FGFBP3

Summary

FGFBP3 (fibroblast growth factor binding protein 3, HGNC:23428) is a protein-coding gene on chromosome 10q23.32, encoding Fibroblast growth factor-binding protein 3 (Q8TAT2). 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 permeabili….

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.

Source: NCBI Gene 143282 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_152429

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23428
Approved symbol	FGFBP3
Name	fibroblast growth factor binding protein 3
Location	10q23.32
Locus type	gene with protein product
Status	Approved
Aliases	MGC39320
Ensembl gene	ENSG00000174721
Ensembl biotype	protein_coding
OMIM	620879
Entrez	143282

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000311575

RefSeq mRNA: 1 — MANE Select: NM_152429 NM_152429

CCDS: CCDS7418

Canonical transcript exons

ENST00000311575 — 2 exons

Exon	Start	End
ENSE00001197955	91909398	91909486
ENSE00001338095	91906584	91909047

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 98.42.

FANTOM5 (CAGE): breadth broad, TPM avg 3.9852 / max 168.0918, expressed in 344 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
110644	3.6032	342
110643	0.3820	142

Top tissues by expression

232 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	98.42	gold quality
embryo	UBERON:0000922	95.52	gold quality
ganglionic eminence	UBERON:0004023	95.52	gold quality
cortical plate	UBERON:0005343	86.21	gold quality
dorsal root ganglion	UBERON:0000044	81.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.61	silver quality
buccal mucosa cell	CL:0002336	77.06	gold quality
trigeminal ganglion	UBERON:0001675	75.00	gold quality
anterior cingulate cortex	UBERON:0009835	73.25	gold quality
amygdala	UBERON:0001876	72.98	gold quality
hypothalamus	UBERON:0001898	72.95	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	71.48	gold quality
prefrontal cortex	UBERON:0000451	71.31	gold quality
right frontal lobe	UBERON:0002810	70.10	gold quality
spinal cord	UBERON:0002240	70.05	gold quality
neocortex	UBERON:0001950	70.04	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	69.60	gold quality
nucleus accumbens	UBERON:0001882	69.32	gold quality
putamen	UBERON:0001874	69.19	gold quality
Brodmann (1909) area 9	UBERON:0013540	68.97	gold quality
cerebral cortex	UBERON:0000956	68.78	gold quality
frontal cortex	UBERON:0001870	68.52	gold quality
frontal lobe	UBERON:0016525	68.52	gold quality
forebrain	UBERON:0001890	67.87	gold quality
tibial nerve	UBERON:0001323	67.74	gold quality
caudate nucleus	UBERON:0001873	67.71	gold quality
hindlimb stylopod muscle	UBERON:0004252	67.66	gold quality
brain	UBERON:0000955	67.61	gold quality
pigmented layer of retina	UBERON:0001782	67.08	silver quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	1483.39
E-GEOD-93593	yes	1130.72
E-MTAB-10485	yes	717.07
E-MTAB-10018	yes	639.49
E-MTAB-8894	yes	629.35
E-HCAD-5	yes	43.56
E-MTAB-6524	no	258.04
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting FGFBP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-4729	99.69	72.18	4233

Literature-anchored findings (GeneRIF, showing 1)

• the FGF binding domain and the heparin binding domain are necessary for the hBP3 interaction with endogenous FGF and the activation of FGFR signaling in vivo (PMID:18669637)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fgfbp3	ENSDARG00000040162
mus_musculus	Fgfbp3	ENSMUSG00000047632
rattus_norvegicus	Fgfbp3	ENSRNOG00000022796

Paralogs (2): FGFBP1 (ENSG00000137440), FGFBP2 (ENSG00000137441)

Protein

Protein identifiers

Fibroblast growth factor-binding protein 3 — Q8TAT2 (reviewed: Q8TAT2)

All UniProt accessions (1): Q8TAT2

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Interacts with FGF2.

Subcellular location. Secreted.

Similarity. Belongs to the fibroblast growth factor-binding protein family.

