PBX2

gene
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Also known as G17HOX12PBX2MHC

Summary

PBX2 (PBX homeobox 2, HGNC:8633) is a protein-coding gene on chromosome 6p21.32, encoding Pre-B-cell leukemia transcription factor 2 (P40425). Transcriptional activator that binds the sequence 5’-ATCAATCAA-3'.

This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias. This protein is a transcriptional activator which binds to the TLX1 promoter. The gene is located within the major histocompatibility complex (MHC) on chromosome 6.

Source: NCBI Gene 5089 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 59 total
  • MANE Select transcript: NM_002586

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8633
Approved symbolPBX2
NamePBX homeobox 2
Location6p21.32
Locus typegene with protein product
StatusApproved
AliasesG17, HOX12, PBX2MHC
Ensembl geneENSG00000204304
Ensembl biotypeprotein_coding
OMIM176311
Entrez5089

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 retained_intron, 1 protein_coding

ENST00000375050, ENST00000478678, ENST00000480254, ENST00000495300, ENST00000496171

RefSeq mRNA: 1 — MANE Select: NM_002586 NM_002586

CCDS: CCDS4748

Canonical transcript exons

ENST00000375050 — 9 exons

ExonStartEnd
ENSE000013486443218473332186474
ENSE000016355563218969532190202
ENSE000017398093218660432186690
ENSE000017596103218681332186901
ENSE000017955413218724232187395
ENSE000035302373218764732187782
ENSE000035321543218872332188796
ENSE000035393923218796632188156
ENSE000035857753218825732188504

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.3840 / max 126.8765, expressed in 1787 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
7292115.38401787
729220.178161
729230.130237
729240.069820

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of thyroid glandUBERON:000111998.14gold quality
left lobe of thyroid glandUBERON:000112097.99gold quality
granulocyteCL:000009497.98gold quality
thyroid glandUBERON:000204697.88gold quality
right ovaryUBERON:000211897.60gold quality
spleenUBERON:000210697.58gold quality
body of uterusUBERON:000985397.56gold quality
pituitary glandUBERON:000000797.49gold quality
left ovaryUBERON:000211997.46gold quality
ovaryUBERON:000099297.29gold quality
adenohypophysisUBERON:000219697.26gold quality
left uterine tubeUBERON:000130397.25gold quality
bloodUBERON:000017897.19gold quality
right uterine tubeUBERON:000130297.15gold quality
right adrenal gland cortexUBERON:003582796.96gold quality
right adrenal glandUBERON:000123396.92gold quality
metanephros cortexUBERON:001053396.87gold quality
endocervixUBERON:000045896.81gold quality
myometriumUBERON:000129696.79gold quality
vermiform appendixUBERON:000115496.77gold quality
placentaUBERON:000198796.70gold quality
lymph nodeUBERON:000002996.69gold quality
muscle layer of sigmoid colonUBERON:003580596.69gold quality
fundus of stomachUBERON:000116096.67gold quality
fallopian tubeUBERON:000388996.63gold quality
gall bladderUBERON:000211096.52gold quality
esophagogastric junction muscularis propriaUBERON:003584196.44gold quality
left adrenal gland cortexUBERON:003582596.37gold quality
prostate glandUBERON:000236796.31gold quality
left adrenal glandUBERON:000123496.26gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-6911no10.40
E-ANND-3no1.24

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1113.1PBX2TALE-type homeo domain factors
MA1113.2PBX2TALE-type homeo domain factors
MA1113.3PBX2TALE-type homeo domain factors

JASPAR matrix evidence (PMIDs): PMID:10082572, PMID:12054735

miRNA regulators (miRDB)

179 targeting PBX2, 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-6867-5P100.0082.213464
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-450099.9972.722367
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-6870-5P99.9968.552115
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-60799.9773.625593
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-LET-7D-5P99.9671.761632

Literature-anchored findings (GeneRIF, showing 11)

