GPBP1

gene
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Also known as DKFZp761C169

Summary

GPBP1 (GC-rich promoter binding protein 1, HGNC:29520) is a protein-coding gene on chromosome 5q11.2, encoding Vasculin (Q86WP2). Functions as a GC-rich promoter-specific transactivating transcription factor.

This gene was originally isolated by subtractive hybridization of cDNAs expressed in atherosclerotic plaques with a thrombus, and was found to be expressed only in vascular smooth muscle cells. However, a shorter splice variant was found to be more ubiquitously expressed. This protein is suggested to play a role in the development of atherosclerosis. Studies in mice suggest that it may also function as a GC-rich promoter-specific trans-activating transcription factor. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene.

Source: NCBI Gene 65056 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 71 total
  • MANE Select transcript: NM_022913

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29520
Approved symbolGPBP1
NameGC-rich promoter binding protein 1
Location5q11.2
Locus typegene with protein product
StatusApproved
AliasesDKFZp761C169
Ensembl geneENSG00000062194
Ensembl biotypeprotein_coding
OMIM608412
Entrez65056

Gene structure

Transcript identifiers

Ensembl transcripts: 53 — 49 protein_coding, 4 retained_intron

ENST00000264779, ENST00000309096, ENST00000424459, ENST00000506184, ENST00000511209, ENST00000513524, ENST00000513732, ENST00000514387, ENST00000515484, ENST00000899283, ENST00000899284, ENST00000899285, ENST00000899286, ENST00000899287, ENST00000899288, ENST00000899289, ENST00000899290, ENST00000899291, ENST00000899292, ENST00000899293, ENST00000899294, ENST00000899295, ENST00000899296, ENST00000899297, ENST00000899298, ENST00000899299, ENST00000899300, ENST00000899301, ENST00000899302, ENST00000899303, ENST00000899304, ENST00000899305, ENST00000899306, ENST00000935644, ENST00000935645, ENST00000935646, ENST00000935647, ENST00000935648, ENST00000935649, ENST00000935650, ENST00000935651, ENST00000935652, ENST00000935653, ENST00000952538, ENST00000952539, ENST00000952540, ENST00000952541, ENST00000952542, ENST00000952543, ENST00000952544, ENST00000952545, ENST00000952546, ENST00000952547

RefSeq mRNA: 5 — MANE Select: NM_022913 NM_001127235, NM_001127236, NM_001203246, NM_001331037, NM_022913

CCDS: CCDS34162, CCDS47211, CCDS47212, CCDS56368, CCDS82998

Canonical transcript exons

ENST00000506184 — 12 exons

ExonStartEnd
ENSE000012242475721407457214193
ENSE000013531065717544857176400
ENSE000015053965726118057261282
ENSE000020877935726259457264673
ENSE000021068155717405957174211
ENSE000034742235723596657236032
ENSE000034923925724630057246484
ENSE000035003375724940957249576
ENSE000035256875725095457251141
ENSE000035287205724707557247215
ENSE000035693425723084657230969
ENSE000036490505723109857231321

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 98.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.6016 / max 972.7196, expressed in 1804 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
5652425.95141795
5652110.79131611
565231.0775656
565300.8606229
565250.4919247
565270.3675155
565290.3235137
565260.2910119
565280.223571
565220.2232104

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305398.29gold quality
cardiac muscle of right atriumUBERON:000337998.08gold quality
calcaneal tendonUBERON:000370198.06gold quality
corpus callosumUBERON:000233698.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099198.04gold quality
left ventricle myocardiumUBERON:000656698.00gold quality
mucosa of paranasal sinusUBERON:000503097.93gold quality
epithelium of nasopharynxUBERON:000195197.84gold quality
nasopharynxUBERON:000172897.82gold quality
embryoUBERON:000092297.78gold quality
ganglionic eminenceUBERON:000402397.78gold quality
kidney epitheliumUBERON:000481997.61gold quality
ileal mucosaUBERON:000033197.54gold quality
myocardiumUBERON:000234997.54gold quality
spermCL:000001997.37gold quality
endothelial cellCL:000011597.34gold quality
upper arm skinUBERON:000426397.29gold quality
tendonUBERON:000004397.27gold quality
palpebral conjunctivaUBERON:000181297.27gold quality
adrenal tissueUBERON:001830397.27gold quality
tibialis anteriorUBERON:000138597.22gold quality
buccal mucosa cellCL:000233697.20gold quality
amniotic fluidUBERON:000017397.20gold quality
cartilage tissueUBERON:000241897.19gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047397.18gold quality
bronchial epithelial cellCL:000232897.13gold quality
bronchusUBERON:000218597.13gold quality
right testisUBERON:000453497.10gold quality
deltoidUBERON:000147697.05gold quality
cerebellar hemisphereUBERON:000224597.05gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-6075yes1028.83
E-GEOD-135922yes22.81
E-CURD-135no1057.55
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

