CFAP61
protein-codingcilia and flagella associated protein 61, the group of Cilia and flagella associated
Gene summary
Acts upstream of or within sperm mitochondrial sheath assembly. Located in axoneme and sperm flagellum. Implicated in spermatogenic failure 84. [provided by Alliance of Genome Resources, Jun 2026]
- C20orf26
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~308.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
Clinical Genomic Database (CGD)
Manifestation: Genitourinary
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CFAP61 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015585.4. 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 | 2 | 3 | 5 | |||
| missense | 2 | 2 | 199 | 14 | 217 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 1 | 3 | ||
| Total | 5 | 3 | 202 | 17 | 0 | 227 |
Highest pathogenic variant AF is 0.00007558598
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056400.3 | 26 | MANE Select | |
| Ensembl | ENSP00000245957.5 | 26 | MANE Select | |
| RefSeq | NP_001161288.1 | 13 | Standard | |
| Ensembl | ENSP00000345553.6 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cilium movement
- cilium organization
Cellular Component
- radial spoke stalk
- axoneme
- motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000245957
- Coding exons
- 26
- Length
- 308189
- Individuals with no LoFs
- 125496
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 251
- Defined
- 125748
- p
- 0.00100
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.245 | 700 | 718 | 0.974 | 0.0000404 | 8196 |
| Missense (PolyPhen) | 196 | 220.14 | 0.89034 | 2553 | ||
| Synonymous | 0.449 | 274 | 284 | 0.966 | 0.0000177 | 2340 |
| Loss of Function | 3.31 | 34 | 62.2 | 0.547 | 0.00000330 | 724 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0034 | 0.0034 | notable |
| Latino/Admixed American | 0.0010 | 0.0010 | notable |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00087 | 0.00087 | rare |
| South Asian | 0.0011 | 0.0011 | notable |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May regulate cilium motility through its role in the assembly of the axonemal radial spokes. {ECO:0000250|UniProtKB:A8IF44, ECO:0000250|UniProtKB:Q23F13}.;
Intolerance Scores
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.87
Essentials
- Essential (gene trap)
- N