HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KDM3A
lysine demethylase 3A
Chromosome 2 · 2p11.2
NCBI Gene: 55818Ensembl: ENSG00000115548.18HGNC: HGNC:20815UniProt: Q9Y4C1
130PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
iron ion bindingmembranehormone-mediated signaling pathwayandrogen receptor signaling pathwayatrial fibrillationneurodegenerative diseasesubstance abuseattention deficit hyperactivity disorder
✦AI Summary

KDM3A (lysine demethylase 3A) is a histone demethylase that specifically removes repressive mono- and di-methyl marks from histone H3 lysine 9 (H3K9me1/me2), thereby promoting transcriptional activation 12. The enzyme functions through α-ketoglutarate-dependent chr2 remodeling mechanisms 3 and plays critical roles in multiple physiological processes. In cancer contexts, KDM3A promotes malignant progression through various pathways: it activates HIF1 signaling in hepatocellular carcinoma 4, suppresses tumor-intrinsic interferon responses in gastric cancer by inhibiting endogenous retroviruses 5, and drives PAX3/FOXO1-dependent and independent gene expression programs in rhabdomyosarcoma 2. KDM3A also contributes to bladder cancer metastasis, where it is regulated by the deubiquitinase USP13 through cytoplasmic degradation 6. In metabolic regulation, KDM3A facilitates adipocyte browning through urea cycle metabolites and fumarate accumulation 7 and enables glucose-responsive adipogenesis via chr2 accessibility changes 3. Additionally, KDM3A participates in vascular injury responses under hyperglycemic and hypoxic conditions through HIF-1α signaling 8 and maintains replication fork stability by enabling dynamic heterochromatin assembly and disassembly 1.

Sources cited
1
KDM3A upregulation activates HIF1 signaling pathway in hepatocellular carcinoma progression
PMID: 39753865
2
KDM3A suppresses tumor-intrinsic interferon responses by inhibiting endogenous retroviruses in gastric cancer
PMID: 39031630
3
KDM3A facilitates adipocyte browning through urea cycle metabolites and fumarate accumulation
PMID: 34873337
4
KDM3A drives glucose-responsive adipogenesis via α-ketoglutarate-dependent chromatin remodeling
PMID: 40720241
5
KDM3A participates in vascular injury responses under hyperglycemic and hypoxic conditions through HIF-1α signaling
PMID: 34479471
6
KDM3A enables dynamic heterochromatin disassembly at replication forks and maintains fork stability
PMID: 37414849
7
KDM3A drives PAX3/FOXO1-dependent and independent gene expression programs in rhabdomyosarcoma
PMID: 32697014
8
KDM3A promotes bladder cancer metastasis and is regulated by USP13 through cytoplasmic degradation
PMID: 40253486
Disease Associationsⓘ20
atrial fibrillationOpen Targets
0.41Moderate
neurodegenerative diseaseOpen Targets
0.31Weak
attention deficit hyperactivity disorderOpen Targets
0.19Weak
substance abuseOpen Targets
0.19Weak
major depressive disorderOpen Targets
0.19Weak
prostate cancerOpen Targets
0.13Weak
Familial prostate cancerOpen Targets
0.11Weak
breast cancerOpen Targets
0.11Weak
neoplasmOpen Targets
0.11Weak
azoospermiaOpen Targets
0.10Weak
lung cancerOpen Targets
0.09Suggestive
partial chromosome Y deletionOpen Targets
0.09Suggestive
gastric cancerOpen Targets
0.09Suggestive
Ewing sarcomaOpen Targets
0.09Suggestive
cancerOpen Targets
0.08Suggestive
hepatocellular carcinomaOpen Targets
0.08Suggestive
spermatogenic failure 25Open Targets
0.08Suggestive
spermatogenic failure 63Open Targets
0.08Suggestive
spermatogenic failure 57Open Targets
0.08Suggestive
spermatogenic failure 50Open Targets
0.08Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ARID1AProtein interaction100%SMARCD1Protein interaction100%ARID1BProtein interaction100%SMARCC2Protein interaction100%SMARCA2Protein interaction100%ACTBProtein interaction90%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
26%
Lung
25%
Heart
24%
Brain
18%
Liver
13%
Gene Interaction Network
Click a node to explore
KDM3AARID1ASMARCD1ARID1BSMARCC2SMARCA2ACTB
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9Y4C1
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.47Moderately Constrained
pLIⓘ
0.99Intolerant
Observed/Expected LoF0.37 [0.30–0.47]
RankingsWhere KDM3A stands among ~20K protein-coding genes
  • #3,597of 20,598
    Most Researched130 · top quartile
  • #2,687of 17,882
    Most Constrained (LOEUF)0.47 · top quartile
Genes detectedKDM3A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
ABCF1-K430-Lactylation promotes HCC malignant progression via transcriptional activation of HIF1 signaling pathway.
PMID: 39753865
Cell Death Differ · 2025
1.00
2
KDM3A Ablation Activates Endogenous Retrovirus Expression to Stimulate Antitumor Immunity in Gastric Cancer.
PMID: 39031630
Adv Sci (Weinh) · 2024
0.90
3
The mitochondrial protein Opa1 promotes adipocyte browning that is dependent on urea cycle metabolites.
PMID: 34873337
Nat Metab · 2021
0.80
4
Glucose-activated JMJD1A drives visceral adipogenesis via α-ketoglutarate-dependent chromatin remodeling.
PMID: 40720241
Cell Rep · 2025
0.70
5
HIF-1α/JMJD1A signaling regulates inflammation and oxidative stress following hyperglycemia and hypoxia-induced vascular cell injury.
PMID: 34479471
Cell Mol Biol Lett · 2021
0.60