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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.
KDM6B
lysine demethylase 6B
Chromosome 17 Β· 17p13.1
NCBI Gene: 23135Ensembl: ENSG00000132510.12HGNC: HGNC:29012UniProt: O15054
165PubMed Papers
21Diseases
0Drugs
112Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
histone H3K27me2/H3K27me3 demethylase activityprotein bindingpositive regulation of cold-induced thermogenesisnucleusneurodevelopmental disorder with coarse facies and mild distal skeletal abnormalitiesgenetic disorderdevelopmental disorder of mental healthsyndromic intellectual disability
✦AI Summary

KDM6B (lysine demethylase 6B) is a histone demethylase that specifically removes di- and trimethyl groups from lysine 27 of histone H3 (H3K27me2/me3), playing crucial roles in chr17 remodeling and gene expression regulation 1. The enzyme functions as an Ξ±-ketoglutarate-dependent demethylase, utilizing this metabolite as a cofactor for its catalytic activity 2. KDM6B demonstrates significant clinical relevance through its involvement in multiple disease processes. De novo variants in KDM6B cause a neurodevelopmental disorder characterized by cognitive deficits, hypotonia, and behavioral abnormalities, though the phenotypic spectrum is broader than initially described 3. In cancer, KDM6B promotes tumor progression through multiple mechanisms: it enhances osteosarcoma metastasis by demethylating the LDHA promoter 1, drives immunosuppression in prostate cancer through iron-dependent activation 4, and its downregulation by cancer-derived exosomal miR-138-5p promotes tumor-associated macrophage M2 polarization 5. Additionally, KDM6B regulates hepatic autophagy and lipid metabolism through FGF21 signaling 6 and contributes to interferon-stimulated gene expression in systemic lupus erythematosus 2. These diverse functions establish KDM6B as a critical epigenetic regulator with significant therapeutic potential across multiple pathological conditions.