141 targeting GPBP1, 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-4262100.0073.263931
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-9-3P99.9670.882068
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-539-5P99.9370.302855
HSA-MIR-22-3P99.9368.13917
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877

Literature-anchored findings (GeneRIF, showing 3)

  • This publication discusses both human and mouse GC-rich promoter binding protein. (PMID:11256614)
  • Vasculin is a novel vascular protein differentially expressed in human atherogenesis (PMID:12842993)
  • occurrence of an unusual TG 3’ splice site in intron 9 (PMID:17672918)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusGpbp1ENSMUSG00000032745
rattus_norvegicusGpbp1ENSRNOG00000013002

Paralogs (1): GPBP1L1 (ENSG00000159592)

Protein

Protein identifiers

VasculinQ86WP2 (reviewed: Q86WP2)

Alternative names: GC-rich promoter-binding protein 1, Vascular wall-linked protein

All UniProt accessions (2): Q86WP2, D4PHA4

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a GC-rich promoter-specific transactivating transcription factor.

Subunit / interactions. Interacts with GTF2B, GTF2F2, RNA polymerase II and TBP.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Widely expressed. Some isoforms may be specifically expressed in veins and arteries (at protein level). Isoform 4 is widely expressed. Isoform 1, isoform 2 and isoform 3 may be specifically expressed in vascular smooth muscle cells.

Similarity. Belongs to the vasculin family.

Isoforms (4)

UniProt IDNamesCanonical?
Q86WP2-11yes
Q86WP2-22
Q86WP2-33
Q86WP2-44

RefSeq proteins (5): NP_001120707, NP_001120708, NP_001190175, NP_001317966, NP_075064* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR028128Vasculin_famFamily

Pfam: PF15337

UniProt features (21 total): modified residue 6, compositionally biased region 5, region of interest 4, splice variant 3, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86WP2-F154.540.04

Functional residue map

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

Post-translational modifications (6): 49, 87, 274, 276, 322, 381

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): ATF_B, CREL_01, TAATAAT_MIR126, GCM_GSPT1, CREBP1_Q2, AP2_Q3, CAGCTG_AP4_Q5, SRF_Q5_01, CREB_Q4, NFKB_C, E2F1DP1_01, E2F1DP2_01, FREAC3_01, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, TGCTGAY_UNKNOWN

GO Biological Process (4): DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (4): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription2
regulation of DNA-templated transcription2
nucleic acid binding2
cellular anatomical structure2
gene expression1
RNA biosynthetic process1
regulation of gene expression1
regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
intracellular membrane-bounded organelle1
cytoplasm1
membrane1
cell periphery1
intracellular anatomical structure1

Protein interactions and networks

STRING

822 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPBP1TOP2AP11388670
GPBP1GTF2BQ00403584
GPBP1PSMC1P49014469
GPBP1SSH3Q8TE77447
GPBP1EP300Q09472411
GPBP1EAPPQ56P03401
GPBP1CCDC174Q6PII3371
GPBP1SH3D19Q5HYK7370
GPBP1DRG2P55039365
GPBP1SLC9A1P19634362
GPBP1ZCCHC4Q9H5U6356
GPBP1ARFGEF3Q5TH69353
GPBP1FAM120BQ96EK7352
GPBP1CERT1Q9Y5P4348
GPBP1ZNF730Q6ZMV8348

