CFAP58
protein-codingcilia and flagella associated protein 58, the group of Cilia and flagella associated
Gene summary
Involved in protein localization to motile cilium; sperm axoneme assembly; and sperm mitochondrial sheath assembly. Located in sperm midpiece and sperm principal piece. Implicated in spermatogenic failure 49. [provided by Alliance of Genome Resources, Jun 2026]
- C10orf80
- CCDC147
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~101.3 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 CFAP58 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001008723.2. 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 | 1 | 5 | 6 | |||
| missense | 132 | 5 | 2 | 139 | ||
| nonsense | 3 | 1 | 4 | |||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 5 | 1 | 134 | 10 | 2 | 152 |
Highest pathogenic variant AF is 0.0002659268
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001008723.1 | 18 | MANE Select | |
| Ensembl | ENSP00000358718.3 | 18 | MANE Select | |
| RefSeq | NP_001387155.1 | 17 | Standard | |
| RefSeq | NP_001387156.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- extracellular space
- cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369704
- Coding exons
- 18
- Length
- 101327
- Individuals with no LoFs
- 125393
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 354
- Defined
- 125748
- p
- 0.00141
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.161 | 466 | 456 | 1.02 | 0.0000247 | 5793 |
| Missense (PolyPhen) | 99 | 105.96 | 0.93434 | 1400 | ||
| Synonymous | 0.0881 | 169 | 170 | 0.991 | 0.00000915 | 1501 |
| Loss of Function | 1.53 | 41 | 53.0 | 0.773 | 0.00000286 | 646 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00075 | 0.00074 | rare |
| Latino/Admixed American | 0.0019 | 0.0019 | notable |
| Ashkenazi Jewish | 0.011 | 0.011 | notable |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00072 | 0.00071 | rare |
| South Asian | 0.0018 | 0.0018 | notable |
| Other | 0.0021 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.35
- RVIS percentile EVS
- 29.59
Essentials
- Essential (gene trap)
- N