Sources cited
1
De novo KDM6B variants cause neurodevelopmental disorder with cognitive deficits and variable phenotype
PMID: 37196654
2
KDM6B demethylates H3K27me2/me3 and promotes osteosarcoma lung metastasis via LDHA regulation
PMID: 33664867
3
Iron-dependent KDM6B activation drives immunosuppression in prostate cancer
PMID: 39426954
4
Cancer-derived exosomal miR-138-5p downregulates KDM6B to promote M2 macrophage polarization
PMID: 34093857
5
FGF21 signaling activates KDM6B to regulate hepatic autophagy and lipid degradation
PMID: 32042044
6
KDM6B functions as Ξ±-ketoglutarate-dependent demethylase regulating interferon-stimulated genes in lupus
PMID: 37800478
Disease Associationsβ“˜21
neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalitiesOpen Targets
0.79Strong
genetic disorderOpen Targets
0.53Moderate
developmental disorder of mental healthOpen Targets
0.41Moderate
syndromic intellectual disabilityOpen Targets
0.37Weak
autosomal recessive non-syndromic intellectual disabilityOpen Targets
0.37Weak
Neurodevelopmental abnormalityOpen Targets
0.33Weak
Abnormality of the skeletal systemOpen Targets
0.27Weak
Neurodevelopmental delayOpen Targets
0.27Weak
Intellectual disabilityOpen Targets
0.27Weak
autism spectrum disorderOpen Targets
0.26Weak
ArthropathyOpen Targets
0.14Weak
clonal hematopoiesisOpen Targets
0.13Weak
Mobius syndromeOpen Targets
0.11Weak
Moebius syndromeOpen Targets
0.11Weak
neoplasmOpen Targets
0.11Weak
acute myeloid leukemiaOpen Targets
0.10Weak
cancerOpen Targets
0.10Suggestive
gastric cancerOpen Targets
0.10Suggestive
breast cancerOpen Targets
0.10Suggestive
neuroblastomaOpen Targets
0.10Suggestive
Stolerman neurodevelopmental syndromeUniProt
Pathogenic Variants112
NM_001348716.2(KDM6B):c.1085_1088del (p.Glu362fs)Pathogenic
not provided|Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜…β˜†β˜†2025β†’ Residue 362
NM_001348716.2(KDM6B):c.685C>T (p.Arg229Ter)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|not provided|Intellectual disability
β˜…β˜…β˜†β˜†2025β†’ Residue 229
NM_001348716.2(KDM6B):c.4187_4189del (p.Phe1396del)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1396
NM_001348716.2(KDM6B):c.1483C>T (p.Arg495Ter)Pathogenic
Neurodevelopmental delay|Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 495
NM_001348716.2(KDM6B):c.2865dup (p.Ala956fs)Likely pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜…β˜†β˜†2025β†’ Residue 956
NM_001348716.2(KDM6B):c.1416_1417del (p.Cys473fs)Pathogenic
not provided|Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜…β˜†β˜†2025β†’ Residue 473
NM_001348716.2(KDM6B):c.1299_1300del (p.His434fs)Pathogenic
See cases|Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜…β˜†β˜†2025β†’ Residue 434
NM_001348716.2(KDM6B):c.595C>T (p.Arg199Ter)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 199
NM_001348716.2(KDM6B):c.4495C>T (p.Arg1499Ter)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜…β˜†β˜†2022β†’ Residue 1499
NM_001348716.2(KDM6B):c.4436ACA[1] (p.Asn1480del)Likely pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜†β˜†β˜†2025β†’ Residue 1480
NM_001348716.2(KDM6B):c.2118del (p.Arg707fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 707
NM_001348716.2(KDM6B):c.4737+2T>CPathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|Gastric cancer
β˜…β˜†β˜†β˜†2025
NM_001348716.2(KDM6B):c.4506_4510del (p.Trp1502_Glu1504delinsTer)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜†β˜†β˜†2025β†’ Residue 1502
NM_001348716.2(KDM6B):c.1507G>T (p.Glu503Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 503
NM_001348716.2(KDM6B):c.1087_1088del (p.Ser363fs)Likely pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜†β˜†β˜†2025β†’ Residue 363
NM_001348716.2(KDM6B):c.2584C>T (p.Gln862Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 862
NM_001348716.2(KDM6B):c.1172del (p.Pro391fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 391
NM_001348716.2(KDM6B):c.1108_1115delinsCGTTTCACCAGCAG (p.Met370_Asp371delinsArgPheThrSer)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 370
NM_001348716.2(KDM6B):c.2041C>T (p.Gln681Ter)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
β˜…β˜†β˜†β˜†2024β†’ Residue 681
NM_001348716.2(KDM6B):c.1537dup (p.Arg513fs)Pathogenic
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 513
View on ClinVar β†—
Related Genes

No related genes found for this gene.

Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network

No interaction data available for this gene.

PROTEIN STRUCTURE
Preparing viewer…
PDB2XXZ Β· 1.80 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.21Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.15 [0.10–0.21]
RankingsWhere KDM6B stands among ~20K protein-coding genes
  • #2,711of 20,598
    Most Researched165 Β· top quartile
  • #699of 5,498
    Most Pathogenic Variants112 Β· top quartile
  • #509of 17,882
    Most Constrained (LOEUF)0.21 Β· top 5%
Genes detectedKDM6B
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder.
PMID: 37196654
Am J Hum Genet Β· 2023
1.00
2
Dysfunction of autophagy in high-fat diet-induced non-alcoholic fatty liver disease.
PMID: 37700498
Autophagy Β· 2024
0.90
3
KDM6B-mediated histone demethylation of LDHA promotes lung metastasis of osteosarcoma.
PMID: 33664867
Theranostics Β· 2021
0.80
4
Iron-loaded cancer-associated fibroblasts induce immunosuppression in prostate cancer.
PMID: 39426954
Nat Commun Β· 2024
0.70
5
The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism.
PMID: 31221981
Exp Mol Med Β· 2019
0.64