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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.
KDM2B
lysine demethylase 2B
Chromosome 12 Β· 12q24.31
NCBI Gene: 84678Ensembl: ENSG00000089094.21HGNC: HGNC:13610UniProt: A0ABB0MV36
128PubMed Papers
20Diseases
0Drugs
19Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmprotein bindingPcG protein complexzinc ion bindingNeurodevelopmental disorderhypertensionessential hypertensiongenetic disorder
✦AI Summary

KDM2B is a histone demethylase that catalyzes removal of methyl groups from histone H3, primarily demethylating trimethylated H3 lysine-4 and dimethylated H3 lysine-36 12. Beyond its canonical demethylase activity, KDM2B functions in non-canonical PRC1.1 complex as a chr12-binding component regulating H2AK119 monoubiquitylation 34. KDM2B exhibits context-dependent transcriptional roles: it represses ribosomal RNA gene transcription 1, but independently of demethylase activity, it promotes IL-6 production through Brg1-mediated chr12 remodeling 5 and regulates metabolic enzyme expression in concert with MYC and ATF4 6. Pathogenic KDM2B variants cause neurodevelopmental disorder presenting with developmental delay, intellectual disability, autism, and congenital organ anomalies, with an identifiable epigenetic signature in peripheral blood 7. KDM2B hyperactivity associates with tumorigenesis; KDM2B fusions characterize soft tissue sarcomas within the BCOR-associated sarcoma family 8. In immune contexts, KDM2B regulates regulatory T cell plasticity and activation, and its deletion enhances anti-tumor immunity 4. KDM2B's demethylase activity can be inhibited by oncometabolite 2-hydroxyglutarate in IDH-mutant cancers, altering genome-wide methylation patterns 9.

Sources cited
1
KDM2B demethylates H3K4me3 and H3K36me2, represses ribosomal RNA genes
PMID: 16362057
2
KDM2B preferentially demethylates trimethylated H3K4 and dimethylated H3K36
PMID: 17994099
3
KDM2B promotes IL-6 production through Brg1-mediated chromatin remodeling independent of demethylase activity
PMID: 31197256
4
Pathogenic KDM2B variants cause neurodevelopmental disorder with developmental delay, intellectual disability, autism, and congenital anomalies
PMID: 36322151
5
KDM2B fusions characterize soft tissue sarcomas within BCOR-associated sarcoma family
PMID: 37634866
6
KDM2B acts as chromatin-binding component in PRC1.1 regulating H2AK119ub1 and bone formation
PMID: 40341537
7
KDM2B in PRC1.1 regulates regulatory T cell plasticity; deletion enhances anti-tumor immunity
PMID: 40527320
8
KDM2B regulates metabolic enzyme expression in concert with MYC and ATF4 in triple-negative breast cancer
PMID: 37935302
9
2-Hydroxyglutarate competitively inhibits KDM2B and other histone demethylases in IDH-mutant cancers
PMID: 21251613
Disease Associationsβ“˜20
Neurodevelopmental disorderOpen Targets
0.52Moderate
hypertensionOpen Targets
0.47Moderate
essential hypertensionOpen Targets
0.43Moderate
genetic disorderOpen Targets
0.42Moderate
type 2 diabetes mellitusOpen Targets
0.41Moderate
diabetes mellitusOpen Targets
0.40Weak
Intellectual disabilityOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.36Weak
diabetic retinopathyOpen Targets
0.35Weak
diabetic eye diseaseOpen Targets
0.35Weak
atrial fibrillationOpen Targets
0.29Weak
Increased blood pressureOpen Targets
0.28Weak
Global developmental delayOpen Targets
0.26Weak
microcephalyOpen Targets
0.26Weak
HypotoniaOpen Targets
0.26Weak
infantile spasmsOpen Targets
0.26Weak
alcohol drinkingOpen Targets
0.25Weak
obstructive sleep apneaOpen Targets
0.24Weak
brain aneurysmOpen Targets
0.24Weak
cardiovascular diseaseOpen Targets
0.20Weak
Pathogenic Variants19
