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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KDM5A
lysine demethylase 5A
Chromosome 12 Β· 12p13.33
NCBI Gene: 5927Ensembl: ENSG00000073614.13HGNC: HGNC:9886UniProt: P29375
138PubMed Papers
21Diseases
0Drugs
11Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
histone H3K4me/H3K4me2/H3K4me3 demethylase activityhistone bindingDNA bindingtranscription cis-regulatory region bindingEl Hayek-Chahrour neurodevelopmental disorderIntellectual disabilitySeizureacute myeloid leukemia
✦AI Summary

KDM5A is a histone demethylase that specifically removes di- and tri-methyl groups from lysine 4 of histone H3 (H3K4me2/3), playing a crucial role in chr12 regulation and transcriptional control 1. The enzyme functions through its demethylase activity to modulate gene expression during key developmental processes, including maternal-to-zygotic transition in early embryogenesis where KDM5A helps remove broad H3K4me3 domains to enable proper zygotic genome activation 1. Beyond its catalytic function, KDM5A acts as an epigenetic regulator controlling the expression of various genes, including promoting WTAP expression in nucleus pulposus cells and NSUN2 expression in endometrial cancer through H3K4me3 modifications at their promoters 23. Clinically, KDM5A is significant in cancer biology, where it contributes to drug tolerance in cancer cell subpopulations by maintaining an altered chr12 state 4. Most notably, KDM5A forms oncogenic fusion proteins, particularly NUP98-KDM5A, which drives pediatric acute myeloid leukemia through aberrant transcriptional programs and represents a major therapeutic challenge with poor clinical outcomes 567. The NUP98-KDM5A fusion creates nuclear puncta through liquid-liquid phase separation mechanisms that are essential for leukemic transformation 8.

Sources cited
1
KDM5A removes broad H3K4me3 domains during maternal-to-zygotic transition and is required for normal zygotic genome activation
PMID: 27626377
2
KDM5A increases H3K4me3 at WTAP promoter in senescent nucleus pulposus cells
PMID: 35304463
3
KDM5A downregulation leads to increased H3K4me3 and NSUN2 upregulation in endometrial cancer
PMID: 38042059
4
KDM5A/RBP2 maintains drug-tolerant phenotype in cancer cell subpopulations through altered chromatin state
PMID: 20371346
5
NUP98-KDM5A fusions comprise 1.4% of pediatric AML cases with distinct molecular profiles and poor outcomes
PMID: 36815378
6
NUP98-KDM5A directly regulates essential target genes and creates druggable vulnerabilities in AML
PMID: 40389480
7
NUP98-KDM5A forms nuclear puncta through liquid-liquid phase separation mechanisms essential for transformation
PMID: 34903620
8
NUP98-KDM5A is a chimeric oncogene in pediatric non-Down syndrome acute megakaryoblastic leukemia
PMID: 28112737
Disease Associationsβ“˜21
El Hayek-Chahrour neurodevelopmental disorderOpen Targets
0.63Moderate
Intellectual disabilityOpen Targets
0.56Moderate
SeizureOpen Targets
0.44Moderate
acute myeloid leukemiaOpen Targets
0.39Weak
autism spectrum disorderOpen Targets
0.37Weak
cutaneous melanomaOpen Targets
0.37Weak
esophageal adenocarcinomaOpen Targets
0.37Weak
bile duct carcinomaOpen Targets
0.37Weak
carcinoma of liver and intrahepatic biliary tractOpen Targets
0.37Weak
colorectal adenocarcinomaOpen Targets
0.37Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.37Weak
gastric carcinomaOpen Targets
0.37Weak
hemangioblastomaOpen Targets
0.37Weak
Hepatobiliary NeoplasmOpen Targets
0.37Weak
lung carcinomaOpen Targets
0.37Weak
Ovarian Endometrioid Adenocarcinoma with Squamous DifferentiationOpen Targets
0.37Weak
skin basal cell carcinomaOpen Targets
0.37Weak
skin squamous cell carcinomaOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.32Weak
type 2 diabetes mellitusOpen Targets
0.30Weak
El Hayek-Chahrour neurodevelopmental syndromeUniProt
Pathogenic Variants11
NM_001042603.3(KDM5A):c.4074+1G>ALikely pathogenic
El Hayek-Chahrour neurodevelopmental disorder|Clear cell carcinoma of kidney|not provided
β˜…β˜…β˜†β˜†2025
NC_000012.12:g.333650delPathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001042603.3(KDM5A):c.50del (p.Pro17fs)Likely pathogenic
El Hayek-Chahrour neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 17
NM_001042603.3(KDM5A):c.1807C>T (p.Arg603Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 603
NM_001042603.3(KDM5A):c.2494C>T (p.Gln832Ter)Pathogenic
El Hayek-Chahrour neurodevelopmental disorder
β˜…β˜†β˜†β˜†2024β†’ Residue 832
NM_001042603.3(KDM5A):c.23dup (p.Tyr9fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 9
NM_001042603.3(KDM5A):c.1A>T (p.Met1Leu)Likely pathogenic
Intellectual disability;Seizure
β˜…β˜†β˜†β˜†2023β†’ Residue 1
NM_001042603.3(KDM5A):c.4283G>T (p.Arg1428Leu)Likely pathogenic
Intellectual disability;Seizure
β˜…β˜†β˜†β˜†2023β†’ Residue 1428
NM_001042603.3(KDM5A):c.2541+1G>TPathogenic
El Hayek-Chahrour neurodevelopmental disorder
β˜†β˜†β˜†β˜†2024
NM_001042603.3(KDM5A):c.1429T>G (p.Phe477Val)Pathogenic
El Hayek-Chahrour neurodevelopmental disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 477
NM_001042603.3(KDM5A):c.672+1488_1149+711delPathogenic
El Hayek-Chahrour neurodevelopmental disorder
β˜†β˜†β˜†β˜†2024
View on ClinVar β†—
Related Genes
ATP5F1AProtein interaction100%ATP5PDProtein interaction100%ATP5POProtein interaction100%ATP5PBProtein interaction100%ATP5F1CProtein interaction100%EHMT2Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
51%
Ovary
45%
Brain
43%
Liver
32%
Heart
31%
Gene Interaction Network
Click a node to explore
KDM5AATP5F1AATP5PDATP5POATP5PBATP5F1CEHMT2
PROTEIN STRUCTURE
Preparing viewer…
PDB6BGY Β· 1.22 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.27Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.20 [0.16–0.27]
RankingsWhere KDM5A stands among ~20K protein-coding genes
  • #3,339of 20,598
    Most Researched138 Β· top quartile
  • #2,745of 5,498
    Most Pathogenic Variants11
  • #909of 17,882
    Most Constrained (LOEUF)0.27 Β· top 10%
Genes detectedKDM5A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations.
PMID: 20371346
Cell Β· 2010
1.00
2
Phase Separation Mediates NUP98 Fusion Oncoprotein Leukemic Transformation.
PMID: 34903620
Cancer Discov Β· 2022
0.90
3
WTAP-mediated m
PMID: 35304463
Nat Commun Β· 2022
0.80
4
Comprehensive molecular and clinical characterization of
PMID: 36815378
Haematologica Β· 2023
0.70
5
Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition.
PMID: 27626377
Nature Β· 2016
0.60