FBF1
protein-codingFas binding factor 1
Gene summary
Involved in apical junction assembly and establishment of epithelial cell polarity. Acts upstream of or within cilium assembly. Located in apical junction complex and cytoskeleton. Part of ciliary transition fiber. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.6 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 FBF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001319193.2. 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 | 4 | 1 | 5 | |||
| missense | 23 | 4 | 27 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 0 | 38 | 5 | 0 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001306122.1 | 29 | MANE Select | |
| Ensembl | ENSP00000490726.1 | 29 | MANE Select | |
| Ensembl | ENSP00000324292.7 | 25 | Standard | |
| Ensembl | ENSP00000475294.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Anchoring of the basal body to the plasma membrane
- Cilium Assembly
- Organelle biogenesis and maintenance
Biological Process
- apical junction assembly
- cilium assembly
- establishment of epithelial cell polarity
- ciliary basal body-plasma membrane docking
Molecular Function
- protein binding
Cellular Component
- spindle pole
- centrosome
- centriole
- cytosol
- apical junction complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000319129
- Coding exons
- 28
- Length
- 31567
- Individuals with no LoFs
- 124555
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 116
- Defined
- 124671
- p
- 0.000465
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 604 | 682 | 0.886 | 0.0000447 | 7186 |
| Missense (PolyPhen) | 148 | 160.93 | 0.91963 | 1800 | ||
| Synonymous | 0.690 | 262 | 277 | 0.947 | 0.0000175 | 2292 |
| Loss of Function | 2.37 | 41 | 61.0 | 0.672 | 0.00000297 | 693 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00094 | 0.00090 | rare |
| Latino/Admixed American | 0.00045 | 0.00041 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0013 | 0.0012 | notable |
| Finnish | 0.000093 | 0.000093 | rare |
| European (Non-Finnish) | 0.00047 | 0.00044 | rare |
| South Asian | 0.00040 | 0.00039 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Keratin-binding protein required for epithelial cell polarization. Involved in apical junction complex (AJC) assembly via its interaction with PARD3. Required for ciliogenesis. {ECO:0000269|PubMed:18838552, ECO:0000269|PubMed:23348840}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.992
- RVIS EVS
- -0.69
- RVIS percentile EVS
- 14.84
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.569