| Cilia-related | Wdr16 | Regulate cilia signal transduction | Affect cell polarity such as water homeostasis or osmoregulation to induce hydrocephalus, but ependymal disorganization or impaired ciliary motility was not observed | Anatomical structure abnormalities | Morpholino | Zebrafish | [44,45] |
| | Wdr78 | Encode motile cilium- specific protein and is involved in axon-dynein complex assembly and ciliary movement | Affect cilia assembly and movement | Abnormal otolith, pronephric cysts | Morpholino | Zebrafish | [46] |
| | Nphp7 | Encode the Kruppel-like zincfinger transcription factor GLIS2 and has an interaction with BBS1 | Disrupt cilia beat | Cystic pronephros | Morpholino | Zebrafish | [47] |
| | Ccp5 | Encode a metal carboxypeptidase belonging to the M14 peptidase family and involved in the process of post-translational modification of tubulin | Uncoordinated movement and reduce the amplitude of cilia | Ventral body curvature, pronephric cysts | Morpholino | Zebrafish | [48,49] |
| | Exoc5 | Encode a protein component of the exocyst complex and play a crucial role in ciliogenesis | Affect ciliogenesis | Cardiac edema | Mutation | Zebrafish | [50] |
| | Efcab1 | Encode Ca2+-binding dyneinassociated protein and serve as a crucial regulator in coordinating ciliary movement | Block cilia movement and impair CSF flow | PCD phenotypes like situs inversus | Mutation | Mice | [51] |
| | Adamts9 | A substrate for B3glct, encode secreted extracellular metalloproteinase and is critical in the formation and maintenance of primary cilia’s functional integrity | Mediate cilia shorten | Ciliopathic phenotypes like renal cysts | Morpholino | Zebrafish | [52] |
| | B3glct | β3-glucosyltransferase | Reduce cilia basal bodies and changes inner epithelium polarity; and reduce secretion of SSPO | Skeletal abnormalities, white spotting | Mutation | Mice | [53] |
| | Dyx1c1 | Encode a dynein protein axon assembly factor and is critical to ciliary assembly and functional integrity | Affect IDA and ODA assembly and ciliary dyskinesia | Body curvature, situs inversus, and kidney cysts | Morpholino | Zebrafish | [54] |
| | Zmynd10 | Encode a cytoplasmic protein in cilia | Affect IDA and ODA assembly | PCD-like laterality defects | Mutation | Mice | [55] |
| | Chmp4b | Encode a protein in the CHMP family, and is a subunit of the endosomal sorting complexes required for transport | Affect cilia assembly | Curved body axis, otolith malformation, and kidney cyst | Morpholino | Zebrafish | [56] |
| | Ttc30 | Involve in protein polyglutamylation in cilia and axonal microtubules | Affect ciliogenesis | Kidney cysts, left-right asymmetry | Mutation | Zebrafish | [57] |
| | Dnaaf3 | Encode a cytoplasmic factor and is essential for the preassembly of axonemal IDA and ODA | Affect IDA and ODA assembly | PCD-like axis curvature defects, kidney cysts, perturbed otolith development, and laterality defects | Morpholino | Zebrafish | [58] |
| | Nphp3 | Encode a protein with a coiled-coil domain, a tubulin-tyrosine ligase domain, and a tetratrico peptide repeat domain | Reduce cilia length and number | Pronephric cysts | Morpholino | Zebrafish | [59] |
| | Wtip | Encode an LIM domain protein of the Ajuba/Zyxin family and is involved in cell mitosis | Affect the PCP | Pronephric cysts, cloaca malfor-mation, body curvature, and pericardial edema | Morpholino | Zebrafish | [60] |
| | Ptk7 | Encode a protein that regulates signaling at the cell membrane and is critical for cell polarity and adhesion | Affects EC cilia function | Idiopathic scoliosis | Mutation | Zebrafish | [61] |
| | Pard3 | Encode a polarity protein that cooperates with microtubules to regulate cell polarity | Impair ciliary growth | – | Morpholino | Zebrafish | [62] |
| | Nherf1 | Encode a protein of the PDZ family and is abundantly expressed in ependymal epithelial cells | Impair cilia function | Renal dysfunction | Mutation/morpholino | Mice/Zebrafish | [63,64] |
| | Cep120 | Encode a protein involved in coupling centrosome microtubules, exhibiting a significant role in ciliogenesis | Affect ciliogenesis | Cerebellar hypoplasia/ventrally curved body axis, otolith defects, and cardiac edema | Mutation/Morpholino | Mice/Zebrafish | [65] |
| | Pkd1 & Pkd2 | Encode polycystin, a kind of large membrane proteins that form a receptorchannel complex expressed throughout the body, and its expression in ependymal cells and choroid plexus | Affect cilia function | Dorsal axis curvature, pronephric cyst/nephric cyst | Morpholino/conditional inactivation or knockout | Mice/Zebrafish | [66,67] |
| | Pde1a | Encode cAMP or cGMP hydrolyzed protein is activated by the Ca2+-calmodulin complex and plays an important role in signal transduction | Affect ciliary movement | Pronephric cysts, body curvature | Morpholino | Zebrafish | [68] |
| | Pih1d3 | An X-linked gene is associated with the defects of dynein arms | Regulating the integrity structure and function of IDA and ODA | Situs inversus, defects in spermato-cyte survival and mucociliary clearance | TALEN | Rats | [69] |
| | Snx27 | Participate in the trafficking of multiple transmembrane receptors; regular β-amyloid and Notch intracellular domain generation | Reduce ependymal cells and cilia density | – | Mutation | Mice | [70] |
