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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
NKX3-2
NK3 homeobox 2
Chromosome 4 Β· 4p15.33
NCBI Gene: 579Ensembl: ENSG00000109705.8HGNC: HGNC:951UniProt: P78367
25PubMed Papers
21Diseases
0Drugs
9Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingprotein bindingnucleuschromatinspondylo-megaepiphyseal-metaphyseal dysplasiaconnective tissue diseasegenetic disorderautosomal recessive spondylocostal dysostosis
✦AI Summary

NKX3-2 is a transcriptional repressor belonging to the NK homeobox gene family with diverse developmental and pathological roles. Developmentally, NKX3-2 acts as a negative regulator of chondrocyte maturation 1 and is essential for axial skeleton patterning, particularly vertebral centrum and intervertebral disc development 2. It also regulates gastric mesenchyme development and antral-pyloric morphogenesis 2. Beyond skeletal development, NKX3-2 has emerged as a multifunctional transcription factor in disease contexts. In ovarian cancer, NKX3-2 promotes cell migration by suppressing autophagy through HDAC6-mediated lysosome repositioning 3, and represents a negative prognostic factor when highly expressed and not subject to P53-induced autophagy degradation 4. In T-cell acute lymphoblastic leukemia, NKX3-2 is aberrantly activated in 18% of pediatric patients, deregulating BMP and MAPK signaling to suppress T-cell differentiation 5. In immune function, NKX3-2 maintains ADGRB3 expression in T cells through non-muscle myosin II signaling, reducing traction force and anti-tumor cytotoxicity 6. Conversely, in retinal pigment epithelium, NKX3-2 provides protective effects by suppressing inflammation and necroptosis through RIP3 degradation 7. NKX3-2 is currently in clinical trials for osteoarthritis gene therapy 8.

Sources cited
1
NKX3-2 (Bapx1) is required for vertebral centrum and intervertebral disc development; targeted mutation shows ventromedial skeletal element deficiency and abnormal gastric mesenchyme
PMID: 11523821
2
NKX3-2 is a negative regulator of chondrocyte differentiation; enhancer deletions at Nkx3-2 locus confirm its role in regulating chondrogenic gene expression
PMID: 38844479
3
NKX3-2 is hyperexpressed in LPA-stimulated ovarian cancer cells and promotes cell migration by inhibiting autophagy through HDAC6-mediated lysosome repositioning
PMID: 39513923
4
NKX3-2 is upregulated in ovarian cancer, negatively correlates with P53 expression, and represents a negative prognostic factor; P53 induces NKX3-2 degradation via autophagy-lysosome pathway
PMID: 40497941
5
NKX3-2 is aberrantly activated in 18% of pediatric T-ALL patients; deregulates BMP and MAPK signaling and suppresses T-cell differentiation through downstream targets
PMID: 29746601
6
NKX3-2 maintains ADGRB3 expression in T cells via non-muscle myosin II, reducing T cell traction force and anti-tumor cytotoxicity
PMID: 39485850
7
NKX3-2 is expressed in retinal pigment epithelium and inhibits retinal degeneration by downregulating pro-inflammatory cytokines and inducing RIP3 degradation to prevent necroptosis
PMID: 40891783
8
NKX3-2 transcription factor is being tested in human clinical trials for osteoarthritis gene therapy (Phase I/II)
PMID: 36508307
Disease Associationsβ“˜21
spondylo-megaepiphyseal-metaphyseal dysplasiaOpen Targets
0.73Strong
connective tissue diseaseOpen Targets
0.32Weak
genetic disorderOpen Targets
0.19Weak
autosomal recessive spondylocostal dysostosisOpen Targets
0.08Suggestive
acute lymphoblastic leukemiaOpen Targets
0.07Suggestive
progressive deafness with stapes fixationOpen Targets
0.07Suggestive
ovarian cancerOpen Targets
0.06Suggestive
luminal B breast carcinomaOpen Targets
0.06Suggestive
Thickened earlobes - conductive deafnessOpen Targets
0.06Suggestive
thickened earlobes-conductive deafness syndromeOpen Targets
0.06Suggestive
Familial Scheuermann diseaseOpen Targets
0.05Suggestive
Scheuermann diseaseOpen Targets
0.05Suggestive
HirsutismOpen Targets
0.05Suggestive
central nervous system cancerOpen Targets
0.05Suggestive
autosomal dominant brachyolmiaOpen Targets
0.05Suggestive
spondylocostal dysostosis 2, autosomal recessiveOpen Targets
0.05Suggestive
X-linked mixed deafness with perilymphatic gusherOpen Targets
0.05Suggestive
X-linked mixed hearing loss with perilymphatic gusherOpen Targets
0.05Suggestive
spondyloepiphyseal dysplasia tardaOpen Targets
0.05Suggestive
Deafness - ear malformation - facial palsyOpen Targets
0.05Suggestive
Spondylo-megaepiphyseal-metaphyseal dysplasiaUniProt
Pathogenic Variants9
NM_001189.4(NKX3-2):c.104_110del (p.Ala35fs)Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 35
NM_001189.4(NKX3-2):c.304G>T (p.Glu102Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 102
NM_001189.4(NKX3-2):c.295G>T (p.Glu99Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 99
NM_001189.4(NKX3-2):c.362dup (p.Ser122fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 122
NM_001189.4(NKX3-2):c.59del (p.Lys20fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 20
NM_001189.4(NKX3-2):c.94_100dup (p.Pro34fs)Likely pathogenic
Connective tissue disorder
β˜…β˜†β˜†β˜†2020β†’ Residue 34
NM_001189.4(NKX3-2):c.507_508del (p.Gly171fs)Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia
β˜†β˜†β˜†β˜†2019β†’ Residue 171
NM_001189.4(NKX3-2):c.336_337delinsT (p.Ala113fs)Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia
β˜†β˜†β˜†β˜†2009β†’ Residue 113
NM_001189.4(NKX3-2):c.337dup (p.Ala113fs)Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia
β˜†β˜†β˜†β˜†2009β†’ Residue 113
View on ClinVar β†—
Related Genes
RUNX2Protein interaction89%TCF21Protein interaction80%HAND2Protein interaction73%ETS2Shared pathway50%PAX1Shared pathway40%ETV1Shared pathway40%
Tissue Expression6 tissues
Ovary
100%
Brain
32%
Lung
5%
Bone Marrow
5%
Liver
0%
Heart
0%
Gene Interaction Network
Click a node to explore
NKX3-2RUNX2TCF21HAND2ETS2PAX1ETV1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P78367
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.20LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.76 [0.49–1.20]
RankingsWhere NKX3-2 stands among ~20K protein-coding genes
  • #13,023of 20,598
    Most Researched25
  • #2,994of 5,498
    Most Pathogenic Variants9
  • #12,643of 17,882
    Most Constrained (LOEUF)1.20
Genes detectedNKX3-2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The role of Bapx1 (Nkx3.2) in the development and evolution of the axial skeleton.
PMID: 11523821
J Anat Β· 2001
1.00
2
NKX3-2 Induces Ovarian Cancer Cell Migration by HDAC6-Mediated Repositioning of Lysosomes and Inhibition of Autophagy.
PMID: 39513923
Cells Β· 2024
0.90
3
Suppression of non-muscle myosin II boosts T cell cytotoxicity against tumors.
PMID: 39485850
Sci Adv Β· 2024
0.80
4
Osteoarthritis gene therapy in 2022.
PMID: 36508307
Curr Opin Rheumatol Β· 2023
0.70
5
Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development.
PMID: 38844479
Nat Commun Β· 2024
0.60