IntAct

75 interactions, top by confidence:

ABTypeScore
FNDC11GPBP1psi-mi:“MI:0915”(physical association)0.830
GPBP1FNDC11psi-mi:“MI:0915”(physical association)0.830
GPBP1MCRS1psi-mi:“MI:0915”(physical association)0.700
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
GPBP1PLEKHF2psi-mi:“MI:0915”(physical association)0.560
PLEKHF2GPBP1psi-mi:“MI:0915”(physical association)0.560
HSF2BPGPBP1psi-mi:“MI:0915”(physical association)0.560
CCDC57GPBP1psi-mi:“MI:0915”(physical association)0.560
GPBP1NXF1psi-mi:“MI:0915”(physical association)0.560
FAM161AGPBP1psi-mi:“MI:0915”(physical association)0.560
GPBP1PRPF18psi-mi:“MI:0915”(physical association)0.560
RACK1GPBP1psi-mi:“MI:0915”(physical association)0.560
QARS1GPBP1psi-mi:“MI:0915”(physical association)0.560
MORF4L2GPBP1psi-mi:“MI:0915”(physical association)0.560
PSMB1GPBP1psi-mi:“MI:0915”(physical association)0.560
SLX1ABACH1psi-mi:“MI:0914”(association)0.530
TPD52TPD52L2psi-mi:“MI:0914”(association)0.530
ankXGPBP1psi-mi:“MI:0915”(physical association)0.520
GPBP1ACTN3psi-mi:“MI:0915”(physical association)0.400
GPBP1PCNApsi-mi:“MI:0915”(physical association)0.370

BioGRID (100): C20orf195 (Two-hybrid), PLEKHF2 (Two-hybrid), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Affinity Capture-MS), GPBP1 (Two-hybrid), GPBP1 (Affinity Capture-MS), PKP3 (Affinity Capture-MS), PLCD1 (Affinity Capture-MS)

ESM2 similar proteins: A4FVR1, A8MQL1, F4IUY8, G5CEW6, O43024, O48772, O64768, O80386, P42775, Q0JDM0, Q0P5K1, Q0WPF2, Q14444, Q14671, Q1LZB6, Q2VB19, Q38796, Q56XU4, Q5M9G3, Q5R4E9, Q5R5X3, Q60865, Q642J5, Q66KI6, Q6K977, Q6NXH3, Q76E23, Q7XM16, Q80U78, Q86WP2, Q8IH18, Q8LPQ9, Q8RXE7, Q8RY18, Q8VY15, Q8VZS6, Q93ZJ9, Q94C33, Q94KE2, Q9C658

Diamond homologs: Q0P5K1, Q28FE5, Q3KR53, Q5R4E9, Q5R9C3, Q6DD19, Q6NXH3, Q6NZP2, Q86WP2, Q9HC44

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 47 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria5126.9×4e-08
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex5112.0×4e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways5112.0×4e-08
Activation of BH3-only proteins582.8×2e-07
RHO GTPases activate PKNs552.9×1e-06
Intrinsic Pathway for Apoptosis548.8×2e-06
SARS-CoV-1-host interactions635.1×8e-07
SARS-CoV-1 Infection628.6×2e-06

GO biological processes:

GO termPartnersFoldFDR
intracellular protein localization513.8×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance54
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2950 predictions. Top by Δscore:

