FGFBP3
protein-codingfibroblast growth factor binding protein 3
Gene summary
Enables fibroblast growth factor binding activity and heparin binding activity. Acts upstream of or within positive regulation of fibroblast growth factor receptor signaling pathway and positive regulation of vascular permeability. Located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
- C10orf13
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.9 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 FGFBP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152429.5. 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 | 59 | 1 | 60 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 59 | 1 | 0 | 60 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689642.3 | 1 | MANE Select | |
| Ensembl | ENSP00000339067.3 | 1 | MANE Select | |
| Ensembl | ENSP00000807769.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- FGFR2b ligand binding and activation
- FGFR2 ligand binding and activation
- Signaling by FGFR2
- Signal Transduction
- Signaling by FGFR
Biological Process
- cell-cell signaling
- positive regulation of vascular permeability
- positive regulation of fibroblast growth factor receptor signaling pathway
Molecular Function
- heparin binding
- fibroblast growth factor binding
Cellular Component
- extracellular region
- collagen-containing extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000311575
- Coding exons
- 1
- Length
- 2895
- Individuals with no LoFs
- 118258
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 118262
- p
- 0.0000169
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.662 | 119 | 100 | 1.19 | 0.00000466 | 1566 |
| Missense (PolyPhen) | 28 | 25.805 | 1.085 | 473 | ||
| Synonymous | -0.424 | 52 | 48.3 | 1.08 | 0.00000246 | 585 |
| Loss of Function | -0.335 | 4 | 3.34 | 1.20 | 1.42e-7 | 61 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000038 | 0.000032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000029 | 0.000028 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Heparin-binding protein which binds to FGF2, prevents binding of FGF2 to heparin and probably inhibits immobilization of FGF2 on extracellular matrix glycosaminoglycans, allowing its release and subsequent activation of FGFR signaling which leads to increased vascular permeability. {ECO:0000269|PubMed:18669637}.;
Recessive Scores
- pRec
- 0.0930
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0155
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |