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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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NKX2-4
NK2 homeobox 4
Chromosome 20 · 20p11.22
NCBI Gene: 644524Ensembl: ENSG00000125816.5HGNC: HGNC:7837UniProt: Q9H2Z4
13PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingcell differentiationDNA-binding transcription factor activity, RNA polymerase II-specificregulation of transcription by RNA polymerase IIneurodegenerative diseaseAbnormal pupillary functionobesitycentral nervous system cancer
✦AI Summary

NKX2-4 is a homeodomain-containing transcription factor belonging to the NK2.1 family, homologous to the Drosophila scro gene 1. As a DNA-binding transcription factor, it functions in regulating gene expression through RNA polymerase II-mediated mechanisms and chr20 interactions. NKX2-4 plays developmental roles in central nervous system ventral region specification and organ development, particularly in thyroid organogenesis where it is required for early thyroid specification and cell fate commitment 2. In the embryonic brain, NKX2-4 transcription is activated through H2A.z-mediated epigenetic regulation, promoting neurogenesis and neuronal differentiation 3. NKX2-4 is increasingly recognized for disease relevance in hematologic and solid malignancies. In acute myeloid leukemia (AML), aberrant NKX2-4 expression disrupts megakaryocytic-erythroid differentiation by repressing the master lineage factor FLI1 and activating endothelial signature genes 45. In cancer contexts, NKX2-4 demonstrates allele-specific binding at the TERT/CLPTM1L risk locus in uveal melanoma, where it suppresses TERT and CLPTM1L expression in an allele-dependent manner 6. Clinically, NKX2-4 DNA methylation is a promising biomarker for non-invasive bladder urothelial carcinoma diagnosis, with inclusion in a four-gene detection panel achieving 92.39% diagnostic accuracy 7. Additionally, NKX2-4 hypermethylation has been identified in salivary gland adenoid cystic carcinoma 8, suggesting broader tumor suppressor functions.

Sources cited
1
NKX2-4 is a homeodomain-containing transcription factor belonging to the NK2.1 family, homologous to the Drosophila scro gene .
PMID: 37492711
2
NKX2-4 plays developmental roles in central nervous system ventral region specification and organ development, particularly in thyroid organogenesis where it is required for early thyroid specification and cell fate commitment .
PMID: 31797737
3
In the embryonic brain, NKX2-4 transcription is activated through H2A.z-mediated epigenetic regulation, promoting neurogenesis and neuronal differentiation .
PMID: 29294103
4
In cancer contexts, NKX2-4 demonstrates allele-specific binding at the TERT/CLPTM1L risk locus in uveal melanoma, where it suppresses TERT and CLPTM1L expression in an allele-dependent manner .
PMID: 36459980
5
Clinically, NKX2-4 DNA methylation is a promising biomarker for non-invasive bladder urothelial carcinoma diagnosis, with inclusion in a four-gene detection panel achieving 92.39% diagnostic accuracy .
PMID: 41420251
6
Additionally, NKX2-4 hypermethylation has been identified in salivary gland adenoid cystic carcinoma , suggesting broader tumor suppressor functions.
PMID: 21692051
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.37Weak
Abnormal pupillary functionOpen Targets
0.32Weak
obesityOpen Targets
0.31Weak
central nervous system cancerOpen Targets
0.30Weak
placenta praeviaOpen Targets
0.21Weak
heart failureOpen Targets
0.17Weak
autism spectrum disorderOpen Targets
0.09Suggestive
acute myeloid leukemiaOpen Targets
0.08Suggestive
attention deficit hyperactivity disorderOpen Targets
0.07Suggestive
atrial fibrillationOpen Targets
0.06Suggestive
cardiac arrhythmiaOpen Targets
0.06Suggestive
insomniaOpen Targets
0.05Suggestive
chronic obstructive pulmonary diseaseOpen Targets
0.04Suggestive
autismOpen Targets
0.04Suggestive
risk-taking behaviourOpen Targets
0.03Suggestive
food allergyOpen Targets
0.03Suggestive
type 2 diabetes mellitusOpen Targets
0.02Suggestive
bladder transitional cell carcinomaOpen Targets
0.02Suggestive
hepatocellular carcinomaOpen Targets
0.01Suggestive
B-cell non-Hodgkins lymphomaOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
DCUN1D1Protein interaction90%MEF2BShared pathway50%TLX1Shared pathway50%TLX2Shared pathway50%TLX3Shared pathway50%TIGD5Shared pathway50%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
7%
Heart
0%
Ovary
0%
Liver
0%
Lung
0%
Gene Interaction Network
Click a node to explore
NKX2-4DCUN1D1MEF2BTLX1TLX2TLX3TIGD5
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9H2Z4
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.97LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF2.48 [0.98–1.97]
RankingsWhere NKX2-4 stands among ~20K protein-coding genes
  • #16,234of 20,598
    Most Researched13
  • #17,780of 17,882
    Most Constrained (LOEUF)1.97
Genes detectedNKX2-4
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
NK2 homeobox gene cluster: Functions and roles in human diseases.
PMID: 37492711
Genes Dis · 2023
1.00
2
NKL Homeobox Genes NKX2-3 and NKX2-4 Deregulate Megakaryocytic-Erythroid Cell Differentiation in AML.
PMID: 34768865
Int J Mol Sci · 2021
0.90
3
Novel DNA methylation biomarkers in urine for non-invasive diagnosis of bladder urothelial carcinoma.
PMID: 41420251
Clin Epigenetics · 2025
0.80
4
Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor.
PMID: 36459980
Am J Hum Genet · 2022
0.70
5
Conserved linkage of NK-2 homeobox gene pairs Nkx2-2/2-4 and Nkx2-1/2-9 in mammals.
PMID: 10818213
Mamm Genome · 2000
0.60