HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KDM5B
lysine demethylase 5B
Chromosome 1 Β· 1q32.1
NCBI Gene: 10765Ensembl: ENSG00000117139.18HGNC: HGNC:18039UniProt: A0A3B3IS40
160PubMed Papers
21Diseases
0Drugs
95Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleusnegative regulation of DNA-templated transcriptiontranscription corepressor activityprotein bindingintellectual disability, autosomal recessive 65Neurodevelopmental disordergenetic disorderneurodegenerative disease
✦AI Summary

KDM5B is a histone H3K4 demethylase that regulates gene expression through removal of methylation marks at lysine 4 of histone H3 1. It demethylates trimethylated, dimethylated, and monomethylated H3K4 modifications but does not target H3K9 or H3K27 1. KDM5B functions as a transcriptional corepressor, suppressing tumor suppressor genes like BRCA1 and HOXA5 in breast cancer cells 1, while its role in melanoma appears context-dependent. Mechanistically, KDM5B promotes immune evasion in melanoma by recruiting SETDB1 to silence retroelements in a demethylase-independent manner, and depletion of KDM5B derepresses these elements to trigger interferon responses and enhance immunotherapy sensitivity 2. In nasopharyngeal carcinoma, KDM5B stabilized by deubiquitinase USP7 promotes cisplatin resistance by reducing H3K4me3 at the ZBTB16 promoter, ultimately increasing TOP2A expression 3. KDM5B also drives smooth muscle phenotypic transformation in diabetic vasculature 4 and hijacking by Epstein-Barr virus enhances metastatic potential 5. During early embryogenesis, KDM5B removes broad H3K4me3 domains required for zygotic genome activation 6. Clinically, biallelic KDM5B variants cause autosomal recessive intellectual developmental disorder 65 with developmental delay and facial dysmorphism 78, while dominant variants associate with neurodevelopmental disorders and growth abnormalities 8.

Sources cited
1
KDM5B is an H3K4 demethylase that demethylates trimethylated, dimethylated, and monomethylated H3K4; acts as transcriptional corepressor for tumor suppressors
PMID: 24952722
2
KDM5B depletion in melanoma recruits SETDB1 to silence retroelements and enhance interferon responses and immunotherapy responses
PMID: 34671158
3
USP7 stabilizes KDM5B which promotes cisplatin resistance in nasopharyngeal carcinoma via H3K4me3 reduction at ZBTB16 promoter
PMID: 38287116
4
KDM5B drives smooth muscle phenotypic transformation in diabetic macroangiopathy
PMID: 39395983
5
EBV hijacks KDM5B through chromatin interactions to promote metastatic potential in nasopharyngeal carcinoma
PMID: 40759888
6
KDM5B removes broad H3K4me3 domains required for normal zygotic genome activation in early embryos
PMID: 27626377
7
Biallelic KDM5B variants cause autosomal recessive intellectual developmental disorder with developmental delay and facial dysmorphism
PMID: 29276005
8
Dominant KDM5B variants associate with neurodevelopmental disorders, autistic behaviors, sleep disorders, and overgrowth
PMID: 39202393
Disease Associationsβ“˜21
intellectual disability, autosomal recessive 65Open Targets
0.74Strong
Neurodevelopmental disorderOpen Targets
0.60Moderate
genetic disorderOpen Targets
0.54Moderate
neurodegenerative diseaseOpen Targets
0.46Moderate
autismOpen Targets
0.37Weak
autosomal recessive non-syndromic intellectual disabilityOpen Targets
0.37Weak
autism spectrum disorderOpen Targets
0.37Weak
Neurodevelopmental abnormalityOpen Targets
0.27Weak
psoriasisOpen Targets
0.24Weak
Intellectual disabilityOpen Targets
0.22Weak
colorectal carcinomaOpen Targets
0.17Weak
Alzheimer diseaseOpen Targets
0.15Weak
behaviorOpen Targets
0.13Weak
atrial fibrillationOpen Targets
0.13Weak
atrial flutterOpen Targets
0.13Weak
bladder exstrophyOpen Targets
0.12Weak
developmental disorder of mental healthOpen Targets
0.12Weak
diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtypeOpen Targets
0.12Weak
dystonia, early-onset, and/or spastic paraplegiaOpen Targets
0.12Weak
familial thoracic aortic aneurysm and aortic dissectionOpen Targets
0.12Weak
Intellectual developmental disorder, autosomal recessive 65UniProt
Pathogenic Variants95
