic renal failure. The Pcy phenotype can be slowed by diet modification such as protein restriction, administration of soy-based proteins, administration of methylprednisolone or treatment with V2R antagonist. In contrast administration of bicarbonate/citrate has no effect. Mice show situs inversus, congenital heart defects, and embryonic lethality. Extended C-terminus. Extended N-terminus.