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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.
LHX2
LIM homeobox 2
Chromosome 9 Β· 9q33.3
NCBI Gene: 9355Ensembl: ENSG00000106689.11HGNC: HGNC:6594UniProt: B3KNJ5
38PubMed Papers
20Diseases
0Drugs
7Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingDNA-binding transcription factor activity, RNA polymerase II-specificRNA polymerase II transcription regulatory region sequence-specific DNA bindingregulation of transcription by RNA polymerase IIneurodegenerative diseasehair colorNeurodevelopmental disordercomplex neurodevelopmental disorder
✦AI Summary

LHX2 is a LIM homeobox transcription factor that functions as a DNA-binding transcriptional regulator with critical roles across multiple developmental and disease contexts. It acts as a transcriptional activator controlling cell differentiation in lymphoid and neural cell types 1, with essential functions in forebrain, eye, olfactory system, and liver development 2. During limb development, LHX2 is regulated by Fgf and Wnt signaling through tissue-specific cis-regulatory modules and coordinates proliferation and patterning 3. In disease contexts, LHX2 haploinsufficiency causes variable neurodevelopmental disorders characterized by developmental delays, autism spectrum disorder, intellectual disability, and microcephaly through loss-of-function mechanisms 4. In hepatic disease, HSC-specific LHX2 expression promotes liver regeneration while inhibiting fibrosis by upregulating pro-regenerative factors like HGF and blocking TGF-Ξ² signaling via SMAD6 upregulation 5. Conversely, LHX2 drives aggressive tumor phenotypes: in prostate cancer, it forms a positive feedback loop with glycolytic metabolism and histone lactylation to promote neuroendocrine transdifferentiation 6, while in medulloblastoma, it enhances oncogenic BMP signaling, promotes stemness, and increases chemoresistance and metastatic potential 7. In cholangiocarcinoma, fibroblast-specific LHX2 expression contributes to tumor-promoting microenvironment remodeling 8.

Sources cited
1
LHX2 expressed in hepatic stellate cells promotes liver regeneration and inhibits fibrosis by upregulating HGF and blocking TGF-Ξ² signaling via SMAD6
PMID: 39693275
2
LHX2 drives neuroendocrine prostate cancer progression through a feedback loop coupling glycolysis to histone lactylation and DNMT1-mediated epigenetic rewiring
PMID: 40899980
3
LHX2 is a fibroblast-specific transcriptional motif in intrahepatic cholangiocarcinoma associated with tumor-promoting microenvironment remodeling
PMID: 38702814
4
LHX2 is a homeodomain transcription factor required for early eye development and cell fate determination
PMID: 35817658
5
LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma, promoting stemness, chemoresistance, and tumor propagation
PMID: 40148468
6
LHX2 haploinsufficiency causes variable neurodevelopmental disorder through loss-of-function mechanisms affecting transcriptional activation and protein interactions
PMID: 37057675
7
LHX2 is regulated by Fgf and Wnt signaling through limb-specific cis-regulatory modules during vertebrate limb development
PMID: 40052149
8
LHX2 is essential for forebrain, eye, olfactory system, and liver development with tissue-specific enhancers regulating its expression
PMID: 21629789
Disease Associationsβ“˜20
neurodegenerative diseaseOpen Targets
0.54Moderate
hair colorOpen Targets
0.52Moderate
Neurodevelopmental disorderOpen Targets
0.51Moderate
complex neurodevelopmental disorderOpen Targets
0.42Moderate
type 2 diabetes mellitusOpen Targets
0.34Weak
alcohol drinkingOpen Targets
0.33Weak
ankylosing spondylitisOpen Targets
0.32Weak
adolescent idiopathic scoliosisOpen Targets
0.17Weak
systemic lupus erythematosusOpen Targets
0.12Weak
cholelithiasisOpen Targets
0.11Weak
non-small cell lung carcinomaOpen Targets
0.10Weak
nasopharyngeal carcinomaOpen Targets
0.10Weak
neoplasmOpen Targets
0.10Suggestive
breast cancerOpen Targets
0.09Suggestive
mathematical abilityOpen Targets
0.09Suggestive
osteosarcomaOpen Targets
0.08Suggestive
esophageal squamous cell carcinomaOpen Targets
0.07Suggestive
triple-negative breast cancerOpen Targets
0.07Suggestive
epilepsyOpen Targets
0.07Suggestive
cervical cancerOpen Targets
0.07Suggestive
Pathogenic Variants7
NM_004789.4(LHX2):c.240C>A (p.Cys80Ter)Pathogenic
LHX2-associated neurodevelopmental disorder
β˜…β˜†β˜†β˜†2026β†’ Residue 80
NM_004789.4(LHX2):c.673_694del (p.Pro225fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 225
NM_004789.4(LHX2):c.750del (p.Asp250fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 250
NM_004789.4(LHX2):c.289_293del (p.Lys96_Asp97insTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 96
NM_004789.4(LHX2):c.948C>G (p.Asn316Lys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 316
NM_004789.4(LHX2):c.437G>A (p.Cys146Tyr)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 146
NM_004789.4(LHX2):c.182_187delinsACCT (p.Ser61fs)Likely pathogenic
Variable neurodevelopmental disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 61
View on ClinVar β†—
Related Genes
NEUROG2Protein interaction98%LDB2Protein interaction94%EBF1Protein interaction94%CITED2Protein interaction90%SSBP3Protein interaction89%ROBO2Protein interaction83%
Tissue Expression6 tissues
Brain
100%
Liver
8%
Bone Marrow
0%
Ovary
0%
Heart
0%
Lung
0%
Gene Interaction Network
Click a node to explore
LHX2NEUROG2LDB2EBF1CITED2SSBP3ROBO2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P50458
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.37Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.19 [0.10–0.37]
RankingsWhere LHX2 stands among ~20K protein-coding genes
  • #10,505of 20,598
    Most Researched38
  • #3,237of 5,498
    Most Pathogenic Variants7
  • #1,698of 17,882
    Most Constrained (LOEUF)0.37 Β· top 10%
Genes detectedLHX2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Lhx2 specifically expressed in HSCs promotes liver regeneration and inhibits liver fibrosis.
PMID: 39693275
Hepatology Β· 2025
1.00
2
LHX2 Rewires the Metabolic and Epigenetic Landscape to Drive Tumor Progression in Prostate Cancer.
PMID: 40899980
Cancer Res Β· 2025
0.90
3
Integrative analyses of bulk and single-cell transcriptomics reveals the infiltration and crosstalk of cancer-associated fibroblasts as a novel predictor for prognosis and microenvironment remodeling in intrahepatic cholangiocarcinoma.
PMID: 38702814
J Transl Med Β· 2024
0.80
4
Cell fate decisions, transcription factors and signaling during early retinal development.
PMID: 35817658
Prog Retin Eye Res Β· 2022
0.70
5
The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma.
PMID: 40148468
Cell Death Differ Β· 2025
0.60