  • a PBX2 Regulatory Element PRE-1048 has been identified which contains a novel DNA-binding sequence and mediates significant activation of the HOX11 gene in K562 cells. (PMID:12054735)
  • these studies demonstrate that the homeodomain proteins, MEIS1, PBX1B, and PBX2, play an important role in megakaryocytic gene expression. (PMID:12609849)
  • PBX2 increases in F9 teratocarcinoma cells because PREP-1 prevents its degradation (PMID:12871956)
  • PBX2 expression pattern is similar to HOXA7 expression in ovarian follicular development (PMID:18973687)
  • Expression levels of PBX2 and VCP were immunohistochemically examined and compared with each other in 206 non-small cell lung cancer cases (PMID:19356220)
  • Pre B cell leukemia homeobox 2 has a role in poor prognosis of gastric adenocarcinoma and esophageal squamous cell carcinoma (PMID:20126986)
  • a high level of PBX2 is a poor prognosticator for disease-free survival and overall survival in gingival squamous cell carcinoma (PMID:22374608)
  • findings suggest the disruption of the HOXB7/PBX2 complexes, miR-221&222 inhibition or even better their combination, as innovative therapeutic approaches (PMID:23400877)
  • miR19153p functions as a silencer of apoptosis, which regulates lung cancer apoptosis via targeting DRG2/PBX2. (PMID:26572100)
  • The findings from the present study that a SNP of the PBX2 gene in the MHC region (at 6p21.3) was associated with allergic rhinitis (AR) in allele and genotypic analysis suggests a new susceptibility gene for AR in the MHC region and another gene associated with both asthma and AR in Chinese subjects. (PMID:26852910)
  • Coexpression of HOXA6 and PBX2 promotes metastasis in gastric cancer. (PMID:33535170)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
mus_musculusPbx2ENSMUSG00000034673
rattus_norvegicusPbx2ENSRNOG00000000440
drosophila_melanogasterexdFBGN0000611
drosophila_melanogasterhthFBGN0001235
drosophila_melanogastervisFBGN0033748
drosophila_melanogasterachiFBGN0033749
caenorhabditis_elegansWBGENE00000443
caenorhabditis_elegansWBGENE00006796
caenorhabditis_elegansWBGENE00017690

Paralogs (13): MEIS3 (ENSG00000105419), PBX4 (ENSG00000105717), TGIF2 (ENSG00000118707), MEIS2 (ENSG00000134138), MEIS1 (ENSG00000143995), TGIF2LX (ENSG00000153779), PKNOX1 (ENSG00000160199), PKNOX2 (ENSG00000165495), PBX3 (ENSG00000167081), TGIF2LY (ENSG00000176679), TGIF1 (ENSG00000177426), PBX1 (ENSG00000185630), MEIS3P2 (ENSG00000188013)

Protein

Protein identifiers

Pre-B-cell leukemia transcription factor 2P40425 (reviewed: P40425)

Alternative names: Homeobox protein PBX2, Protein G17

All UniProt accessions (2): A0A024RCR3, P40425

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional activator that binds the sequence 5’-ATCAATCAA-3’. Activates transcription of PF4 in complex with MEIS1.

Subunit / interactions. Forms heterodimers with MEIS1 and heterotrimers with MEIS1 and HOXA9. Interacts with PBXIP1.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the TALE/PBX homeobox family.

RefSeq proteins (1): NP_002577* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR005542PBX_PBC_domDomain
IPR008422KN_HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR050224TALE_homeoboxFamily

Pfam: PF03792, PF05920

UniProt features (17 total): modified residue 5, region of interest 5, compositionally biased region 3, chain 1, domain 1, sequence conflict 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P40425-F171.300.32

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 (5): 136, 151, 159, 330, 395

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 267 (showing top): HOFMANN_CELL_LYMPHOMA_UP, SP3_Q3, RIZ_ERYTHROID_DIFFERENTIATION_CCNE1, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_NEUROGENESIS, HNF1_Q6, BOYLAN_MULTIPLE_MYELOMA_D_DN, GOBP_PROXIMAL_DISTAL_PATTERN_FORMATION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN, GOBP_APPENDAGE_DEVELOPMENT, GOBP_HEAD_DEVELOPMENT, HNF1_C, TGGNNNNNNKCCAR_UNKNOWN

GO Biological Process (9): eye development (GO:0001654), brain development (GO:0007420), animal organ morphogenesis (GO:0009887), proximal/distal pattern formation (GO:0009954), embryonic limb morphogenesis (GO:0030326), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic organ development (GO:0048568), neuron development (GO:0048666), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (8): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), chromatin binding (GO:0003682), DNA-binding transcription factor binding (GO:0140297), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), transcription regulator complex (GO:0005667)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
animal organ development3
regulation of transcription by RNA polymerase II2
transcription cis-regulatory region binding2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
binding2
sensory organ development1
visual system development1
central nervous system development1
head development1
anatomical structure morphogenesis1
regionalization1
limb morphogenesis1
embryonic appendage morphogenesis1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
embryo development1
neuron differentiation1
cell development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
transcription factor binding1
nucleic acid binding1
regulation of DNA-templated transcription1
transcription regulator activity1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1
protein-containing complex1