| | Cfap54 | Localize to the C1D projection of the central microtubule apparatus | Decrease the ciliary beat frequency and perturb ciliadriven flow | PCD-relevant phenotypes | Knockout | Mice | [71] |
| | Ccdc39 | Is essential for the dynein motor protein regulatory complex | Disturb the axonemal organization and ciliary beating | – | Mutation | Mice | [72] |
| | Stk36 | Encode a kind of serinethreonine protein kinases of the Unc-51–like kinase family | Affect the length and ultrastructure of the cilia | Respiratory infections | Knockout | Mice | [73] |
| | Spag6l | A key component of the central apparatus | Reduced ciliary beating frequency or uncoordinated beating | Growth retardation, structural abnormalities in the spleen | Conditional knockout | Mice | [74] |
| Ion transport-related | CaV1.2 | Encode the Ca2+ channel protein α-1 subunit for regulating Ca2+ transportation | Destroy the balance of cellular homeostasis | Primary cilia defects related diseases like renal cysts, left-right asymmetry defects | Morpholino | Zebrafish | [75] |
| | Calb2a & Calb2b | Encode a member of the troponin C superfamily of Ca2+ binding protein plays a role in Ca2+ transportation | Destroy nervous system development by regulating calcium concentration of synaptic | Axial curvature defect, and yolk sac edema | Morpholino | Zebrafish | [76] |
| | Tmem67 | Regulate choroid plexus epithelial cell fluid and electrolyte homeostasis | Osmotic gradient increase in the choroid plexus epithelial cells | Polycystic kidney disease | Mutation | Rats | [77] |
| | Atp1a3 | Encode a crucial enzyme responsible for transporting ions across membranes and regulate Na+ and K+ gradients, and is essential for the transmission of electrical excitation in both nerves and muscles | Destroy transmembrane ion transport | Neuronal excitability impaired | Morpholino | Zebrafish | [78] |
| | Slc41a1 | Encode Mg2+ transporter a protein located in the basolateral plasma membrane and involved in the trans-membrane transportation of Mg2+ | Perturb intracellular Mg2+ homeo-stasis | Body curvature, cystic kidneys | Morpholino | Zebrafish | [79] |
| CNS-related | Pank2 | Encode a key regulatory enzyme in the biosynthesis of coenzyme A | Impair neuronal development, particularly in the anterior part of the CNS | Perturbed brain morphology, heart region, and caudal plexus edema | Morpholino | Zebrafish | [95] |
| | Ecrg4 | Encode auguring protein, is expressed in the CP epithelial, brain ventricular and central canal cells of the spinal cord | Inhibit CNS injury | – | Morpholino | Zebrafish | [96] |
| | Ccdc85c | Encode a protein belonging to the delta-interacting protein A family, and plays a necessary role in epithelial cell proliferation and cortex development | Reduce NPC number | Subcortical heterotopia, intra-cranial hemorrhage | Mutation | Mice | [97] |
| | α-Snap | Encode a key protein in intracellular trafficking | Result in abnormal transport of N-cadherin to the plasma membrane of NSCs | Abnormal neurogenesis | Mutation | Mice | [82] |
| | Smarcb1 | The core subunit of the BAF chromatin remodeling complex is essential for the regulation of DNA accessibility and gene expression during neuronal differentiation | Affect neurodevelopment | Neuronal signaling disturbance | Mutation | Mice | [98] |
| | Idh1 | Located in the cytoplasm and peroxisome where it acts in lipid and glucose metabolism and protects against ROS | SVZ cells proliferate ectopically, infiltrate the brain parenchyma, and form nodules; self-renewal and proliferation of NSCs and NPCs increase | Grossly dilated lateral ventricles and gliomagenesis | Mutation | Mice | [99] |
| | Lgi1b | Encode a kind of secreted protein in the leucine-rich repeat (LRR) superfamily, it is highly expressed in the choroid plexus and involved in neuronal growth and survival | Mediate neuronal apoptosis | Brain dysplasia and pericardial edema | Morpholino | Zebrafish | [100] |
| RF-related | Camel | A novel distantly related member of the L1CAM family and involved in cell adhesion | Affect RF synthesis; abnormal development of CVOs and axial structures | Scoliosis (tail curled down) | Morpholino | Zebrafish | [105] |
| | Msx1 | Regulate the activity of DNA-binding transcription factor is widely expressed in neuroepithelial cells, such as the fimbria and the medulla | Affect RF synthesis | – | Mutation | Mice | [110] |
| Others | Hrg1 | Encode transmembrane protein, play an essential role in the formation and maturation of the erythrocytes | Affect heme homeostasis | Yolk tube malformations, anemia | Morpholino | Zebrafish | [111] |
| | β-Pix | Expressed in the brain and blood vessels | Disruption of vascular stability | Cranial hemorrhage | Mutation and morpholino | Zebrafish | [112] |
| | Dio3 | Inactivate 2 main thyroid hormones and reduce the levels of THs during the early development of mammals | Affect the development | Cleft palate, choanal atresia, Chiari malformations | Mutation | Mice | [113] |
| | Mks1 | Encode a 559 amino acid B9-domain-containing protein that localized to the basal body of mammalian cells | Wnt/β-catenin signal increase and cellular over-proliferation | Dandy-Walker malformation and renal cystic dysplasia | Knockout | Mice | [114] |
| | Thioredoxin1 | Encode antioxidant protein | Mediate ventricular epithelial cell apoptosis | Brain dysplasia | Morpholino | Zebrafish | [115] |