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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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KDM4B
lysine demethylase 4B
Chromosome 19 Β· 19p13.3
NCBI Gene: 23030Ensembl: ENSG00000127663.16HGNC: HGNC:29136UniProt: A0A0C4DFL8
110PubMed Papers
21Diseases
0Drugs
35Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmhistone H3K9 demethylase activityhistone H3K36 demethylase activityhistone H3K9me2/H3K9me3 demethylase activityintellectual developmental disorder, autosomal dominant 65hypertensiongenetic disorderessential hypertension
✦AI Summary

KDM4B (lysine demethylase 4B) is a histone-modifying enzyme that specifically demethylates trimethylated and dimethylated lysine 9 on histone H3 (H3K9me3/2), playing crucial roles in gene expression regulation and chr19 remodeling 1. The enzyme functions by removing repressive H3K9me3 marks, thereby activating gene transcription and coordinating Ξ²-catenin/Smad1-mediated signaling pathways 2. KDM4B is essential for normal brain development, with high expression levels in the hippocampus during neurogenesis 1. Loss-of-function variants cause autosomal dominant intellectual developmental disorder 65, characterized by global developmental delay, language and motor impairments, seizures, and brain malformations including corpus callosum agenesis and hippocampal abnormalities 13. The protein also regulates mesenchymal stem cell fate decisions, promoting osteogenic differentiation while suppressing adipogenesis through DLX gene expression control 42. In cancer biology, KDM4B dysfunction contributes to DNA repair defects, as oncometabolites can inhibit KDM4B activity, leading to aberrant H3K9 hypermethylation at DNA break sites and impaired homologous recombination repair 5. These diverse functions make KDM4B a potential therapeutic target for both developmental disorders and cancer treatment 6.

Sources cited
1
KDM4B demethylates H3K9me3/2, is highly expressed in hippocampus during brain development, and variants cause intellectual developmental disorder with brain malformations
PMID: 33232677
2
KDM4B coordinates Ξ²-catenin/Smad1 signaling by removing repressive H3K9me3 marks and regulates mesenchymal stem cell fate
PMID: 33571444
3
Oncometabolite-induced KDM4B inhibition causes aberrant H3K9 hypermethylation at DNA breaks and impaired homologous recombination repair
PMID: 32494005
4
KDM4B promotes osteogenic differentiation of mesenchymal stem cells by removing H3K9me3 and controlling DLX expression
PMID: 22770241
5
Biallelic KDM4B frameshift variants are viable in humans and cause more severe phenotypes than heterozygous variants
PMID: 37526414
6
KDM4B represents a potential therapeutic target for cancer treatment due to its oncogenic functions
PMID: 37923555
Disease Associationsβ“˜21
intellectual developmental disorder, autosomal dominant 65Open Targets
0.71Strong
hypertensionOpen Targets
0.52Moderate
genetic disorderOpen Targets
0.47Moderate
essential hypertensionOpen Targets
0.47Moderate
atrial fibrillationOpen Targets
0.40Moderate
developmental disorder of mental healthOpen Targets
0.40Weak
Increased blood pressureOpen Targets
0.40Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
goutOpen Targets
0.36Weak
insomniaOpen Targets
0.34Weak
Neurodevelopmental delayOpen Targets
0.33Weak
substance-related disorderOpen Targets
0.33Weak
health study participationOpen Targets
0.33Weak
type 2 diabetes mellitusOpen Targets
0.32Weak
smoking initiationOpen Targets
0.32Weak
pericarditisOpen Targets
0.32Weak
mathematical abilityOpen Targets
0.31Weak
mouth diseaseOpen Targets
0.28Weak
Neurodevelopmental disorderOpen Targets
0.28Weak
response to xenobiotic stimulusOpen Targets
0.27Weak
Intellectual developmental disorder, autosomal dominant 65UniProt
Pathogenic Variants35
NM_015015.3(KDM4B):c.432+1G>APathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025
NM_015015.3(KDM4B):c.1198_1222del (p.Ala399_Leu400insTer)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜…β˜†β˜†2025β†’ Residue 399
NM_015015.3(KDM4B):c.2303A>G (p.His768Arg)Likely pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2022β†’ Residue 768
NM_015015.3(KDM4B):c.2407C>T (p.Arg803Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 803
NM_015015.3(KDM4B):c.3005_3006insA (p.Ser1003fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 1003
NM_015015.3(KDM4B):c.432+1delPathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_015015.3(KDM4B):c.2269_2270del (p.Leu757fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 757
NM_015015.3(KDM4B):c.2954T>C (p.Leu985Pro)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 985
NM_015015.3(KDM4B):c.1771del (p.Ala591fs)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 591
NM_015015.3(KDM4B):c.253C>T (p.Gln85Ter)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 85
NM_015015.3(KDM4B):c.398A>G (p.Tyr133Cys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 133
NM_015015.3(KDM4B):c.1980G>A (p.Trp660Ter)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 660
NM_015015.3(KDM4B):c.432+2dupLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_015015.3(KDM4B):c.1217del (p.Gly406fs)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 406
NM_015015.3(KDM4B):c.994_998del (p.Leu332fs)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 332
NM_015015.3(KDM4B):c.432+1G>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_015015.3(KDM4B):c.2442-5_2445delinsGCLikely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024
NM_015015.3(KDM4B):c.2329G>T (p.Glu777Ter)Likely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2024β†’ Residue 777
NM_015015.3(KDM4B):c.2550+2T>CLikely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2023
NM_015015.3(KDM4B):c.2901+59_2901+60insTCCCGAGAGCATCACGGTGAGCTGTGGGGTGGGGCAGGGGGCGGGGGGAGGCTGGGAGCACAGCGACAACCTGTALikely pathogenic
Intellectual developmental disorder, autosomal dominant 65
β˜…β˜†β˜†β˜†2023
View on ClinVar β†—
Related Genes
JMJD1CProtein interaction95%ESR1Protein interaction92%KDM3AProtein interaction84%H4C6Protein interaction80%SMARCA4Protein interaction78%KDM2BProtein interaction78%
Tissue Expression6 tissues
Liver
100%
Ovary
96%
Lung
92%
Brain
75%
Heart
45%
Bone Marrow
35%
Gene Interaction Network
Click a node to explore
KDM4BJMJD1CESR1KDM3AH4C6SMARCA4KDM2B
PROTEIN STRUCTURE
Preparing viewer…
PDB9H44 Β· 1.74 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.37Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.27 [0.20–0.37]
RankingsWhere KDM4B stands among ~20K protein-coding genes
  • #4,323of 20,598
    Most Researched110 Β· top quartile
  • #1,673of 5,498
    Most Pathogenic Variants35
  • #1,721of 17,882
    Most Constrained (LOEUF)0.37 Β· top 10%
Genes detectedKDM4B
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.
PMID: 33232677
Am J Hum Genet Β· 2020
1.00
2
Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging.
PMID: 33571444
Cell Stem Cell Β· 2021
0.90
3
Oncometabolites suppress DNA repair by disrupting local chromatin signalling.
PMID: 32494005
Nature Β· 2020
0.80
4
KDM4B: A Nail for Every Hammer?
PMID: 30759871
Genes (Basel) Β· 2019
0.70
5
The Diverse Roles of Histone Demethylase KDM4B in Normal and Cancer Development and Progression.
PMID: 35186950
Front Cell Dev Biol Β· 2021
0.60