| Disease | Main features | Genes involved | Corresponding protein | Protein localization | Postulated functions |
| Autosomal recessive PKD (ARPKD) | Renal cyst, enlarged kidneys, hepatic fibrosis | PKHD1 | Fibrocystin/polyductin (FPC) | Cilia and secreted | Calcium response; proliferation/differentiation |
| Autosomal dominant PKD (ADPKD) | Renal, hepatic, pancreatic and brain cysts | PKD1, PKD2 | Polycystin 1 (PC1), Polycystin 2 (PC2) | Cilia, Golgi apparatus, focal adhesions | Calcium response; proliferation/differentiation |
| Nephronophthisis (NPHP) and Senior Løken Syndrome (SNLS) | Renal fibrosis, renal cysts, tubular atrophy, retinal dystrophy (in SNLS) | NPHP1-NPHP11 | Nephrocystin-1, 2/inversin, 3, 4, 5, 6/CEP290, 7/GLIS2, 8/RPGRIP1L, 9/NEK8, 11/Meckelin | Cilia, basal bodies, centrosomes, focal adhesions | Cell-cell and cell-matrix adhesion; actin cytoskeleton; cell division; Wnt and Shh signaling |
| Joubert syndrome (JS) | NPHP and cerebellar ataxia | AHI1, NPHP1, CEP290, JBTS6/TMEM67, RPGRIP1L, ARL13B, CC2D2A, INPP5E, JBTS2/TMEM216 | Jouberin, Nephrocystin, CEP290, Meckelin, RPGRIP1L, ARL13B, CC2D2A, INPP5E, TMEM216 | Cilia, basal bodies, centrosomes, cell junctions | Ciliogenesis, Sonic Hedgehog signaling |
| Bardet-Biedl syndrome (BBS) | Renal cysts, obesity, polydactyly, retinal dystrophy, mental retardation | BBS1-12, MKS1, CEP290, FRITZ, SDCCAG8 | BBS1-12, MKS1, CEP290, FRITZ, SDCCAG8 | Centrosomes, basal bodies | Pericentriolar organization, ciliogenesis, Wnt signaling |
| Meckel-Gruber syndrome (MKS) | Occipital meningoencephalocele, cystic kidneys, liver fibrosis, polydactyly | MKS1, MKS3/TMEM67, NPHP3, CEP290, RPGRIP1L, CC2D2A, MKS2/TMEM216 | MKS1, Meckelin, Nephrocystin 3, CEP290, RPGRIP1L, CC2D2A, TMEM216 | Centrosomes, cilia, plasma membrane | Basal body localization, ciliogenesis, Hedgehog signaling |
| Oral-facial-digital syndrome 1 (OFD1) | Malformations of face, oral cavity and digits, renal cysts, polydactyly | OFD1 | OFD1 | Cilia, basal bodies, centrosomes, nucleus | Ciliogenesis, L-R asymmetry, possibly gene regulation |
| Short-Rib Polydactily (including Jeune Asphyxiating Thoracic Dystrophy) | Renal cysts, shortened bones, polydactyly, situs inversus | DYN2CH1, IFT80 | Cytoplasmic dynein 2 heavy chain, IFT80 | Chondrocyte cilia, basal bodies | Intraflagelar transport, Hedgehog signaling |
| Tuberous sclerosis complex | Renal cysts, beningn tumors in multiple organs, dermatologic abnormalities inlcuding hypopigmented macules (ash-leaf spots), angiofibromas, shagreen patches, and brown fibrous plaque of the forehead | TSC1, TSC2 | Hamartin (TSC1), Tuberin (TSC2) | Centrosome, cytoplasm, | Cellular signaling by regulating the mammalian target of rapamycin (mTOR) signaling pathway |
| Uromodulin associated kidney diseases (MCKD2, FJHN, GCKD) | Renal cysts, fibrosis, hypertension, hypoeruricemia | UMOD, MCKD1, MCKD2 | Uromodulin | Cilia, basal bodies, centrosomes, secreted | Unknown ciliary role |
