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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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NKX3-1
NK3 homeobox 1
Chromosome 8 · 8p21.2
NCBI Gene: 4824Ensembl: ENSG00000167034.10HGNC: HGNC:7838UniProt: Q99801
131PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription FactorTumor Suppressor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
transcription cis-regulatory region bindingRNA polymerase II cis-regulatory region sequence-specific DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specifichistone deacetylase bindingprostate carcinomaprostate cancerneurodegenerative diseasebenign prostatic hyperplasia
✦AI Summary

NKX3.1 is an androgen-regulated homeodomain transcription factor that serves as a critical regulator of prostate development and tumor suppression 12. The protein functions as a pioneer factor, binding to chr8 at enhancers to integrate androgen-regulated signaling pathways in prostate epithelial cells 3. NKX3.1 acts primarily as a transcriptional repressor and plays essential roles in normal prostate organogenesis, regulating epithelial proliferation and ductal formation 1. In prostate cancer, NKX3.1 functions as a tumor suppressor, with its loss representing an initiating event in carcinogenesis 12. The protein directly binds to TMPRSS2 promoter sequences and negatively regulates ERG oncogene expression through TMPRSS2-ERG gene fusions, a common mechanism in prostate cancer progression 4. NKX3.1 expression is frequently reduced in prostate cancer through multiple mechanisms including allelic loss, haploinsufficiency, and post-translational modifications that affect protein stability 54. Single-cell analysis has revealed that NKX3.1-positive differentiated luminal cells contribute significantly to prostate regeneration following androgen deprivation 6. Due to its prostate specificity, NKX3.1 serves as a valuable immunohistochemical marker in clinical practice, though rare expression in non-prostatic tumors has been documented 37.

Sources cited
1
NKX3.1 is an androgen-regulated homeodomain transcription factor that serves as a critical regulator of prostate development and tumor suppression .
PMID: 14648854
2
NKX3.1 is an androgen-regulated homeodomain transcription factor that serves as a critical regulator of prostate development and tumor suppression .
PMID: 18557759
3
The protein functions as a pioneer factor, binding to chr8 at enhancers to integrate androgen-regulated signaling pathways in prostate epithelial cells .
PMID: 34996754
4
The protein directly binds to TMPRSS2 promoter sequences and negatively regulates ERG oncogene expression through TMPRSS2-ERG gene fusions, a common mechanism in prostate cancer progression .
PMID: 24418414
5
NKX3.1 expression is frequently reduced in prostate cancer through multiple mechanisms including allelic loss, haploinsufficiency, and post-translational modifications that affect protein stability .
PMID: 26841725
6
Single-cell analysis has revealed that NKX3.1-positive differentiated luminal cells contribute significantly to prostate regeneration following androgen deprivation .
PMID: 32355025
7
Due to its prostate specificity, NKX3.1 serves as a valuable immunohistochemical marker in clinical practice, though rare expression in non-prostatic tumors has been documented .
PMID: 38525603
Disease Associationsⓘ20
prostate carcinomaOpen Targets
0.53Moderate
prostate cancerOpen Targets
0.48Moderate
neurodegenerative diseaseOpen Targets
0.46Moderate
benign prostatic hyperplasiaOpen Targets
0.15Weak
major depressive disorderOpen Targets
0.11Weak
neoplasmOpen Targets
0.10Weak
acute lymphoblastic leukemiaOpen Targets
0.10Suggestive
posterior cortical atrophyOpen Targets
0.09Suggestive
gliomaOpen Targets
0.07Suggestive
hypertensionOpen Targets
0.07Suggestive
Hereditary breast and ovarian cancer syndromeOpen Targets
0.07Suggestive
prostate intraepithelial neoplasiaOpen Targets
0.07Suggestive
adamantinomaOpen Targets
0.06Suggestive
ovarian cancerOpen Targets
0.05Suggestive
Salivary Gland Pleomorphic AdenomaOpen Targets
0.05Suggestive
ovarian carcinomaOpen Targets
0.05Suggestive
van der Woude syndromeOpen Targets
0.05Suggestive
breast-ovarian cancer, familial, susceptibility to, 1Open Targets
0.05Suggestive
breast-ovarian cancer, familial, susceptibility to, 2Open Targets
0.05Suggestive
reticulum cell sarcomaOpen Targets
0.05Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
AKT1Protein interaction99%TMPRSS2Protein interaction97%SPDEFProtein interaction88%AKT2Protein interaction83%AKT3Protein interaction83%KLK3Protein interaction71%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
97%
Liver
86%
Ovary
56%
Lung
39%
Brain
35%
Gene Interaction Network
Click a node to explore
NKX3-1AKT1TMPRSS2SPDEFAKT2AKT3KLK3
PROTEIN STRUCTURE
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PDB2L9R · NMR
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.18LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.75 [0.50–1.18]
RankingsWhere NKX3-1 stands among ~20K protein-coding genes
  • #3,569of 20,598
    Most Researched131 · top quartile
  • #12,354of 17,882
    Most Constrained (LOEUF)1.18
Genes detectedNKX3-1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages.
PMID: 40516530
Cell Stem Cell · 2025
1.00
2
Regenerative potential of prostate luminal cells revealed by single-cell analysis.
PMID: 32355025
Science · 2020
0.90
3
NKX3.1 Expression in Non-Prostatic Tumors and Characterizing its Expression in Esophageal/Gastroesophageal Adenocarcinoma.
PMID: 38525603
Adv Anat Pathol · 2024
0.80
4
Gene of the month: NKX3.1.
PMID: 34996754
J Clin Pathol · 2022
0.70
5
Regulating NKX3.1 stability and function: Post-translational modifications and structural determinants.
PMID: 26841725
Prostate · 2016
0.60