PBX4

gene
On this page

Summary

PBX4 (PBX homeobox 4, HGNC:13403) is a protein-coding gene on chromosome 19p13.11, encoding Pre-B-cell leukemia transcription factor 4 (Q9BYU1).

This gene encodes a member of the pre-B cell leukemia transcription factor family. These proteins are homeobox proteins that play critical roles in embryonic development and cellular differentiation both as Hox cofactors and through Hox-independent pathways. The encoded protein contains a homeobox DNA-binding domain, but specific functions of the protein have not been determined. Alternatively spliced transcript variants have been observed for this gene.

Source: NCBI Gene 80714 — RefSeq curated summary.

At a glance

  • GWAS associations: 35
  • Clinical variants (ClinVar): 76 total
  • MANE Select transcript: NM_025245

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13403
Approved symbolPBX4
NamePBX homeobox 4
Location19p13.11
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000105717
Ensembl biotypeprotein_coding
OMIM608127
Entrez80714

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000251203, ENST00000557978, ENST00000558222, ENST00000558276, ENST00000559735, ENST00000885656, ENST00000885657

RefSeq mRNA: 1 — MANE Select: NM_025245 NM_025245

CCDS: CCDS12406

Canonical transcript exons

ENST00000251203 — 8 exons

ExonStartEnd
ENSE000008660511957058619570833
ENSE000025466241961851119618687
ENSE000033112601956171319562117
ENSE000035006251959929219599365
ENSE000035378451956493319565089
ENSE000035428951956944919569584
ENSE000035515091956350919563615
ENSE000036846751957010919570299

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 94.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0003 / max 121.2479, expressed in 948 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1801543.7870937
1801530.213393

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of thyroid glandUBERON:000111994.38gold quality
left lobe of thyroid glandUBERON:000112094.31gold quality
thyroid glandUBERON:000204693.43gold quality
granulocyteCL:000009485.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.85gold quality
left testisUBERON:000453381.40gold quality
right testisUBERON:000453481.31gold quality
ventricular zoneUBERON:000305380.13gold quality
testisUBERON:000047378.78gold quality
right uterine tubeUBERON:000130278.29gold quality
small intestine Peyer’s patchUBERON:000345478.29gold quality
lymph nodeUBERON:000002978.07gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.04gold quality
spleenUBERON:000210677.66gold quality
embryoUBERON:000092277.58gold quality
ganglionic eminenceUBERON:000402377.58gold quality
mucosa of transverse colonUBERON:000499177.37gold quality
vermiform appendixUBERON:000115477.20gold quality
cortical plateUBERON:000534376.14gold quality
bloodUBERON:000017876.11gold quality
skin of legUBERON:000151174.69gold quality
skin of abdomenUBERON:000141674.50gold quality
adenohypophysisUBERON:000219674.50gold quality
small intestineUBERON:000210873.91gold quality
olfactory segment of nasal mucosaUBERON:000538673.70gold quality
upper lobe of left lungUBERON:000895273.60gold quality
right ovaryUBERON:000211873.49gold quality
body of stomachUBERON:000116173.48gold quality
tibial nerveUBERON:000132373.23gold quality
right lungUBERON:000216772.86gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.43

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
FGF8Unknown
LPAR1
PGK2

miRNA regulators (miRDB)

19 targeting PBX4, 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-428299.9975.366408
HSA-MIR-590-3P99.9674.346478
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-1211999.8768.351653
HSA-MIR-1213299.4768.901341
HSA-MIR-4795-5P99.1166.90876
HSA-MIR-3124-3P98.8768.952123
HSA-MIR-6889-3P98.8467.351198
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-6878-5P98.4967.912142
HSA-MIR-477398.3567.301710
HSA-MIR-1233-5P98.1966.711201
HSA-MIR-6778-5P98.1966.591239
HSA-MIR-430398.0168.132304
HSA-MIR-6788-5P97.8066.411532
HSA-MIR-30C-1-3P97.8066.361499
HSA-MIR-30C-2-3P97.8066.451499
HSA-MIR-548AD-3P94.3966.04350

Literature-anchored findings (GeneRIF, showing 3)