NM_006618.5(KDM5B):c.895C>T (p.Arg299Ter)Pathogenic
Intellectual disability, autosomal recessive 65|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 299
NM_006618.5(KDM5B):c.1321C>T (p.Arg441Ter)Pathogenic
not provided|Intellectual disability, autosomal recessive 65
β˜…β˜…β˜†β˜†2025β†’ Residue 441
NM_006618.5(KDM5B):c.3139C>T (p.Arg1047Ter)Pathogenic
not provided|Intellectual disability, autosomal recessive 65
β˜…β˜…β˜†β˜†2025β†’ Residue 1047
NM_006618.5(KDM5B):c.2945+1G>ALikely pathogenic
Intellectual disability, autosomal recessive 65|not provided
β˜…β˜…β˜†β˜†2025
NM_006618.5(KDM5B):c.1708C>T (p.Arg570Ter)Pathogenic
not provided|Intellectual disability, autosomal recessive 65
β˜…β˜…β˜†β˜†2025β†’ Residue 570
NM_006618.5(KDM5B):c.3841C>T (p.Arg1281Ter)Pathogenic
not provided|Neurodevelopmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 1281
NM_006618.5(KDM5B):c.365_366del (p.His122fs)Likely pathogenic
Intellectual disability, autosomal recessive 65|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 122
NM_006618.5(KDM5B):c.3757C>T (p.Arg1253Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1253
NM_006618.5(KDM5B):c.775C>T (p.Arg259Ter)Pathogenic
See cases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 259
NM_006618.5(KDM5B):c.2265C>G (p.Tyr755Ter)Pathogenic
Intellectual disability, autosomal recessive 65|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 755
NM_006618.5(KDM5B):c.1454del (p.Pro485fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 485
NM_006618.5(KDM5B):c.3640C>T (p.Arg1214Ter)Likely pathogenic
KDM5B-related disorder|Intellectual disability, autosomal recessive 65
β˜…β˜…β˜†β˜†2023β†’ Residue 1214
NM_006618.5(KDM5B):c.4276C>T (p.Arg1426Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 1426
NM_006618.5(KDM5B):c.4198C>T (p.Arg1400Ter)Pathogenic
Intellectual disability, autosomal recessive 65
β˜…β˜†β˜†β˜†2025β†’ Residue 1400
NM_006618.5(KDM5B):c.1969dup (p.Ile657fs)Likely pathogenic
Intellectual disability, autosomal recessive 65
β˜…β˜†β˜†β˜†2025β†’ Residue 657
NM_006618.5(KDM5B):c.2345T>G (p.Leu782Ter)Likely pathogenic
Intellectual disability, autosomal recessive 65
β˜…β˜†β˜†β˜†2025β†’ Residue 782
NM_006618.5(KDM5B):c.4422T>G (p.Tyr1474Ter)Pathogenic
Intellectual disability, autosomal recessive 65
β˜…β˜†β˜†β˜†2025β†’ Residue 1474
NM_006618.5(KDM5B):c.280G>A (p.Glu94Lys)Likely pathogenic
Neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 94
NM_006618.5(KDM5B):c.454T>G (p.Trp152Gly)Likely pathogenic
Neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 152
NM_006618.5(KDM5B):c.1103delinsAAA (p.Phe368Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 368
View on ClinVar β†—
Related Genes
ATP5F1AProtein interaction100%ATP5PDProtein interaction100%ATP5POProtein interaction100%ATP5PBProtein interaction100%ATP5F1CProtein interaction100%CBX3Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
78%
Ovary
41%
Lung
29%
Heart
21%
Liver
15%
Gene Interaction Network
Click a node to explore
KDM5BATP5F1AATP5PDATP5POATP5PBATP5F1CCBX3
PROTEIN STRUCTURE
Preparing viewer…
PDB5FYZ Β· 1.75 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.86LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.74 [0.64–0.86]
RankingsWhere KDM5B stands among ~20K protein-coding genes
  • #2,806of 20,598
    Most Researched160 Β· top quartile
  • #810of 5,498
    Most Pathogenic Variants95 Β· top quartile
  • #7,500of 17,882
    Most Constrained (LOEUF)0.86
Genes detectedKDM5B
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.
PMID: 34671158
Nature Β· 2021
1.00
2
Targeting NPM1 Epigenetically Promotes Postinfarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism.
PMID: 38390737
Circulation Β· 2024
0.90
3
Deubiquitinase USP7 stabilizes KDM5B and promotes tumor progression and cisplatin resistance in nasopharyngeal carcinoma through the ZBTB16/TOP2A axis.
PMID: 38287116
Cell Death Differ Β· 2024
0.80
4
ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer.
PMID: 39570746
Cell Rep Β· 2024
0.72
5
Spatial multiomics atlas reveals smooth muscle phenotypic transformation and metabolic reprogramming in diabetic macroangiopathy.
PMID: 39395983
Cardiovasc Diabetol Β· 2024
0.70