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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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KDM3B
lysine demethylase 3B
Chromosome 5 Β· 5q31.2
NCBI Gene: 51780Ensembl: ENSG00000120733.16HGNC: HGNC:1337UniProt: Q7LBC6
105PubMed Papers
21Diseases
0Drugs
43Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmchromatin DNA bindinghistone H3K9 demethylase activitytranscription coregulator activityDiets-Jongmans syndromegenetic disorderNeurodevelopmental delaysyndromic intellectual disability
✦AI Summary

KDM3B (lysine demethylase 3B) is a histone demethylase that specifically removes mono- and dimethyl marks from lysine 9 of histone H3 (H3K9me1/2), thereby regulating chr5 structure and gene transcription 1. This enzymatic activity involves demethylation generating formaldehyde and succinate as byproducts. KDM3B functions as a context-dependent epigenetic regulator with both tumor-suppressive and tumor-promoting roles depending on cancer type 1. Mechanistically, KDM3B controls transcription through H3K9 demethylation and coordinates with other epigenetic factors. For example, KDM3B balances H3K9 methylation at the MLL/KMT2A locus in cooperation with methyltransferase G9a, regulating CTCF occupancy and preventing leukemic amplifications and rearrangements 2. In fusion-positive rhabdomyosarcoma, KDM3B supports PAX3-FOXO1 oncogenic transcriptional activity 3. Clinically, KDM3B shows diverse disease relevance. Dysregulation associates with infertility, obesity, metabolic syndromes, and cancers 1. KDM3B is underexpressed in acute myeloid leukemia with specific translocations 4, while KDM3B-ETF1 fusion promotes breast cancer invasion via WNT/Ξ²-catenin pathway activation 5. Genome-wide association studies identified KDM3B SNPs linked to radiation therapy-induced urinary toxicity in prostate cancer patients through mechanisms involving circular RNA regulation and fibrotic responses 67. KDM3B represents a tractable therapeutic target across multiple malignancies.

Sources cited
1
KDM3B (lysine demethylase 3B) is a histone demethylase that specifically removes mono- and dimethyl marks from lysine 9 of histone H3 (H3K9me1/2), thereby regulating chr5 structure and gene transcription .
PMID: 38926399
2
For example, KDM3B balances H3K9 methylation at the MLL/KMT2A locus in cooperation with methyltransferase G9a, regulating CTCF occupancy and preventing leukemic amplifications and rearrangements .
PMID: 37788669
3
In fusion-positive rhabdomyosarcoma, KDM3B supports PAX3-FOXO1 oncogenic transcriptional activity .
PMID: 38402212
4
KDM3B is underexpressed in acute myeloid leukemia with specific translocations , while KDM3B-ETF1 fusion promotes breast cancer invasion via WNT/Ξ²-catenin pathway activation .
PMID: 28540746
5
KDM3B is underexpressed in acute myeloid leukemia with specific translocations , while KDM3B-ETF1 fusion promotes breast cancer invasion via WNT/Ξ²-catenin pathway activation .
PMID: 33828234
Disease Associationsβ“˜21
Diets-Jongmans syndromeOpen Targets
0.77Strong
genetic disorderOpen Targets
0.51Moderate
Neurodevelopmental delayOpen Targets
0.41Moderate
syndromic intellectual disabilityOpen Targets
0.40Weak
Neurodevelopmental disorderOpen Targets
0.37Weak
Rare genetic epilepsyOpen Targets
0.34Weak
Rare genetic intellectual disabilityOpen Targets
0.34Weak
pilocytic astrocytomaOpen Targets
0.33Weak
autism spectrum disorderOpen Targets
0.28Weak
atrial fibrillationOpen Targets
0.26Weak
medulloblastomaOpen Targets
0.24Weak
Abnormality of the skeletal systemOpen Targets
0.23Weak
esophageal diseaseOpen Targets
0.19Weak
hypertensionOpen Targets
0.19Weak
JaundiceOpen Targets
0.18Weak
obesityOpen Targets
0.18Weak
gastroesophageal reflux diseaseOpen Targets
0.16Weak
mixed connective tissue diseaseOpen Targets
0.15Weak
developmental disorder of mental healthOpen Targets
0.12Weak
smoking initiationOpen Targets
0.10Suggestive
Diets-Jongmans syndromeUniProt
Pathogenic Variants43
NM_016604.4(KDM3B):c.4549C>T (p.Arg1517Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 1517
NM_016604.4(KDM3B):c.4414C>T (p.Arg1472Ter)Pathogenic
Neurodevelopmental delay|KDM3B-related disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1472
NM_016604.4(KDM3B):c.4631A>G (p.Tyr1544Cys)Pathogenic
Diets-Jongmans syndrome|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 1544
NM_016604.4(KDM3B):c.4627G>A (p.Ala1543Thr)Likely pathogenic
Diets-Jongmans syndrome|See cases
β˜…β˜…β˜†β˜†2022β†’ Residue 1543
NM_016604.4(KDM3B):c.4821del (p.Glu1608fs)Likely pathogenic
Diets-Jongmans syndrome
β˜…β˜†β˜†β˜†2026β†’ Residue 1608
NM_016604.4(KDM3B):c.3768del (p.Leu1257fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1257
NM_016604.4(KDM3B):c.2845C>T (p.Arg949Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 949
NM_016604.4(KDM3B):c.3256C>T (p.Gln1086Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1086
NM_016604.4(KDM3B):c.2409del (p.Leu804fs)Pathogenic
Diets-Jongmans syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 804
NM_016604.4(KDM3B):c.4606dup (p.Leu1536fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 1536
NM_016604.4(KDM3B):c.4622A>G (p.Tyr1541Cys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1541
NM_016604.4(KDM3B):c.2752C>T (p.Arg918Cys)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 918
NM_016604.4(KDM3B):c.3749_3750del (p.Glu1250fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 1250
NM_016604.4(KDM3B):c.2144del (p.Pro715fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 715
NM_016604.4(KDM3B):c.4616A>G (p.Lys1539Arg)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1539
NM_016604.4(KDM3B):c.344C>T (p.Ala115Val)Likely pathogenic
Diets-Jongmans syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 115
NM_016604.4(KDM3B):c.2827C>T (p.Arg943Trp)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 943
NM_016604.4(KDM3B):c.4888C>T (p.Arg1630Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1630
NM_016604.4(KDM3B):c.4981C>T (p.Arg1661Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1661
NM_016604.4(KDM3B):c.4201A>G (p.Asn1401Asp)Likely pathogenic
Diets-Jongmans syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 1401
View on ClinVar β†—
Related Genes
MSL1Shared pathway100%HDGFL1Shared pathway100%HIPK4Shared pathway100%HMGB4Shared pathway100%NAA40Shared pathway100%NSD1Shared pathway100%
Tissue Expression6 tissues
Ovary
100%
Bone Marrow
93%
Heart
90%
Brain
88%
Lung
79%
Liver
39%
Gene Interaction Network
Click a node to explore
KDM3BMSL1HDGFL1HIPK4HMGB4NAA40NSD1
PROTEIN STRUCTURE
Preparing viewer…
PDB5R7X Β· 1.44 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.12Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.07 [0.04–0.12]
RankingsWhere KDM3B stands among ~20K protein-coding genes
  • #4,534of 20,598
    Most Researched105 Β· top quartile
  • #1,464of 5,498
    Most Pathogenic Variants43
  • #104of 17,882
    Most Constrained (LOEUF)0.12 Β· top 1%
Genes detectedKDM3B
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Epigenetic roles of KDM3B and KDM3C in tumorigenesis and their therapeutic implications.
PMID: 38926399
Cell Death Dis Β· 2024
1.00
2
CRISPR Dependency Screens in Primary Hematopoietic Stem Cells Identify KDM3B as a Genotype-specific Vulnerability in IDH2- and TET2-mutant Cells.
PMID: 38819218
Cancer Discov Β· 2024
0.90
3
Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement.
PMID: 37788669
Cell Β· 2023
0.80
4
KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma.
PMID: 38402212
Nat Commun Β· 2024
0.70
5
KDM3B Regulates Postradiation Fibrotic Responses in Prostate Stroma via N
PMID: 40588066
Int J Radiat Oncol Biol Phys Β· 2025
0.60