  • up-regulation of PREP1 and PBX genes could be implicated in the modulation of the cellular response to chemotherapeutic-induced apoptosis. (PMID:22185299)
  • Sex (male)-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels is observed both the Mulao and Han ethnic groups. (PMID:22208664)
  • Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. (PMID:35740947)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_reriopbx2ENSDARG00000019717
mus_musculusPbx4ENSMUSG00000031860
rattus_norvegicusPbx4ENSRNOG00000010736
drosophila_melanogasterexdFBGN0000611
drosophila_melanogasterhthFBGN0001235
drosophila_melanogastervisFBGN0033748
drosophila_melanogasterachiFBGN0033749
caenorhabditis_elegansWBGENE00000443
caenorhabditis_elegansWBGENE00006796
caenorhabditis_elegansWBGENE00017690

Paralogs (13): MEIS3 (ENSG00000105419), TGIF2 (ENSG00000118707), MEIS2 (ENSG00000134138), MEIS1 (ENSG00000143995), TGIF2LX (ENSG00000153779), PKNOX1 (ENSG00000160199), PKNOX2 (ENSG00000165495), PBX3 (ENSG00000167081), TGIF2LY (ENSG00000176679), TGIF1 (ENSG00000177426), PBX1 (ENSG00000185630), MEIS3P2 (ENSG00000188013), PBX2 (ENSG00000204304)

Protein

Protein identifiers

Pre-B-cell leukemia transcription factor 4Q9BYU1 (reviewed: Q9BYU1)

Alternative names: Homeobox protein PBX4

All UniProt accessions (2): Q9BYU1, H0YL59

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the TALE/PBX homeobox family.

RefSeq proteins (1): NP_079521* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR005542PBX_PBC_domDomain
IPR008422KN_HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR050224TALE_homeoboxFamily

Pfam: PF03792, PF05920

UniProt features (11 total): region of interest 3, sequence variant 3, chain 1, domain 1, sequence conflict 1, DNA-binding region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BYU1-F174.290.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): MODULE_511, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_HEAD_DEVELOPMENT, AFFAR_YY1_TARGETS_UP, GOBP_EMBRYO_DEVELOPMENT, GOBP_SENSORY_ORGAN_DEVELOPMENT, RGAGGAARY_PU1_Q6, GOBP_EMBRYONIC_ORGAN_DEVELOPMENT, GOCC_SEX_CHROMOSOME, GOCC_XY_BODY, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II

GO Biological Process (8): eye development (GO:0001654), brain development (GO:0007420), animal organ morphogenesis (GO:0009887), positive regulation of DNA-templated transcription (GO:0045893), embryonic organ development (GO:0048568), neuron development (GO:0048666), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (5): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), XY body (GO:0001741), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
animal organ development3
regulation of DNA-templated transcription3
DNA-templated transcription2
sensory organ development1
visual system development1
central nervous system development1
head development1
anatomical structure morphogenesis1
positive regulation of RNA biosynthetic process1
embryo development1
neuron differentiation1
cell development1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription by RNA polymerase II1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
DNA binding1
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
chromosome1
cellular anatomical structure1
sex chromosome1
condensed chromatin of inactivated sex chromosome1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

666 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PBX4CILP2Q8IUL8823
PBX4MEIS3Q99687822
PBX4HOXA10P31260566
PBX4NCANO14594543
PBX4HDAC1Q13547517
PBX4PSRC1Q6PGN9513
PBX4GALNT2Q10471507
PBX4MMABQ96EY8507
PBX4CELSR2Q9HCU4471
PBX4MVB12AQ96EY5449
PBX4TRIB1Q96RU8447
PBX4ZNF619Q8N2I2420
PBX4YJEFN3A6XGL0418
PBX4ETNK2Q9NVF9418
PBX4SORT1Q99523415

IntAct

258 interactions, top by confidence:

ABTypeScore
PBX4IPO13psi-mi:“MI:0915”(physical association)0.830
PBX4TFIP11psi-mi:“MI:0915”(physical association)0.830
IPO13PBX4psi-mi:“MI:0915”(physical association)0.830
TFIP11PBX4psi-mi:“MI:0915”(physical association)0.830
PKNOX1PBX4psi-mi:“MI:0915”(physical association)0.670
PKNOX2PBX4psi-mi:“MI:0915”(physical association)0.670
USP20PBX4psi-mi:“MI:0915”(physical association)0.560
HOXC8PBX4psi-mi:“MI:0915”(physical association)0.560
PBX4psi-mi:“MI:0915”(physical association)0.560
KDM1APBX4psi-mi:“MI:0915”(physical association)0.560
MEIS2PBX4psi-mi:“MI:0915”(physical association)0.560
PBX4SERTAD1psi-mi:“MI:0915”(physical association)0.560
PPLPBX4psi-mi:“MI:0915”(physical association)0.560
HOXB2PBX4psi-mi:“MI:0915”(physical association)0.560
PBX4PICK1psi-mi:“MI:0915”(physical association)0.560
MBD3PBX4psi-mi:“MI:0915”(physical association)0.560
PBX4C14orf119psi-mi:“MI:0915”(physical association)0.560
PBX4CCM2Lpsi-mi:“MI:0915”(physical association)0.560

BioGRID (91): PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Affinity Capture-MS), PBX4 (Affinity Capture-MS), PBX4 (Affinity Capture-MS), PBX4 (Affinity Capture-MS), PBX4 (Affinity Capture-MS), TFIP11 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid), PBX4 (Two-hybrid)

ESM2 similar proteins: A0A1W2PQ72, A7J1T0, A7J1T2, A7MBB4, A8MZ59, D3ZXW3, M0R5D6, O36371, O43283, O43310, O73622, O95073, P03177, P10242, P21705, P46200, Q0P4H6, Q1HKZ5, Q1HVD1, Q1LVK9, Q22811, Q2NKQ1, Q3KSQ2, Q3UPF5, Q535K8, Q562B4, Q567C6, Q5R8X7, Q5ZI27, Q6DGX3, Q6INH1, Q6J1H4, Q6PEE2, Q6ZTZ1, Q71M44, Q7SXL7, Q80T85, Q8BFX3, Q8BIL2, Q8BKE5

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

2 interactions.

AEffectBMechanism
PBX4“down-regulates quantity by repression”FGF8“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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
anterior/posterior pattern specification515.6×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance61
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1802 predictions. Top by Δscore:

VariantEffectΔscore
19:19563504:CTCA:Cdonor_loss1.0000
19:19563506:CACC:Cdonor_loss1.0000
19:19563508:C:CGdonor_loss1.0000
19:19569375:C:Adonor_gain1.0000
19:19570097:ACAGG:Adonor_gain1.0000
19:19570098:CAGGC:Cdonor_gain1.0000
19:19570831:CCA:Cacceptor_gain1.0000
19:19570832:CAC:Cacceptor_gain1.0000
19:19570834:C:CCacceptor_gain1.0000
19:19618526:T:TAdonor_gain1.0000
19:19563507:A:ACdonor_gain0.9900
19:19563508:C:CCdonor_gain0.9900
19:19564926:CACT:Cdonor_loss0.9900
19:19564927:ACTC:Adonor_loss0.9900
19:19564929:TCACC:Tdonor_loss0.9900
19:19564930:CA:Cdonor_loss0.9900
19:19564931:A:ACdonor_gain0.9900
19:19564932:C:Adonor_loss0.9900
19:19564932:C:CCdonor_gain0.9900
19:19564983:T:TAdonor_gain0.9900
19:19565086:AGACC:Aacceptor_loss0.9900
19:19565088:ACC:Aacceptor_loss0.9900
19:19565090:C:CAacceptor_loss0.9900
19:19565091:T:Cacceptor_loss0.9900
19:19569374:T:TAdonor_gain0.9900
19:19569443:CGTCA:Cdonor_loss0.9900
19:19569444:GTCA:Gdonor_loss0.9900
19:19569445:TCA:Tdonor_loss0.9900
19:19569446:CACCT:Cdonor_loss0.9900
19:19569447:A:Tdonor_loss0.9900

AlphaMissense

2444 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:19565066:T:AK264N0.996
19:19565066:T:GK264N0.996
19:19565075:A:CF261L0.994
19:19565075:A:TF261L0.994
19:19565077:A:GF261L0.994
19:19565063:T:AR265S0.992
19:19565063:T:GR265S0.992
19:19569477:G:TA247D0.992
19:19569488:T:AK243N0.992
19:19569488:T:GK243N0.992
19:19570274:A:TV156D0.992
19:19565067:T:AK264I0.991
19:19570265:A:GL159P0.991
19:19565080:A:GW260R0.990
19:19565080:A:TW260R0.990
19:19565088:A:TV257D0.990
19:19569530:A:CF229L0.989
19:19569530:A:TF229L0.989
19:19569532:A:GF229L0.989
19:19565078:C:AW260C0.988
19:19565078:C:GW260C0.988
19:19569531:A:GF229S0.988
19:19570285:G:CF152L0.988
19:19570285:G:TF152L0.988
19:19570287:A:GF152L0.988
19:19565061:A:GI266T0.985
19:19565076:A:GF261S0.984
19:19599302:C:AK61N0.984
19:19599302:C:GK61N0.984
19:19565064:C:GR265T0.983