VariantEffectΔscore
5:57176095:T:TAacceptor_gain1.0000
5:57230834:A:AGacceptor_gain1.0000
5:57230834:AATTT:Aacceptor_gain1.0000
5:57230835:A:Gacceptor_gain1.0000
5:57230838:T:TAacceptor_gain1.0000
5:57230842:TCAGT:Tacceptor_loss1.0000
5:57230843:CA:Cacceptor_loss1.0000
5:57230844:A:AGacceptor_gain1.0000
5:57230844:A:Cacceptor_loss1.0000
5:57230844:AGTC:Aacceptor_gain1.0000
5:57230845:G:Aacceptor_loss1.0000
5:57230845:G:GTacceptor_gain1.0000
5:57230845:GT:Gacceptor_gain1.0000
5:57230845:GTC:Gacceptor_gain1.0000
5:57230845:GTCG:Gacceptor_gain1.0000
5:57230845:GTCGT:Gacceptor_gain1.0000
5:57230966:GGAG:Gdonor_gain1.0000
5:57230967:G:GTdonor_gain1.0000
5:57230967:GAGGT:Gdonor_loss1.0000
5:57230968:AGG:Adonor_loss1.0000
5:57230969:GG:Gdonor_loss1.0000
5:57230970:GTAA:Gdonor_loss1.0000
5:57230971:T:Adonor_loss1.0000
5:57230980:C:Gdonor_gain1.0000
5:57231090:A:AGacceptor_gain1.0000
5:57231091:A:Gacceptor_gain1.0000
5:57231093:TAAA:Tacceptor_loss1.0000
5:57231096:A:ACacceptor_loss1.0000
5:57231097:G:GTacceptor_loss1.0000
5:57231311:C:Gdonor_gain1.0000

AlphaMissense

3154 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:57214158:T:AW10R1.000
5:57214158:T:CW10R1.000
5:57214146:T:CF6L0.999
5:57214148:T:AF6L0.999
5:57214148:T:GF6L0.999
5:57214160:G:CW10C0.999
5:57214160:G:TW10C0.999
5:57249505:T:CF301L0.999
5:57249506:T:CF301S0.999
5:57249507:T:AF301L0.999
5:57249507:T:GF301L0.999
5:57249509:T:CL302S0.999
5:57261185:T:CL389S0.999
5:57261239:T:CL407S0.999
5:57261262:T:CF415L0.999
5:57261263:T:CF415S0.999
5:57261264:C:AF415L0.999
5:57261264:C:GF415L0.999
5:57214162:T:CL11P0.998
5:57251131:G:CA384P0.998
5:57261180:A:CR387S0.998
5:57261180:A:TR387S0.998
5:57261182:T:CL388S0.998
5:57261199:T:AW394R0.998
5:57261199:T:CW394R0.998
5:57261201:G:CW394C0.998
5:57261201:G:TW394C0.998
5:57214159:G:CW10S0.997
5:57214162:T:AL11H0.997
5:57261200:G:CW394S0.997

dbSNP variants (sampled 300 via entrez): RS1000060323 (5:57182225 A>G), RS1000061150 (5:57228011 T>C,G), RS1000065527 (5:57198215 C>T), RS1000092109 (5:57192790 A>C,G), RS1000126922 (5:57192530 G>A), RS1000141791 (5:57214613 A>G), RS1000146094 (5:57254218 C>T), RS1000174319 (5:57177873 AT>A,ATT,ATTTTTT), RS1000176804 (5:57253843 A>G), RS1000208410 (5:57220645 A>T), RS1000213535 (5:57259711 G>A), RS1000252915 (5:57250805 A>G), RS1000303037 (5:57220304 G>A,T), RS1000303201 (5:57182578 G>T), RS1000338193 (5:57203665 A>G)

Disease associations

OMIM: gene MIM:608412 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST002934_22Zinc levels9.000000e-06
GCST007094_185Diastolic blood pressure3.000000e-08
GCST007449_1Normal facial asymmetry (angle of deformation score)8.000000e-08
GCST011155_17Nontraumatic osteonecrosis of the femoral head5.000000e-06
GCST012341_3Asparaginase hypersensitivity in acute lymphoblastic leukemia3.000000e-08

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure
EFO:0009751facial asymmetry measurement
EFO:1001930idiopathic osteonecrosis of the femoral head
EFO:0004881asparaginase hypersensitivity

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, increases oxidation3
sodium arseniteincreases expression, decreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
aflatoxin B2decreases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases oxidation, increases abundance1
K 7174increases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
jinfukangdecreases expression1
PCI 5002affects cotreatment, increases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, decreases expression, increases oxidation, increases abundance1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Coaldecreases expression, increases abundance1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Methotrexateincreases expression1
Ozoneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
Silverincreases expression1
Smokedecreases expression, increases abundance1
Testosteronedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Valproic Aciddecreases expression1

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.