NM_032590.5(KDM2B):c.1841G>C (p.Arg614Pro)Pathogenic
not provided|KDM2B-related syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 614
NM_032590.5(KDM2B):c.758A>G (p.His253Arg)Likely pathogenic
Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜…β˜†β˜†β˜†2026β†’ Residue 253
NM_032590.5(KDM2B):c.1936dup (p.Cys646fs)Likely pathogenic
Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜…β˜†β˜†β˜†2026β†’ Residue 646
NM_032590.5(KDM2B):c.2913del (p.Gln971fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 971
NM_032590.5(KDM2B):c.1945C>T (p.Arg649Trp)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 649
NM_032590.5(KDM2B):c.3005_3023del (p.Asn1002fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1002
NM_032590.5(KDM2B):c.1880G>C (p.Cys627Ser)Pathogenic
KDM2B-related disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 627
NM_032590.5(KDM2B):c.1913G>C (p.Gly638Ala)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 638
NM_032590.5(KDM2B):c.778-2A>GLikely pathogenic
KDM2B-related disorder
β˜…β˜†β˜†β˜†2024
NM_032590.5(KDM2B):c.1913G>A (p.Gly638Asp)Pathogenic
not provided|Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜…β˜†β˜†β˜†2023β†’ Residue 638
NM_032590.5(KDM2B):c.1847G>T (p.Cys616Phe)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2023β†’ Residue 616
NM_032590.5(KDM2B):c.1900AAG[1] (p.Lys635del)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 635
NM_032590.5(KDM2B):c.1846T>C (p.Cys616Arg)Pathogenic
not provided|Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜…β˜†β˜†β˜†2023β†’ Residue 616
NM_032590.5(KDM2B):c.1946G>A (p.Arg649Gln)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 649
NM_032590.5(KDM2B):c.1912G>A (p.Gly638Ser)Pathogenic
Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜†β˜†β˜†β˜†2026β†’ Residue 638
NM_032590.5(KDM2B):c.1889G>C (p.Cys630Ser)Pathogenic
Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
β˜†β˜†β˜†β˜†2026β†’ Residue 630
NM_032590.5(KDM2B):c.1838G>A (p.Cys613Tyr)Likely pathogenic
not provided
β˜†β˜†β˜†β˜†2024β†’ Residue 613
NM_032590.5(KDM2B):c.3325del (p.His1109fs)Likely pathogenic
KDM2B-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 1109
NM_032590.5(KDM2B):c.500G>A (p.Arg167Gln)Likely pathogenic
KDM2B-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 167
View on ClinVar β†—
Related Genes
YAF2Protein interaction100%PHF19Protein interaction100%BCORL1Protein interaction100%BMI1Protein interaction100%CUL1Protein interaction100%POU5F1Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
63%
Brain
57%
Lung
56%
Liver
54%
Heart
31%
Gene Interaction Network
Click a node to explore
KDM2BYAF2PHF19BCORL1BMI1CUL1POU5F1
PROTEIN STRUCTURE
Preparing viewer…
PDB4O64 Β· 2.13 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.27Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.19 [0.14–0.27]
RankingsWhere KDM2B stands among ~20K protein-coding genes
  • #3,656of 20,598
    Most Researched128 Β· top quartile
  • #2,230of 5,498
    Most Pathogenic Variants19
  • #883of 17,882
    Most Constrained (LOEUF)0.27 Β· top 5%
Genes detectedKDM2B
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of Ξ±-ketoglutarate-dependent dioxygenases.
PMID: 21251613
Cancer Cell Β· 2011
1.00
2
Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature.
PMID: 36322151
Genet Med Β· 2023
0.90
3
KDM2B promotes IL-6 production and inflammatory responses through Brg1-mediated chromatin remodeling.
PMID: 31197256
Cell Mol Immunol Β· 2020
0.80
4
KDM2B-Rearranged Soft Tissue Sarcomas Expand the Concept of BCOR-Associated Sarcoma.
PMID: 37634866
Mod Pathol Β· 2023
0.70
5
Targeted disruption of PRC1.1 complex enhances bone remodeling.
PMID: 40341537
Nat Commun Β· 2025
0.60