Protein interactions and networks

STRING

998 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PBX2PKNOX1P55347808
PBX2AGPAT1Q99943805
PBX2HOXA10P31260795
PBX2SLC38A2Q96QD8760
PBX2HOXB7P09629749
PBX2NOTCH4Q99466738
PBX2SLC38A1Q9H2H9719
PBX2HOXA9P31269687
PBX2CREBBPQ92793665
PBX2MEIS3Q99687646
PBX2MEIS2O14770614
PBX2AGERQ15109597
PBX2AGPAT2O15120588
PBX2TLX1P31314533
PBX2EMX2Q04743524

IntAct

150 interactions, top by confidence:

ABTypeScore
STK25STRNpsi-mi:“MI:0914”(association)0.900
PKNOX1PBX2psi-mi:“MI:0915”(physical association)0.740
PBX2PKNOX1psi-mi:“MI:0915”(physical association)0.740
AFF4ELL2psi-mi:“MI:0914”(association)0.730
MEIS2PBX1psi-mi:“MI:0914”(association)0.660
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
PBX2RIPPLY2psi-mi:“MI:0915”(physical association)0.630
RIPPLY2PBX2psi-mi:“MI:0915”(physical association)0.630
MAB21L1PBX2psi-mi:“MI:0915”(physical association)0.620
PBX2HOXA1psi-mi:“MI:0915”(physical association)0.560
PBX2CARD9psi-mi:“MI:0915”(physical association)0.560
CARD9PBX2psi-mi:“MI:0915”(physical association)0.560
HOXC8PBX2psi-mi:“MI:0915”(physical association)0.560
PBX2PPFIBP1psi-mi:“MI:0915”(physical association)0.560
HOXB5PBX2psi-mi:“MI:0915”(physical association)0.560
PBX2FAM90A1psi-mi:“MI:0915”(physical association)0.560
PBX2BFSP2psi-mi:“MI:0915”(physical association)0.560
PBX2EFHC1psi-mi:“MI:0915”(physical association)0.560
HOXC9PBX2psi-mi:“MI:0915”(physical association)0.560
PBX2HOXC5psi-mi:“MI:0915”(physical association)0.560
PBX2BRMS1Lpsi-mi:“MI:0915”(physical association)0.560

BioGRID (100): PBX2 (Two-hybrid), CARD9 (Two-hybrid), PBX2 (Affinity Capture-RNA), PBX2 (Affinity Capture-RNA), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX2 (Affinity Capture-MS)

ESM2 similar proteins: A3KMR8, A7Z017, B3DM47, B4R090, D3ZNT6, O35317, O35984, O42290, O57342, O75030, O75444, P10083, P23091, P25932, P40424, P40425, P40426, P41778, P54841, P54842, P54843, P54844, P56224, P57102, P61295, P61296, P79745, P79746, Q05192, Q0V9K1, Q27350, Q2PFS4, Q32NP8, Q4U1U2, Q504L8, Q61039, Q6DE84, Q6PFG8, Q789F3, Q7RTU3

Diamond homologs: A1YER0, A2D5H2, A6NDR6, A8K0S8, A8WL06, B3DM47, B4F6V6, O00470, O04134, O04135, O14770, O17894, O22299, O35317, O35984, O42406, O46339, O65034, O73916, O80416, O93307, O95343, O95475, P10842, P24345, P40424, P40425, P40426, P40427, P41778, P41779, P41817, P46608, P46609, P46639, P46640, P48731, P53147, P56661, P56662

SIGNOR signaling

4 interactions.

AEffectBMechanism
PBX2“up-regulates quantity by expression”EMX2“transcriptional regulation”
PBXIP1“down-regulates activity”PBX2binding
PBX2“down-regulates quantity by repression”FGF8“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 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.

