CFAP20
protein-codingcilia and flagella associated protein 20, the group of Cilia and flagella associated
Gene summary
Enables RNA binding activity. Involved in several processes, including positive regulation of feeding behavior; protein polyglutamylation; and regulation of cilium beat frequency involved in ciliary motility. Located in microtubule cytoskeleton and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- C16orf80
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.8 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 CFAP20 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013242.3. 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 | 0 | |||||
| missense | 3 | 17 | 20 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 4 | 18 | 0 | 0 | 22 |
Highest pathogenic variant AF is 0.000008054243
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037374.1 | 6 | MANE Select | |
| Ensembl | ENSP00000262498.3 | 6 | MANE Select | |
| Ensembl | ENSP00000455220.1 | 4 | Standard | |
| Ensembl | ENSP00000566600.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- protein polyglutamylation
- cilium assembly
- regulation of cilium beat frequency involved in ciliary motility
- positive regulation of cell motility
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- centriole
- microtubule
- cilium
- motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262498
- Coding exons
- 6
- Length
- 15859
- Individuals with no LoFs
- 125717
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 125747
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.07 | 56 | 120 | 0.467 | 0.00000749 | 1274 |
| Missense (PolyPhen) | 17 | 38.942 | 0.43654 | 361 | ||
| Synonymous | 0.547 | 39 | 43.6 | 0.895 | 0.00000242 | 364 |
| Loss of Function | 1.55 | 6 | 11.7 | 0.511 | 6.70e-7 | 122 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.000079 | 0.000079 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. Involved in the regulation of the size and morphology of cilia (PubMed:24414207). Required for axonemal microtubules polyglutamylation (PubMed:24414207). {ECO:0000269|PubMed:24414207}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.63
Essentials
- Essential (gene trap)
- E