RefSeq proteins (1): NP_689642* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010510	FGF1-bd	Family

Pfam: PF06473

UniProt features (10 total): disulfide bond 3, compositionally biased region 2, sequence variant 2, signal peptide 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAT2-F1	69.02	0.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 59–80, 90–124, 241–249

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-190377	FGFR2b ligand binding and activation

MSigDB gene sets: 116 (showing top): FXR_IR1_Q6, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_CIRCULATORY_SYSTEM_PROCESS, REACTOME_SIGNALING_BY_FGFR, GOBP_CELL_CELL_SIGNALING, NKX61_01, GOBP_RESPONSE_TO_FIBROBLAST_GROWTH_FACTOR, GOBP_REGULATION_OF_FIBROBLAST_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, WTGAAAT_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_POSITIVE_REGULATION_OF_VASCULAR_PERMEABILITY, GOMF_GLYCOSAMINOGLYCAN_BINDING, TATA_C, GOBP_RESPONSE_TO_GROWTH_FACTOR, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN

GO Biological Process (3): cell-cell signaling (GO:0007267), positive regulation of vascular permeability (GO:0043117), positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)

GO Molecular Function (3): heparin binding (GO:0008201), fibroblast growth factor binding (GO:0017134), growth factor binding (GO:0019838)

GO Cellular Component (2): extracellular region (GO:0005576), extracellular matrix (GO:0031012)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
FGFR2 ligand binding and activation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	1
signaling	1
regulation of vascular permeability	1
fibroblast growth factor receptor signaling pathway	1
positive regulation of signal transduction	1
regulation of fibroblast growth factor receptor signaling pathway	1
glycosaminoglycan binding	1
sulfur compound binding	1
growth factor binding	1
protein binding	1
cellular anatomical structure	1
external encapsulating structure	1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FGFBP3	ARHGEF33	A8MVX0	476
FGFBP3	HDHD3	Q9BSH5	469
FGFBP3	MDFIC2	A0A1B0GVS7	456
FGFBP3	DDAH1	O94760	444
FGFBP3	ANO4	Q32M45	436
FGFBP3	ZNF592	Q92610	433
FGFBP3	TTYH1	Q9H313	418
FGFBP3	USP31	Q70CQ4	410
FGFBP3	CDC42BPB	Q9Y5S2	410
FGFBP3	GPC1	P35052	400
FGFBP3	B4GALT3	O60512	395
FGFBP3	MPP3	Q13368	391
FGFBP3	KIF1B	O60333	387
FGFBP3	IDH3A	P50213	387
FGFBP3	SLC25A37	Q9NYZ2	386

IntAct

0 interactions, top by confidence:

BioGRID (1): FGFBP3 (PCA)

ESM2 similar proteins: A0A140LIA7, A0A1B0GTL2, A2VDX9, A3FFS8, A6NCS6, A8MVW0, K9M1U5, O43541, P01588, P03971, P03972, P07321, P07865, P0C7N4, P0DPE3, P13725, P27106, P29676, P33707, P33708, P33709, P48617, P49000, P49157, P53346, P79295, Q02011, Q0Z956, Q16619, Q1HCM0, Q28513, Q29RM6, Q5BLP8, Q5S1V9, Q60753, Q63086, Q65Z15, Q6H8S9, Q6H8T0, Q6H8T1

Diamond homologs: Q1HCM0, Q8TAT2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

54 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

85 predictions. Top by Δscore:

Variant	Effect	Δscore
10:91909391:AACTT:A	donor_loss	0.9800
10:91909392:ACTTA:A	donor_loss	0.9800
10:91909393:CTT:C	donor_loss	0.9800
10:91909394:TTAC:T	donor_loss	0.9800
10:91909395:TACCG:T	donor_loss	0.9800
10:91909396:A:AC	donor_gain	0.9800
10:91909396:ACCG:A	donor_loss	0.9800
10:91909397:C:A	donor_loss	0.9800
10:91909397:C:CC	donor_gain	0.9800
10:91909046:ACCT:A	acceptor_loss	0.9400
10:91909048:CTGCG:C	acceptor_loss	0.9400
10:91909049:T:G	acceptor_loss	0.9400
10:91909390:GAACT:G	donor_loss	0.9300
10:91909397:CCGA:C	donor_gain	0.9100
10:91908240:T:TA	donor_gain	0.9000
10:91909397:CCG:C	donor_gain	0.8900
10:91909397:CCGAG:C	donor_gain	0.8900
10:91909048:C:CC	acceptor_gain	0.8800
10:91909396:AC:A	donor_gain	0.8800
10:91909397:CC:C	donor_gain	0.8800
10:91907335:TCTC:T	acceptor_gain	0.8200
10:91909050:G:C	acceptor_loss	0.8200
10:91907334:GTCT:G	acceptor_gain	0.8100
10:91909389:TGAAC:T	donor_loss	0.7500
10:91909382:TA:T	donor_gain	0.6800
10:91908195:AG:A	donor_gain	0.6700
10:91909038:TCCCC:T	acceptor_gain	0.6700
10:91909045:GAC:G	acceptor_gain	0.6500
10:91909044:GGAC:G	acceptor_gain	0.6400
10:91907336:CTCA:C	acceptor_gain	0.6200

AlphaMissense

1631 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:91908640:C:A	W110C	0.993
10:91908640:C:G	W110C	0.993
10:91908787:C:A	W61C	0.992
10:91908787:C:G	W61C	0.992
10:91908235:C:A	W245C	0.991
10:91908235:C:G	W245C	0.991
10:91908818:A:C	F51C	0.989
10:91908224:C:G	C249S	0.983
10:91908225:A:T	C249S	0.983
10:91908224:C:T	C249Y	0.982
10:91908817:G:C	F51L	0.980
10:91908817:G:T	F51L	0.980
10:91908818:A:G	F51S	0.980
10:91908819:A:G	F51L	0.980
10:91908248:C:G	C241S	0.979
10:91908249:A:T	C241S	0.979
10:91908811:G:C	S53R	0.975
10:91908811:G:T	S53R	0.975
10:91908813:T:G	S53R	0.975
10:91908794:C:T	C59Y	0.973
10:91908566:C:G	C135S	0.972
10:91908567:A:T	C135S	0.972
10:91908599:C:G	C124S	0.972
10:91908600:A:T	C124S	0.972
10:91908237:A:G	W245R	0.971
10:91908237:A:T	W245R	0.971
10:91908248:C:T	C241Y	0.971
10:91908794:C:G	C59S	0.970
10:91908795:A:T	C59S	0.970
10:91908731:C:G	C80S	0.967

dbSNP variants (sampled 300 via entrez): RS1001369496 (10:91907533 A>AG), RS1002364309 (10:91909166 C>T), RS1002880509 (10:91910429 C>A,T), RS1003176829 (10:91907411 C>T), RS1003314074 (10:91907189 G>A,T), RS1004102542 (10:91909451 G>A,C), RS1004373586 (10:91908868 G>C), RS1004928750 (10:91910640 C>A,T), RS1005612886 (10:91907813 A>C), RS1006452497 (10:91907422 TG>T), RS1006878969 (10:91907015 A>G), RS1006927367 (10:91906588 TAC>T,TACAC), RS1007422550 (10:91906212 G>C,T), RS1008084647 (10:91909986 C>T), RS1009124043 (10:91908241 C>G,T)

Disease associations

OMIM: gene MIM:620879 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006585_505	Blood protein levels	6.000000e-28
GCST90011900_59	Serum alkaline phosphatase levels	6.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression, affects cotreatment	8
methylmercuric chloride	increases expression, affects cotreatment	4
trichostatin A	affects cotreatment, increases expression	3
entinostat	increases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	affects expression, decreases expression	2
propionaldehyde	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases response to substance, increases expression	1
jinfukang	affects cotreatment, increases expression	1
LDN 193189	increases expression, affects cotreatment	1
Vorinostat	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Thimerosal	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Cyclosporine	decreases expression	1
Gold Compounds	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.