CEP15
protein-codingcentrosomal protein 15
Gene summary
Predicted to be located in cilium. [provided by Alliance of Genome Resources, Jul 2025]
- C3orf14
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.2 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 CEP15 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001291941.3. 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 | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001278870.1 | 4 | MANE Select | |
| Ensembl | ENSP00000419977.1 | 4 | MANE Select | |
| RefSeq | NP_001278871.1 | 4 | Standard | |
| RefSeq | NP_001278872.1 | 3 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000494481
- Coding exons
- 4
- Length
- 17241
- Individuals with no LoFs
- 125644
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 89
- Defined
- 125733
- p
- 0.000354
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.349 | 57 | 64.9 | 0.878 | 0.00000326 | 824 |
| Missense (PolyPhen) | 11 | 13.968 | 0.78749 | 197 | ||
| Synonymous | 0.397 | 18 | 20.3 | 0.888 | 8.67e-7 | 236 |
| Loss of Function | -0.173 | 7 | 6.52 | 1.07 | 2.75e-7 | 84 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000096 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0038 | 0.0038 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.598
- RVIS EVS
- 0.68
- RVIS percentile EVS
- 84.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |