CEP162
protein-codingcentrosomal protein 162
Gene summary
Involved in cilium assembly. Located in microtubule cytoskeleton and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C6orf84
- KIAA1009
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~103.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CEP162 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014895.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 1 | 5 | ||
| missense | 190 | 18 | 208 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 197 | 19 | 1 | 217 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055710.2 | 26 | MANE Select | |
| Ensembl | ENSP00000385215.3 | 26 | MANE Select | |
| RefSeq | NP_001273135.1 | 24 | Standard | |
| Ensembl | ENSP00000257766.4 | 24 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cep162 | Danio rerio | Structure: whole organism Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Anchoring of the basal body to the plasma membrane
- Cilium Assembly
- Organelle biogenesis and maintenance
Biological Process
- cilium assembly
- ciliary basal body-plasma membrane docking
Molecular Function
- protein binding
Cellular Component
- nucleus
- centrosome
- centriole
- spindle
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000403245
- Coding exons
- 26
- Length
- 103394
- Individuals with no LoFs
- 125439
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 151
- Defined
- 125590
- p
- 0.000601
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.244 | 646 | 629 | 1.03 | 0.0000301 | 9279 |
| Missense (PolyPhen) | 196 | 192.5 | 1.0182 | 3035 | ||
| Synonymous | 0.0378 | 216 | 217 | 0.997 | 0.0000106 | 2358 |
| Loss of Function | 1.70 | 50 | 64.8 | 0.772 | 0.00000284 | 986 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00086 | 0.00086 | rare |
| Latino/Admixed American | 0.00053 | 0.00049 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0018 | 0.0018 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00059 | 0.00056 | rare |
| South Asian | 0.00060 | 0.00056 | rare |
| Other | 0.00052 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required to promote assembly of the transition zone in primary cilia. Acts by specifically recognizing and binding the axonemal microtubule. Localizes to the distal ends of centrioles before ciliogenesis and directly binds to axonemal microtubule, thereby promoting and restricting transition zone formation specifically at the cilia base. Required to mediate CEP290 association with microtubules. {ECO:0000269|PubMed:23644468}.;
Recessive Scores
- pRec
- 0.0891
Intolerance Scores
- RVIS EVS
- 1.13
- RVIS percentile EVS
- 92.13
Essentials
- Essential (gene trap)
- N