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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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HOXD4
homeobox D4
Chromosome 2 · 2q31.1
NCBI Gene: 3233Ensembl: ENSG00000170166.6HGNC: HGNC:5138UniProt: P09016
33PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
embryonic organ developmentnucleoplasmDNA-binding transcription activator activity, RNA polymerase II-specificprotein bindingAbnormality of the skeletal systemskin diseaseandrogenetic alopecialeukemia, acute lymphoblastic, susceptibility to, 3
✦AI Summary

HOXD4 is a sequence-specific transcription factor that regulates anterior-posterior pattern specification during embryonic development 1. It functions as a DNA-binding transcriptional activator, controlling expression through interaction with retinoid-responsive enhancer elements and retinoic acid receptors 12. During early embryogenesis, HOXD4 is activated in a temporal and spatially restricted manner, with retinoic acid serving as a critical developmental regulator 23. The gene directs proper expression in the neural tube and paraxial mesoderm, establishing correct anterior boundaries in the hindbrain up to rhombomere 6/7 3. In disease contexts, HOXD4 overexpression drives tumorigenesis across multiple cancer types. In glioblastoma, HOXD4 activates ESM1 transcription to promote cell proliferation, invasion, migration, and angiogenesis 4. Similarly, elevated HOXD4 expression correlates with poor prognosis in ovarian serous carcinoma and gastric adenocarcinoma, promoting cell proliferation through c-Myc and cyclin D1 upregulation 56. Conversely, HOXD4 loss-of-function mutations cause spinal extradural arachnoid cyst through haplo-insufficiency, indicating HOXD4's essential role in dura mater development 7. Across pan-cancer analysis, HOXD4 downregulation is associated with improved survival outcomes in renal cell carcinoma and other malignancies 8.

Sources cited
1
HOXD4 is developmentally regulated and activated by retinoids through distal enhancer elements containing retinoic acid receptor binding sites
PMID: 7908827
2
HOXD4 contains a 185-bp retinoid-responsive enhancer that directs neural tube expression in transgenic mice and responds to retinoic acid in vivo
PMID: 8674428
3
HOXD4 overexpression in glioblastoma activates ESM1 transcription to promote cell growth, invasion, migration, and angiogenesis
PMID: 40854419
4
HOXD4 downregulation is associated with improved overall survival, disease-specific survival, and progression-free interval in renal cell carcinoma and other cancers
PMID: 37827698
5
High HOXD4 expression in ovarian serous carcinoma correlates with advanced FIGO stage and poorer overall survival
PMID: 35317110
6
Elevated HOXD4 expression in gastric adenocarcinoma associates with tumor progression markers and promotes proliferation via c-Myc and cyclin D1
PMID: 30588951
7
HOXD4 possesses neural and mesodermal enhancers directing expression to specific anterior boundaries in hindbrain and somites with retinoid-responsive components
PMID: 9272954
8
Heterozygous HOXD4 loss-of-function mutations cause spinal extradural arachnoid cyst through haplo-insufficiency, indicating essential role in dura mater development
PMID: 26545093
Disease Associationsⓘ20
Abnormality of the skeletal systemOpen Targets
0.35Weak
skin diseaseOpen Targets
0.32Weak
androgenetic alopeciaOpen Targets
0.31Weak
leukemia, acute lymphoblastic, susceptibility to, 3Open Targets
0.11Weak
gliomaOpen Targets
0.08Suggestive
gastric adenocarcinomaOpen Targets
0.08Suggestive
cancerOpen Targets
0.08Suggestive
autosomal recessive spondylocostal dysostosisOpen Targets
0.07Suggestive
spondylocostal dysostosis 2, autosomal recessiveOpen Targets
0.06Suggestive
brachyolmia, Maroteaux typeOpen Targets
0.06Suggestive
autosomal dominant brachyolmiaOpen Targets
0.06Suggestive
spondylocostal dysostosis 5Open Targets
0.06Suggestive
Klippel-Feil syndrome 3, autosomal dominantOpen Targets
0.06Suggestive
Becker nevus syndromeOpen Targets
0.05Suggestive
motion sicknessOpen Targets
0.05Suggestive
osteomesopyknosisOpen Targets
0.05Suggestive
Prata-Liberal-Goncalves syndromeOpen Targets
0.05Suggestive
thoracolaryngopelvic dysplasiaOpen Targets
0.05Suggestive
Primary basilar impressionOpen Targets
0.05Suggestive
primary basilar invaginationOpen Targets
0.05Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HOXA5Protein interaction94%HOXA6Protein interaction94%HOXA7Protein interaction94%HOXB5Protein interaction94%HOXB6Protein interaction94%HOXC5Protein interaction94%
Tissue Expression6 tissues
Ovary
100%
Heart
3%
Lung
2%
Brain
1%
Liver
0%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
HOXD4HOXA5HOXA6HOXA7HOXB5HOXB6HOXC5
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt P09016
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.98LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.64 [0.42–0.98]
RankingsWhere HOXD4 stands among ~20K protein-coding genes
  • #11,349of 20,598
    Most Researched33
  • #9,330of 17,882
    Most Constrained (LOEUF)0.98
Genes detectedHOXD4
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Regulation of the human HOXD4 gene by retinoids.
PMID: 7908827
Mech Dev · 1993
1.00
2
In vitro and transgenic analysis of a human HOXD4 retinoid-responsive enhancer.
PMID: 8674428
Development · 1996
0.90
3
HOXD4-mediated transcriptional activation of ESM1 drives glioblastoma progression in human tumor cells and mouse models.
PMID: 40854419
Neurosci Lett · 2025
0.80
4
A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma.
PMID: 37827698
Aging (Albany NY) · 2023
0.70
5
Prognostic significance of HOXD4 protein expression in human ovarian cancers.
PMID: 35317110
Iran J Basic Med Sci · 2021
0.60