CEP20
protein-codingcentrosomal protein 20
Gene summary
Enables identical protein binding activity. Involved in cilium assembly. Located in centriolar satellite. [provided by Alliance of Genome Resources, Jun 2026]
- C16orf63
- FOPNL
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.9 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 CEP20 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144600.4. 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 | 1 | 1 | ||||
| missense | 28 | 1 | 29 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 29 | 2 | 0 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653201.1 | 5 | MANE Select | |
| Ensembl | ENSP00000255759.6 | 5 | MANE Select | |
| RefSeq | NP_001291426.1 | 3 | Standard | |
| RefSeq | NP_001291427.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microtubule anchoring
- cilium assembly
Cellular Component
- nucleus
- centrosome
- centriole
- motile cilium
- centriolar satellite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000255759
- Coding exons
- 5
- Length
- 22906
- Individuals with no LoFs
- 125699
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 48
- Defined
- 125747
- p
- 0.000191
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.589 | 103 | 87.5 | 1.18 | 0.00000425 | 1118 |
| Missense (PolyPhen) | 20 | 25.757 | 0.77648 | 329 | ||
| Synonymous | 0.352 | 30 | 32.6 | 0.922 | 0.00000149 | 326 |
| Loss of Function | 0.140 | 9 | 9.46 | 0.951 | 6.34e-7 | 110 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00014 | 0.00012 | rare |
| Latino/Admixed American | 0.000075 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.0013 | 0.0013 | notable |
| European (Non-Finnish) | 0.000081 | 0.000079 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the biogenesis of cilia (PubMed:20551181). Required for the recruitement of PLK1 to centrosomes and S phase progression (PubMed:24018379). {ECO:0000269|PubMed:20551181, ECO:0000269|PubMed:24018379}.;
Intolerance Scores
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |