The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demeth... See more...

Aliases for KDM6B Gene

Aliases for KDM6B Gene

  • Lysine Demethylase 6B 2 3 4 5
  • Jumonji Domain Containing 3, Histone Lysine Demethylase 2 3
  • [Histone H3]-Trimethyl-L-Lysine(27) Demethylase 6B 3 4
  • Jumonji Domain-Containing Protein 3 3 4
  • Lysine (K)-Specific Demethylase 6B 2 3
  • JmjC Domain-Containing Protein 3 3 4
  • Lysine-Specific Demethylase 6B 3 4
  • KIAA0346 2 4
  • JMJD3 3 4
  • Jumonji Domain Containing 3 2
  • EC 1.14.11.68 4
  • EC 1.14.11 50
  • NEDCFSA 3
  • KDM6B 5

External Ids for KDM6B Gene

Previous HGNC Symbols for KDM6B Gene

  • JMJD3

Previous GeneCards Identifiers for KDM6B Gene

  • GC17P007686

Summaries for KDM6B Gene

Entrez Gene Summary for KDM6B Gene

  • The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

GeneCards Summary for KDM6B Gene

KDM6B (Lysine Demethylase 6B) is a Protein Coding gene. Diseases associated with KDM6B include Neurodevelopmental Disorder With Coarse Facies And Mild Distal Skeletal Abnormalities and Agenesis Of Corpus Callosum, Cardiac, Ocular, And Genital Syndrome. Among its related pathways are Chromatin organization and Pathways Affected in Adenoid Cystic Carcinoma. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and dioxygenase activity. An important paralog of this gene is KDM6A.

UniProtKB/Swiss-Prot Summary for KDM6B Gene

  • Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Demethylates trimethylated and dimethylated H3 'Lys-27' (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression by acting as a link between T-box factors and the SMARCA4-containing SWI/SNF remodeling complex (By similarity).

Tocris Summary for KDM6B Gene

  • Histone demethylases (KDMs) are a family of enzymes that catalyze the removal of methyl groups from lysine and arginine residues on histone tails. They reverse the methylation of lysine and arginine residues that is catalyzed by histone methyltransferases.

No data available for CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for KDM6B Gene

Genomics for KDM6B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KDM6B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM6B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KDM6B

Top Transcription factor binding sites by QIAGEN in the KDM6B gene promoter:
  • c-Ets-1
  • HNF-4alpha1
  • HNF-4alpha2
  • LCR-F1
  • NF-kappaB
  • NF-kappaB1
  • Nkx2-5
  • Olf-1
  • Pax-6
  • XBP-1

Genomic Locations for KDM6B Gene

Latest Assembly
chr17:7,834,210-7,854,796
(GRCh38/hg38)
Size:
20,587 bases
Orientation:
Plus strand

Previous Assembly
chr17:7,737,535-7,758,114
(GRCh37/hg19 by Entrez Gene)
Size:
20,580 bases
Orientation:
Plus strand

chr17:7,743,222-7,758,114
(GRCh37/hg19 by Ensembl)
Size:
14,893 bases
Orientation:
Plus strand

Genomic View for KDM6B Gene

Genes around KDM6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM6B Gene

Proteins for KDM6B Gene

  • Protein details for KDM6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15054-KDM6B_HUMAN
    Recommended name:
    Lysine-specific demethylase 6B
    Protein Accession:
    O15054
    Secondary Accessions:
    • C9IZ40
    • Q96G33

    Protein attributes for KDM6B Gene

    Size:
    1643 amino acids
    Molecular mass:
    176632 Da
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with TLE1 (By similarity). Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B (PubMed:17825402). Interacts with TBX21, SMARCA4, SMARCC1 and SMARCC2 (By similarity).
    SequenceCaution:
    • Sequence=BAA21572.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM6B Gene

    Alternative splice isoforms for KDM6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM6B Gene

Selected DME Specific Peptides for KDM6B Gene

O15054:
  • QRPGDLVWINAGTVHWVQA
  • GWCNNIAWNVGPLTA
  • KLNPPTPSIYLE
  • IKFGTNIDLSD
  • SHTTIAKYAQYQA

Post-translational modifications for KDM6B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for KDM6B Gene

Gene Families for KDM6B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for KDM6B Gene

InterPro:
Blocks:
  • Transcription factor jumonji, jmjC

Suggested Antigen Peptide Sequences for KDM6B Gene

GenScript: Design optimal peptide antigens:
  • Lysine demethylase 6B (KDM6B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15054

UniProtKB/Swiss-Prot:

KDM6B_HUMAN :
  • Belongs to the UTX family.
Family:
  • Belongs to the UTX family.
genes like me logo Genes that share domains with KDM6B: view

Function for KDM6B Gene

Molecular function for KDM6B Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Demethylates trimethylated and dimethylated H3 'Lys-27' (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression by acting as a link between T-box factors and the SMARCA4-containing SWI/SNF remodeling complex (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(27)-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L-lysyl(27)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60224, Rhea:RHEA-COMP:15535, Rhea:RHEA-COMP:15544, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, ChEBI:CHEBI:61961; EC=1.14.11.68; Evidence={ECO:0000269|PubMed:17713478, ECO:0000269|PubMed:17825402, ECO:0000269|PubMed:17851529, ECO:0000269|PubMed:18003914};.
UniProtKB/Swiss-Prot Induction:
By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells.

Enzyme Numbers (IUBMB) for KDM6B Gene

Phenotypes From GWAS Catalog for KDM6B Gene

Gene Ontology (GO) - Molecular Function for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 21841772
GO:0008013 beta-catenin binding IEA --
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with KDM6B: view
genes like me logo Genes that share phenotypes with KDM6B: view

Human Phenotype Ontology for KDM6B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for KDM6B Gene

MGI Knock Outs for KDM6B:

miRNA for KDM6B Gene

miRTarBase miRNAs that target KDM6B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM6B

No data available for Transcription Factor Targets and HOMER Transcription for KDM6B Gene

Localization for KDM6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM6B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM6B gene
Compartment Confidence
nucleus 5
extracellular 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus IEA,ISS 23856522
GO:0005654 nucleoplasm TAS --
GO:0044666 MLL3/4 complex IBA 21873635
genes like me logo Genes that share ontologies with KDM6B: view

Pathways & Interactions for KDM6B Gene

genes like me logo Genes that share pathways with KDM6B: view

Pathways by source for KDM6B Gene

1 Cell Signaling Technology pathway for KDM6B Gene
1 GeneTex pathway for KDM6B Gene

SIGNOR curated interactions for KDM6B Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002437 inflammatory response to antigenic stimulus IEA --
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IEA,ISS --
GO:0006954 inflammatory response IEA --
GO:0007507 heart development IBA 21873635
genes like me logo Genes that share ontologies with KDM6B: view

Drugs & Compounds for KDM6B Gene

(8) Drugs for KDM6B Gene - From: ApexBio, DGIdb, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Daminozide Pharma KDM2A inhibitor, Selective KDM2/7 inhibitor 20
GSK J1 Pharma H3K27 demethylase JMJD3 inhibitor, Potent JMJD3/UTX inhibitor 0
GSK J4 free base Pharma 0
GSK J4 HCl Pharma Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 0
JIB-04 Pharma Jumonji histone demethylase inihibitor 0

(1) Additional Compounds for KDM6B Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
GSK J4
1373423-53-0

(5) Tocris Compounds for KDM6B Gene

Compound Action Cas Number
Daminozide Selective KDM2/7 inhibitor 1596-84-5
GSK J1 Potent JMJD3/UTX inhibitor 1373422-53-7
GSK J4 Histone KDM inhibitor; cell permeable 1373423-53-0
IOX 1 Histone demethylase inhibitor; cell permeable 5852-78-8
Tranylcypromine hydrochloride Irreversible inhibitor of LSD1; also inhibits MAO 1986-47-6

(5) ApexBio Compounds for KDM6B Gene

Compound Action Cas Number
Daminozide KDM2A inhibitor 1596-84-5
GSK J1 H3K27 demethylase JMJD3 inhibitor 1373422-53-7
GSK J4 free base
GSK J4 HCl Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 1373423-53-0
JIB-04 Jumonji histone demethylase inihibitor 199596-05-9
genes like me logo Genes that share compounds with KDM6B: view

Drug products for research

Transcripts for KDM6B Gene

mRNA/cDNA for KDM6B Gene

2 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM6B

Alternative Splicing Database (ASD) splice patterns (SP) for KDM6B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b
SP1: -
SP2:
SP3:
SP4:
SP5:

Relevant External Links for KDM6B Gene

GeneLoc Exon Structure for
KDM6B

Expression for KDM6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KDM6B Gene

mRNA differential expression in normal tissues according to GTEx for KDM6B Gene

This gene is overexpressed in Whole Blood (x7.8).

Protein differential expression in normal tissues from HIPED for KDM6B Gene

This gene is overexpressed in Serum (36.7) and Cervix (21.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for KDM6B Gene



Protein tissue co-expression partners for KDM6B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KDM6B

SOURCE GeneReport for Unigene cluster for KDM6B Gene:

Hs.223678

Evidence on tissue expression from TISSUES for KDM6B Gene

  • Nervous system(4.6)
  • Lung(2.6)
  • Skin(2.6)
  • Bone marrow(2.5)
  • Blood(2.5)
  • Intestine(2.5)
  • Liver(2.4)
  • Muscle(2.3)
  • Spleen(2.2)
  • Heart(2.2)
  • Kidney(2.1)
  • Pancreas(2.1)
  • Lymph node(2.1)
genes like me logo Genes that share expression patterns with KDM6B: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM6B Gene

Orthologs for KDM6B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM6B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia KDM6B 29 30
  • 99.58 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia KDM6B 29 30
  • 90.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia KDM6B 29 30
  • 90.43 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Kdm6b 29 16 30
  • 88.36 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Kdm6b 29
  • 87.6 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia KDM6B 30
  • 50 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia KDM6B 30
  • 57 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii KDM6B (2 of 2) 30
  • 32 (a)
OneToMany
kdm6bb 30
  • 30 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea jmjd-3.3 30
  • 20 (a)
OneToMany
jmjd-3.1 30
  • 18 (a)
OneToMany
jmjd-3.2 30
  • 17 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CYC8 30
  • 10 (a)
OneToMany
Species where no ortholog for KDM6B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for KDM6B Gene

ENSEMBL:
Gene Tree for KDM6B (if available)
TreeFam:
Gene Tree for KDM6B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDM6B: view image
Alliance of Genome Resources:
Additional Orthologs for KDM6B

Paralogs for KDM6B Gene

Paralogs for KDM6B Gene

(5) SIMAP similar genes for KDM6B Gene using alignment to 2 proteins:

  • KDM6B_HUMAN
  • I3L0Z0_HUMAN
genes like me logo Genes that share paralogs with KDM6B: view

Variants for KDM6B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KDM6B Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
1030087 Uncertain Significance: Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities 7,848,796(+) G/C
NM_001348716.2(KDM6B):c.2508G>C (p.Gln836His)
MISSENSE
1030088 Uncertain Significance: Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities 7,849,334(+) C/T
NM_001348716.2(KDM6B):c.3046C>T (p.Arg1016Trp)
MISSENSE
873453 Uncertain Significance: Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities 7,848,366(+) A/C
NM_001080424.2(KDM6B):c.2078A>C (p.Asp693Ala)
MISSENSE
975572 Likely Benign: Intellectual disability 7,848,453(+) A/C
NM_001080424.2(KDM6B):c.2165A>C (p.Gln722Pro)
MISSENSE
975573 Likely Benign: Intellectual disability 7,848,568(+) CACCACG/C
NM_001080424.2(KDM6B):c.2281_2286del (p.Thr761_Thr762del)
INFRAME_DELETION

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for KDM6B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for KDM6B Gene

Variant ID Type Subtype PubMed ID
dgv172e215 CNV deletion 23714750
dgv510n67 CNV gain 20364138
esv2715604 CNV deletion 23290073
esv2715605 CNV deletion 23290073
esv2715606 CNV deletion 23290073
esv3204242 CNV deletion 24192839
esv989512 CNV deletion 20482838
nsv1070804 CNV deletion 25765185
nsv833351 CNV loss 17160897

Variation tolerance for KDM6B Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.69; 97.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM6B Gene

Human Gene Mutation Database (HGMD)
KDM6B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM6B
Leiden Open Variation Database (LOVD)
KDM6B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM6B Gene

Disorders for KDM6B Gene

MalaCards: The human disease database

(7) MalaCards diseases for KDM6B Gene - From: OMI, CVR, GTR, SW