GO biological processes:

GO termPartnersFoldFDR
eye development831.2×1e-07
anatomical structure morphogenesis913.9×5e-06
anterior/posterior pattern specification612.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1410 predictions. Top by Δscore:

VariantEffectΔscore
6:32187286:C:CAdonor_gain1.0000
6:32187300:CA:Cdonor_gain1.0000
6:32187300:CACGG:Cdonor_gain1.0000
6:32187331:T:TAdonor_gain1.0000
6:32187345:T:Adonor_gain1.0000
6:32187391:GAGAC:Gacceptor_gain1.0000
6:32187393:GAC:Gacceptor_gain1.0000
6:32187394:AC:Aacceptor_gain1.0000
6:32187395:CC:Cacceptor_gain1.0000
6:32187396:C:CCacceptor_gain1.0000
6:32187643:ATACC:Adonor_loss1.0000
6:32187644:TAC:Tdonor_loss1.0000
6:32187645:ACCTG:Adonor_loss1.0000
6:32187646:C:CTdonor_loss1.0000
6:32187780:CGT:Cacceptor_gain1.0000
6:32187783:C:CCacceptor_gain1.0000
6:32187960:GCCCA:Gdonor_loss1.0000
6:32187961:CCCA:Cdonor_loss1.0000
6:32187962:CCAC:Cdonor_loss1.0000
6:32187963:CACCT:Cdonor_loss1.0000
6:32187965:C:CTdonor_loss1.0000
6:32188152:CATGC:Cacceptor_gain1.0000
6:32188253:TTACC:Tdonor_loss1.0000
6:32188255:A:ACdonor_gain1.0000
6:32188256:C:CCdonor_gain1.0000
6:32188256:CCTG:Cdonor_gain1.0000
6:32188526:T:Cacceptor_gain1.0000
6:32186409:C:CAdonor_gain0.9900
6:32187297:TGA:Tdonor_gain0.9900
6:32187299:A:ACdonor_gain0.9900

AlphaMissense

2808 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:32187329:C:GA313P1.000
6:32187351:G:CN305K1.000
6:32187351:G:TN305K1.000
6:32187354:T:AK304N1.000
6:32187354:T:GK304N1.000
6:32187355:T:AK304I1.000
6:32187355:T:GK304T1.000
6:32187356:T:CK304E1.000
6:32187357:C:AK303N1.000
6:32187357:C:GK303N1.000
6:32187358:T:AK303M1.000
6:32187358:T:GK303T1.000
6:32187359:T:CK303E1.000
6:32187361:T:CY302C1.000
6:32187361:T:GY302S1.000
6:32187362:A:CY302D1.000
6:32187362:A:GY302H1.000
6:32187362:A:TY302N1.000
6:32187364:C:GR301P1.000
6:32187364:C:TR301H1.000
6:32187365:G:AR301C1.000
6:32187365:G:CR301G1.000
6:32187365:G:TR301S1.000
6:32187367:A:CI300S1.000
6:32187367:A:GI300T1.000
6:32187367:A:TI300N1.000
6:32187369:C:AR299S1.000
6:32187369:C:GR299S1.000
6:32187370:C:AR299M1.000
6:32187370:C:GR299T1.000

dbSNP variants (sampled 300 via entrez): RS1000 (6:32186118 T>C), RS1000286697 (6:32184644 C>A), RS1000337149 (6:32184909 C>T), RS1001 (6:32186196 A>G), RS1001508058 (6:32184697 G>A), RS1001796081 (6:32190465 C>G,T), RS1002 (6:32186240 G>A,C), RS1002013736 (6:32189033 C>T), RS1002210751 (6:32190532 A>G), RS1003229811 (6:32187462 G>A), RS1003586041 (6:32191890 G>A), RS1003637966 (6:32187178 T>C), RS1004095 (6:32185632 A>C), RS1004674647 (6:32190731 C>T), RS1005024340 (6:32190344 G>A)

Disease associations

OMIM: gene MIM:176311 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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
Valproic Acidaffects expression, affects cotreatment, increases expression, decreases expression7
Acetaminophendecreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
coumarindecreases phosphorylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
belinostatdecreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
Panobinostataffects cotreatment, affects expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Caffeineincreases phosphorylation1
Carmustinedecreases expression1
Cisplatinaffects expression, affects cotreatment1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Flavonoidsincreases expression1
Hydralazineaffects cotreatment, increases expression1
Methotrexatedecreases expression1
Methyl Methanesulfonatedecreases expression1
Niclosamideincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_GZ92K562 eGFP-PBX2Cancer cell lineFemale

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.