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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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HOXA3
homeobox A3
Chromosome 7 · 7p15.2
NCBI Gene: 3200Ensembl: ENSG00000105997.24HGNC: HGNC:5104UniProt: A4D182
43PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingnucleoplasmangiogenesisDNA-binding transcription factor activity, RNA polymerase II-specificneurodegenerative diseasecardiovascular diseasenon-small cell lung carcinomalung adenocarcinoma
✦AI Summary

HOXA3 is a sequence-specific transcription factor that specifies anterior-posterior positional identity during development 1. During embryogenesis, HOXA3 is essential for pharyngeal arch patterning and third pharyngeal pouch derivatives (thymus and parathyroids), functioning in both neural crest cells and endoderm with tissue-specific roles in morphogenesis, differentiation, and cell survival 12. In adults, HOXA3 promotes angiogenesis and wound repair by inducing endothelial and epithelial cell migration through upregulation of MMP-14 and uPAR, and HOXA3 gene transfer improves wound healing in diabetic mice 3. In cancer contexts, HOXA3 is aberrantly expressed in multiple tumor types and promotes disease progression through distinct mechanisms. In glioblastoma, HOXA3 cooperates with the histone demethylase KDM6A to activate aerobic glycolysis genes (HK2, PKM2) via H3K27 demethylation, accelerating proliferation and tumor growth 4. In renal cell carcinoma, HOXA3 transcriptionally activates USP15, which suppresses autophagy and promotes M2-type macrophage polarization through SQSTM1 deubiquitination and CCL2 secretion 5. HOXA3 is hypermethylated across 16 cancer types, with 3' UTR hypermethylation in oral squamous cell carcinoma associated with poor survival 67. These findings establish HOXA3 as a critical developmental regulator with multifaceted roles in tumor progression.

Sources cited
1
HOXA3 is required for thymus and parathyroid development with tissue-specific roles in endoderm and neural crest cells for patterning, differentiation, and morphogenesis
PMID: 25249461
2
HOXA3 regulates differentiation of third pharyngeal arch expressed in neural crest cells and pharyngeal pouch; null mutants show carotid artery malformation
PMID: 19290546
3
HOXA3 promotes angiogenesis and wound repair by inducing endothelial and epithelial cell migration through MMP-14 and uPAR upregulation; improves healing in diabetic mice
PMID: 15914537
4
HOXA3 is highly expressed in glioblastoma predicting poor prognosis; cooperates with KDM6A to activate glycolytic genes via H3K27 demethylation to promote tumor growth
PMID: 36215227
5
HOXA3 transcriptionally activates USP15 in renal cell carcinoma to suppress autophagy and promote M2-type macrophage polarization via SQSTM1 deubiquitination
PMID: 39740793
6
HOXA3 is hypermethylated in all 16 cancer types analyzed in pan-cancer methylation study, suggesting role in oncogenesis
PMID: 38886487
7
In oral squamous cell carcinoma, HOXA3 expression is epigenetically regulated by promoter and 3' UTR methylation, with 3' UTR hypermethylation associated with poor overall survival
PMID: 39658479
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.25Weak
cardiovascular diseaseOpen Targets
0.10Suggestive
non-small cell lung carcinomaOpen Targets
0.08Suggestive
lung adenocarcinomaOpen Targets
0.07Suggestive
hypertensionOpen Targets
0.07Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.07Suggestive
sign or symptomOpen Targets
0.07Suggestive
central nervous system cancerOpen Targets
0.06Suggestive
hypospadiasOpen Targets
0.06Suggestive
endometriosisOpen Targets
0.06Suggestive
Ovarian EndometriosisOpen Targets
0.06Suggestive
Peyronie diseaseOpen Targets
0.06Suggestive
breast cancerOpen Targets
0.05Suggestive
atrial fibrillationOpen Targets
0.05Suggestive
atrial flutterOpen Targets
0.05Suggestive
gliomaOpen Targets
0.05Suggestive
breast carcinomaOpen Targets
0.05Suggestive
HerniaOpen Targets
0.05Suggestive
Splenogonadal fusion - limb defects - micrognathiaOpen Targets
0.04Suggestive
splenogonadal fusion-limb defects-micrognathia syndromeOpen Targets
0.04Suggestive
Pathogenic Variants1
NM_153631.3(HOXA3):c.562C>T (p.Gln188Ter)Likely pathogenic
See cases
★☆☆☆2026→ Residue 188
View on ClinVar ↗
Related Genes
HOXB3Shared pathway100%HOXA6Protein interaction97%HOXA10Protein interaction88%PBX1Protein interaction83%HOXA2Protein interaction73%HOXA7Protein interaction73%
Tissue Expression6 tissues
Lung
100%
Ovary
26%
Brain
16%
Liver
7%
Bone Marrow
3%
Heart
2%
Gene Interaction Network
Click a node to explore
HOXA3HOXB3HOXA6HOXA10PBX1HOXA2HOXA7
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt O43365
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.54Moderately Constrained
pLIⓘ
0.94Intolerant
Observed/Expected LoF0.30 [0.18–0.54]
RankingsWhere HOXA3 stands among ~20K protein-coding genes
  • #9,742of 20,598
    Most Researched43
  • #5,143of 5,498
    Most Pathogenic Variants1
  • #3,460of 17,882
    Most Constrained (LOEUF)0.54 · top quartile
Genes detectedHOXA3
Sources retrieved10 papers
Response time—
📄 Sources
10â–¼
1
Retraction.
PMID: 34086992
J Cell Biochem · 2021
1.00
2
Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression.
PMID: 36215227
Neuro Oncol · 2023
0.90
3
Homeobox and Polycomb target gene methylation in human solid tumors.
PMID: 38886487
Sci Rep · 2024
0.80
4
Hoxa3 and signaling molecules involved in aortic arch patterning and remodeling.
PMID: 19290546
Cell Tissue Res · 2009
0.70
5
HOXA3 activates USP15 to suppress autophagy and promote M2-type macrophage polarization in renal cell carcinoma via facilitating the deubiquitination of SQSTM1.
PMID: 39740793
Am J Physiol Cell Physiol · 2025
0.60