dbSNP variants (sampled 300 via entrez): RS1000021089 (19:19607306 G>A), RS1000048719 (19:19568208 C>A,T), RS1000065171 (19:19563993 T>A,C), RS1000146440 (19:19589452 C>A), RS1000251754 (19:19577871 TAAAAAA>T,TAAAAA,TAAAAAAA), RS1000275029 (19:19577059 C>T), RS1000283786 (19:19618851 T>C), RS1000384065 (19:19594656 C>T), RS1000410067 (19:19602453 T>C), RS1000518247 (19:19589280 T>C), RS1000545573 (19:19573752 T>C), RS1000563203 (19:19609297 C>A), RS1000626781 (19:19605661 G>A), RS1000685853 (19:19599667 A>G,T), RS1000738750 (19:19619172 G>A,T)

Disease associations

OMIM: gene MIM:608127 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

StudyTraitp-value
GCST000134_2LDL cholesterol3.000000e-08
GCST000138_9Triglycerides4.000000e-09
GCST000286_11Triglycerides4.000000e-11
GCST000287_4LDL cholesterol2.000000e-08
GCST000758_7Triglycerides2.000000e-29
GCST000759_15LDL cholesterol7.000000e-22
GCST000760_8Cholesterol, total3.000000e-38
GCST001762_394Obesity-related traits4.000000e-06
GCST002149_11Schizophrenia3.000000e-09
GCST002539_89Schizophrenia4.000000e-10
GCST003486_3Response to fenofibrate (LDL cholesterol levels)2.000000e-08
GCST003657_1Attention deficit hyperactivity disorder symptom score1.000000e-07
GCST004625_213Monocyte count2.000000e-09
GCST004632_22Lymphocyte percentage of white cells9.000000e-10
GCST004764_1LDL cholesterol change in response to fenofibrate in statin-treated type 2 diabetes9.000000e-08
GCST004765_31Total cholesterol change in response to fenofibrate in statin-treated type 2 diabetes6.000000e-07
GCST004864_18Perceived unattractiveness to mosquitoes3.000000e-06
GCST006614_114Total cholesterol levels6.000000e-12
GCST006803_88Schizophrenia7.000000e-12
GCST007096_62Pulse pressure1.000000e-09
GCST007658_7Triglyceride levels (parental genotype effect)8.000000e-06
GCST007660_1Triglyceride levels in response to fenofibrate treatment (parental genotype effect)3.000000e-06
GCST007660_2Triglyceride levels in response to fenofibrate treatment (parental genotype effect)7.000000e-06
GCST007660_3Triglyceride levels in response to fenofibrate treatment (parental genotype effect)9.000000e-07
GCST008103_10Bipolar disorder1.000000e-09
GCST008115_2Bipolar I disorder3.000000e-09
GCST008116_4Bipolar II disorder4.000000e-06
GCST009240_416Serum metabolite levels (CMS)4.000000e-09
GCST009242_384Serum metabolite levels9.000000e-10
GCST010002_52Refractive error4.000000e-29

EFO canonical traits (16, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0004574total cholesterol measurement
EFO:0007804LDL cholesterol change measurement
EFO:0007860ADHD symptom measurement
EFO:0005091monocyte count
EFO:0007993lymphocyte percentage of leukocytes
EFO:0007806total cholesterol change measurement
EFO:0008380perceived unattractiveness to mosquitos measurement
EFO:0005763pulse pressure measurement
EFO:0005939parental genotype effect measurement
EFO:0009963bipolar I disorder
EFO:0009964bipolar II disorder
EFO:0004346neuroimaging measurement
EFO:0004842eosinophil count
EFO:0007991eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
propionaldehydeincreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Adecreases methylation1
titanium dioxideincreases methylation1
butyraldehydeincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
abrineincreases expression1
theaflavin-3,3’-digallateaffects expression1
Temozolomideincreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Hydrogen Peroxideaffects expression1
Lipopolysaccharidesincreases expression, affects response to substance1
Methyl Methanesulfonateincreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
8-Bromo Cyclic Adenosine Monophosphateincreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1
Acrylamideincreases expression1
Particulate Matterdecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): alcoholic liver cirrhosis