CFAP157
protein-codingcilia and flagella associated protein 157, the group of Cilia and flagella associated
Gene summary
Predicted to enable microtubule binding activity. Predicted to be involved in sperm axoneme assembly. Predicted to be located in cilium. Predicted to be active in ciliary basal body. [provided by Alliance of Genome Resources, Jun 2026]
- C9orf117
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.0 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 CFAP157 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001012502.3. 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 | 2 | 2 | ||||
| missense | 88 | 5 | 93 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 1 | 90 | 5 | 0 | 96 |
Highest pathogenic variant AF is 0.000013703613
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001012520.2 | 9 | MANE Select | |
| Ensembl | ENSP00000362392.1 | 9 | MANE Select | |
| Ensembl | ENSP00000485445.1 | 3 | Standard | |
| Ensembl | ENSP00000478313.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- sperm axoneme assembly
Molecular Function
- microtubule binding
Cellular Component
- cytosol
- plasma membrane
- ciliary basal body
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373295
- Coding exons
- 9
- Length
- 9014
- Individuals with no LoFs
- 124453
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 365
- Defined
- 124818
- p
- 0.00146
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.752 | 271 | 308 | 0.879 | 0.0000188 | 3415 |
| Missense (PolyPhen) | 100 | 92.187 | 1.0848 | 1039 | ||
| Synonymous | 1.35 | 107 | 126 | 0.847 | 0.00000748 | 983 |
| Loss of Function | 0.952 | 20 | 25.1 | 0.795 | 0.00000116 | 280 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.017 | 0.016 | notable |
| Latino/Admixed American | 0.0011 | 0.0011 | notable |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00046 | 0.00045 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0.0012 | 0.0012 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Specifically required during spermatogenesis for flagellum morphogenesis and sperm motility. May be required to suppress the formation of supernumerary axonemes and ensure a correct ultrastructure. {ECO:0000250|UniProtKB:Q0VFX2}.;
Intolerance Scores
- RVIS EVS
- -0.13
- RVIS percentile EVS
- 43.91
Essentials
- Essential (gene trap)
- N