CFAP90
protein-codingcilia and flagella associated protein 90
Gene summary
Predicted to be involved in flagellated sperm motility. Located in axoneme and ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]
- C5orf49
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.8 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 CFAP90 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 | 0 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001083053.1 | 3 | MANE Select | |
| Ensembl | ENSP00000382708.2 | 3 | MANE Select | |
| Ensembl | ENSP00000426019.1 | 3 | Standard | |
| Ensembl | ENSP00000426019.1 | 3 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000399810
- Coding exons
- 3
- Length
- 21113
- Individuals with no LoFs
- 123270
- Homozygous LoFs
- 37
- Heterozygous LoFs
- 1474
- Defined
- 124781
- p
- 0.00607
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.113 | 73 | 75.8 | 0.963 | 0.00000437 | 927 |
| Missense (PolyPhen) | 30 | 26.046 | 1.1518 | 307 | ||
| Synonymous | 0.815 | 25 | 30.8 | 0.813 | 0.00000174 | 285 |
| Loss of Function | 0.477 | 3 | 4.03 | 0.744 | 1.69e-7 | 65 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00045 | 0.00045 | rare |
| Latino/Admixed American | 0.018 | 0.017 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.040 | 0.039 | notable |
| Finnish | 0.0065 | 0.0062 | notable |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.0014 | 0.0013 | notable |
| Other | 0.0045 | 0.0045 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.344
- RVIS EVS
- 0.82
- RVIS percentile EVS
- 87.87
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |