GBP3

gene
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Also known as FLJ10961

Summary

GBP3 (guanylate binding protein 3, HGNC:4184) is a protein-coding gene on chromosome 1p22.2, encoding Guanylate-binding protein 3 (Q9H0R5). Interferon (IFN)-inducible GTPase that plays important roles in innate immunity against a diverse range of bacterial, viral and protozoan pathogens.

This gene encodes a member of the guanylate-binding protein (GBP) family. GBPs specifically bind guanine nucleotides (GMP, GDP, and GTP) and contain two of the three consensus motifs found in typical GTP-binding proteins. The encoded protein interacts with a member of the germinal center kinase family. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 2635 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 102 total
  • MANE Select transcript: NM_018284

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4184
Approved symbolGBP3
Nameguanylate binding protein 3
Location1p22.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10961
Ensembl geneENSG00000117226
Ensembl biotypeprotein_coding
OMIM600413
Entrez2635

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 9 protein_coding, 4 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000235878, ENST00000370481, ENST00000370482, ENST00000445969, ENST00000461384, ENST00000475853, ENST00000489444, ENST00000493594, ENST00000564037, ENST00000564665, ENST00000568006, ENST00000850557, ENST00000879050, ENST00000879051, ENST00000955700, ENST00000955701

RefSeq mRNA: 4 — MANE Select: NM_018284 NM_001319179, NM_001319180, NM_001319181, NM_018284

CCDS: CCDS717

Canonical transcript exons

ENST00000370481 — 11 exons

ExonStartEnd
ENSE000014528338902268489022866
ENSE000025837388900668089007852
ENSE000034583478901318589013427
ENSE000034585588901528789015414
ENSE000034843768901174789012027
ENSE000036070228900894789009140
ENSE000036244278902053289020743
ENSE000036268498901454789014656
ENSE000036308868900939289009494
ENSE000036770748901408389014279
ENSE000036775908901090489011116

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 99.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.1526 / max 811.5466, expressed in 1317 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
131365.29221224
131351.9515664
131331.8011200
131340.107851

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033199.25gold quality
ileumUBERON:000211699.17silver quality
epithelial cell of pancreasCL:000008399.12gold quality
jejunal mucosaUBERON:000039998.90gold quality
pancreatic ductal cellCL:000207998.52gold quality
palpebral conjunctivaUBERON:000181297.98gold quality
colonic mucosaUBERON:000031797.21gold quality
mucosa of sigmoid colonUBERON:000499397.04gold quality
bronchial epithelial cellCL:000232896.91gold quality
bronchusUBERON:000218596.64gold quality
epithelium of nasopharynxUBERON:000195196.61gold quality
nasopharynxUBERON:000172896.60gold quality
germinal epithelium of ovaryUBERON:000130495.88gold quality
pericardiumUBERON:000240795.67gold quality
mucosa of paranasal sinusUBERON:000503094.85gold quality
visceral pleuraUBERON:000240194.63gold quality
seminal vesicleUBERON:000099894.62gold quality
rectumUBERON:000105294.00gold quality
urethraUBERON:000005793.98gold quality
caput epididymisUBERON:000435893.90gold quality
duodenumUBERON:000211493.03gold quality
corpus epididymisUBERON:000435992.02gold quality
superficial temporal arteryUBERON:000161491.78gold quality
pylorusUBERON:000116691.64gold quality
calcaneal tendonUBERON:000370191.33gold quality
nasal cavity epitheliumUBERON:000538491.25gold quality
parietal pleuraUBERON:000240090.96gold quality
oviduct epitheliumUBERON:000480490.51gold quality
endometriumUBERON:000129590.11gold quality
small intestineUBERON:000210889.95gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-ENAD-27yes6.10
E-ANND-3yes6.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting GBP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-314899.9775.066478
HSA-MIR-211099.9666.681930
HSA-MIR-365899.9673.874379
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-651-3P99.9473.485177
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-367199.9073.043897
HSA-MIR-368699.9070.532432
HSA-MIR-17-5P99.8973.832665
HSA-MIR-990299.8969.152250
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-137-3P99.8774.742401
HSA-MIR-612499.8769.783551
HSA-MIR-94499.8270.853042
HSA-MIR-323A-3P99.7970.301739
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-4668-5P99.7970.583782

Literature-anchored findings (GeneRIF, showing 5)

  • Data show that the novel splice variant of guanylate binding protein 3 hGBP-3, named hGBP-3DeltaC, showed the most prominent antiviral activity in epithelial cells. (PMID:22106366)
  • GBP3 over-expression promotes glioma growth in mice and is inversely correlated with patients survival rate. (PMID:29128363)
  • GBP3 promotes glioblastoma resistance to temozolomide by enhancing DNA damage repair. (PMID:35780181)
  • The function of guanylate binding protein 3 (GBP3) in human cancers by pan-cancer bioinformatics. (PMID:37161254)
  • Helical domain of hGBP3 cannot stimulate the second phosphate cleavage of GTP. (PMID:38301888)

Cross-species orthologs

1 orthologs

OrganismSymbolGene ID
drosophila_melanogasteratlFBGN0039213

Paralogs (10): GBP1 (ENSG00000117228), ATL2 (ENSG00000119787), RNF112 (ENSG00000128482), GBP5 (ENSG00000154451), GBP2 (ENSG00000162645), GBP4 (ENSG00000162654), GBP6 (ENSG00000183347), ATL3 (ENSG00000184743), ATL1 (ENSG00000198513), GBP7 (ENSG00000213512)

Protein

Protein identifiers

Guanylate-binding protein 3Q9H0R5 (reviewed: Q9H0R5)

Alternative names: GTP-binding protein 3, Guanine nucleotide-binding protein 3

All UniProt accessions (8): Q9H0R5, F6SPX6, F6X827, H3BNS1, H3BP53, H3BPH2, H3BRX6, Q5T8M0

UniProt curated annotations — full annotation on UniProt →

Function. Interferon (IFN)-inducible GTPase that plays important roles in innate immunity against a diverse range of bacterial, viral and protozoan pathogens. Hydrolyzes GTP very efficiently; GDP rather than GMP is the major reaction product. Following infection, recruited to the pathogen-containing vacuoles or vacuole-escaped bacteria and acts as a positive regulator of inflammasome assembly by promoting the release of inflammasome ligands from bacteria. Acts by promoting lysis of pathogen-containing vacuoles, releasing pathogens into the cytosol. Following pathogen release in the cytosol, promotes recruitment of proteins that mediate bacterial cytolysis: this liberates ligands that are detected by inflammasomes, such as lipopolysaccharide (LPS) that activates the non-canonical CASP4/CASP11 inflammasome or double-stranded DNA (dsDNA) that activates the AIM2 inflammasome. Exhibits antiviral activity against influenza virus. Shows the most prominent antiviral activity in epithelial cells.

Subunit / interactions. Heterodimer with other family members, including GBP1, GBP2 and GBP5. Dimerization regulates subcellular location.

Subcellular location. Cytoplasm. Perinuclear region. Golgi apparatus membrane.

Similarity. Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3 GTPase family. GB1 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H0R5-11yes
Q9H0R5-42, GBP-3DeltaC

RefSeq proteins (4): NP_001306108, NP_001306109, NP_001306110, NP_060754* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003191Guanylate-bd/ATL_CDomain
IPR015894Guanylate-bd_NDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR030386G_GB1_RHD3_domDomain
IPR036543Guanylate-bd_C_sfHomologous_superfamily
IPR037684GBP_CDomain

Pfam: PF02263, PF02841

Catalyzed reactions (Rhea), 1 shown:

  • GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (19 total): sequence variant 6, sequence conflict 3, binding site 3, splice variant 2, chain 1, domain 1, mutagenesis site 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0R5-F188.430.57

Functional residue map

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

Ligand- & substrate-binding residues (3): 45–52; 67–69; 97–101

Mutagenesis-validated functional residues (1):

PositionPhenotype
105promotes ubiquitination and degradation by s. flexneri ipah9.8.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-877300Interferon gamma signaling
R-HSA-9948001CASP4 inflammasome assembly
R-HSA-9953170GBP-mediated host defense
R-HSA-9956593Enterobacterial factors antagonize host defense

MSigDB gene sets: 144 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, ROZANOV_MMP14_TARGETS_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_RESPONSE_TO_INTERLEUKIN_1, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_RESPONSE_TO_LIPID, GOBP_DEFENSE_RESPONSE_TO_VIRUS

GO Biological Process (10): defense response to bacterium (GO:0042742), defense response to virus (GO:0051607), cytolysis in another organism (GO:0051715), cellular response to lipopolysaccharide (GO:0071222), cellular response to type II interferon (GO:0071346), cellular response to interleukin-1 (GO:0071347), cellular response to tumor necrosis factor (GO:0071356), positive regulation of pyroptotic inflammatory response (GO:0140639), immune system process (GO:0002376), innate immune response (GO:0045087)

GO Molecular Function (7): GTPase activity (GO:0003924), GTP binding (GO:0005525), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (7): Golgi membrane (GO:0000139), cytoplasm (GO:0005737), cytosol (GO:0005829), cytoplasmic vesicle (GO:0031410), perinuclear region of cytoplasm (GO:0048471), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Interferon Signaling1
Non-canonical inflammasome activation1
Antimicrobial mechanism of IFN-stimulated genes1
Infection with Enterobacteria1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoplasm4
cellular response to cytokine stimulus3
defense response2
response to bacterium1
response to virus1
cytolysis1
killing of cells of another organism1
response to lipopolysaccharide1
cellular response to molecule of bacterial origin1
cellular response to lipid1
cellular response to oxygen-containing compound1
response to type II interferon1
response to interleukin-11
response to tumor necrosis factor1
positive regulation of inflammatory response1
pyroptotic inflammatory response1
biological_process1
immune response1
defense response to symbiont1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
protein binding1
identical protein binding1
protein dimerization activity1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
catalytic activity1
Golgi apparatus1
bounding membrane of organelle1
intracellular anatomical structure1
intracellular vesicle1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

698 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GBP3ISG15P05161611
GBP3IFNGP01579586
GBP3IRGMA1A4Y4586
GBP3IRF9Q00978572
GBP3IFI44Q8TCB0551
GBP3IL1BP01584535
GBP3RTP4Q96DX8513
GBP3MAP4K4O95819504
GBP3TNFP01375482
GBP3CMPK2Q5EBM0476
GBP3IFIT3O14879474
GBP3GBP2P32456465
GBP3PYHIN1Q6K0P9462
GBP3IFIT1P09914446
GBP3IRF1P10914435
GBP3HERC6Q8IVU3435

IntAct

23 interactions, top by confidence:

ABTypeScore
GBP1GBP3psi-mi:“MI:0915”(physical association)0.790
GBP1GBP2psi-mi:“MI:0914”(association)0.720
GBP2GBP3psi-mi:“MI:0915”(physical association)0.720
GBP3MAP4K4psi-mi:“MI:0915”(physical association)0.590
GBP3MAP4K4psi-mi:“MI:0407”(direct interaction)0.590
MAP4K4GBP3psi-mi:“MI:0915”(physical association)0.590
GBP3GBP3psi-mi:“MI:0915”(physical association)0.510
GBP5GBP3psi-mi:“MI:0915”(physical association)0.510
GBP3S100A10psi-mi:“MI:0915”(physical association)0.400
H1-2GBP3psi-mi:“MI:0915”(physical association)0.400
GBP2HSP90AA1psi-mi:“MI:0914”(association)0.350
GBP3ACTL6Bpsi-mi:“MI:0914”(association)0.350
GBP3tktApsi-mi:“MI:0915”(physical association)0.000

BioGRID (16): GBP3 (Affinity Capture-MS), GBP3 (Affinity Capture-MS), GBP3 (Affinity Capture-MS), GBP3 (Proximity Label-MS), GBP3 (Proximity Label-MS), GBP3 (Reconstituted Complex), MAP4K4 (Affinity Capture-Western), MAP4K4 (Two-hybrid), GBP3 (Affinity Capture-MS), GBP3 (Affinity Capture-MS), GBP2 (Affinity Capture-MS), ACTL6B (Affinity Capture-MS), DECR2 (Affinity Capture-MS), CASP6 (Affinity Capture-MS), GBP3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0G2JDV3, A0MWD1, A1E2I4, A4UUI3, A6QQL3, A7VK00, B0BNF1, B0KWP7, B1H120, B1MTN8, B2KIE9, B3GNI6, B5FW69, P20591, P20592, P32455, P32456, Q01514, Q0VCP4, Q14141, Q1MT80, Q28379, Q2KTC2, Q3SZN0, Q4R555, Q5D1D6, Q5I2P5, Q5R5G3, Q5R9T9, Q5RBE1, Q61107, Q63663, Q642H3, Q6AXA6, Q6IRQ5, Q6ZN66, Q6ZU15, Q8C1B7, Q8C650, Q8CFB4

Diamond homologs: A0A0G2JDV3, A4UUI3, P32455, P32456, Q01514, Q1MT80, Q5D1D6, Q5R9T9, Q5RBE1, Q61107, Q63663, Q6ZN66, Q8CFB4, Q8N8V2, Q91Z40, Q96PP8, Q96PP9, Q9H0R5, Q9Z0E6, A0E2L1, B6K0N7, P0CQ46, P0CQ47, A5DB26, Q4PEQ0, Q525S7, Q9UTE0, A0A386CAB9, Q9P5X6, C4JQN4, Q6BK59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance77
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1738 predictions. Top by Δscore:

VariantEffectΔscore
1:89008942:GATAC:Gdonor_loss1.0000
1:89008943:ATAC:Adonor_loss1.0000
1:89008945:ACC:Adonor_loss1.0000
1:89008946:C:CTdonor_loss1.0000
1:89009136:TTCCA:Tacceptor_gain1.0000
1:89009137:TCCA:Tacceptor_gain1.0000
1:89009138:CCA:Cacceptor_gain1.0000
1:89009138:CCAC:Cacceptor_gain1.0000
1:89009139:CA:Cacceptor_gain1.0000
1:89009139:CAC:Cacceptor_gain1.0000
1:89009140:ACT:Aacceptor_loss1.0000
1:89009141:C:CAacceptor_loss1.0000
1:89009141:C:CCacceptor_gain1.0000
1:89009143:G:GCacceptor_gain1.0000
1:89009496:T:Cacceptor_gain1.0000
1:89009504:C:CTacceptor_gain1.0000
1:89009504:C:Tacceptor_gain1.0000
1:89009505:A:Tacceptor_gain1.0000
1:89011778:T:TAdonor_gain1.0000
1:89013183:A:ACdonor_gain1.0000
1:89013184:C:CCdonor_gain1.0000
1:89013184:CGAGG:Cdonor_gain1.0000
1:89013207:T:TAdonor_gain1.0000
1:89013262:A:ACdonor_gain1.0000
1:89013263:C:CCdonor_gain1.0000
1:89014118:T:Cdonor_gain1.0000
1:89014561:AG:Adonor_gain1.0000
1:89014653:CACC:Cacceptor_gain1.0000
1:89014655:CC:Cacceptor_gain1.0000
1:89014656:CC:Cacceptor_gain1.0000

AlphaMissense

3929 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:89014606:G:CS123R0.970
1:89014606:G:TS123R0.970
1:89014608:T:GS123R0.970
1:89015410:G:CF65L0.961
1:89015410:G:TF65L0.961
1:89015412:A:GF65L0.961
1:89014603:G:CS124R0.957
1:89014603:G:TS124R0.957
1:89014605:T:GS124R0.957
1:89014176:A:GW178R0.953
1:89014176:A:TW178R0.953
1:89013273:A:CF260L0.947
1:89013273:A:TF260L0.947
1:89013275:A:GF260L0.947
1:89011812:C:GA362P0.941
1:89013369:G:CF228L0.941
1:89013369:G:TF228L0.941
1:89013371:A:GF228L0.941
1:89015324:A:TV94D0.940
1:89013351:A:CF234L0.939
1:89013351:A:TF234L0.939
1:89013353:A:GF234L0.939
1:89011911:C:GA329P0.935
1:89020570:T:AK51I0.920
1:89011783:G:CF371L0.915
1:89011783:G:TF371L0.915
1:89011785:A:GF371L0.915
1:89013219:T:AK278N0.904
1:89013219:T:GK278N0.904
1:89011027:G:CF413L0.902

dbSNP variants (sampled 300 via entrez): RS1000386063 (1:89013076 G>A,T), RS1000464213 (1:89011257 T>TA), RS1000565183 (1:89018870 T>C), RS1000733588 (1:89009944 C>A,G), RS1000766409 (1:89010163 C>G), RS1000771786 (1:89012439 C>A,G), RS1000816677 (1:89024713 A>T), RS1000892266 (1:89024780 C>A), RS1000961892 (1:89018620 A>C,G), RS1001078426 (1:89018832 G>T), RS1001204536 (1:89021841 G>A), RS1001340368 (1:89022088 T>C), RS1001453925 (1:89015476 G>A), RS1001512438 (1:89008004 T>C), RS1001654993 (1:89012994 T>C)

Disease associations

OMIM: gene MIM:600413 | 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):

StudyTraitp-value
GCST003114_9Carotid intima media thickness2.000000e-06
GCST012490_650Femur bone mineral density x serum urate levels interaction6.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, increases methylation4
sodium arseniteincreases abundance, increases expression, decreases expression2
Acetaminophendecreases expression, increases expression2
Air Pollutantsdecreases expression, increases abundance2
Arsenicaffects methylation, decreases expression, increases abundance2
Nickeldecreases expression, increases expression2
Smokedecreases expression, increases abundance2
Tetrachlorodibenzodioxinincreases expression2
Tretinoinincreases expression2
fulvic acidaffects cotreatment, decreases reaction, increases expression1
triphenyl phosphateaffects expression1
hydroxyhydroquinoneincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
entinostatincreases expression1
beta-hydroxy simvastatin aciddecreases expression1
abrinedecreases expression1
BIX 01294increases expression, increases reaction1
(+)-JQ1 compounddecreases expression1
Calcimycinaffects cotreatment, decreases reaction, increases expression1
Air Pollutants, Occupationaldecreases expression1
Calcitriolincreases expression, affects cotreatment1
Citrullineincreases expression1
Doxorubicindecreases expression1
Drugs, Chinese Herbalincreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2MWAbcam A-549 GBP3 KOCancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.