Gene Gene information from NCBI Gene database.
Entrez ID 23135
Gene name Lysine demethylase 6B
Gene symbol KDM6B
Synonyms (NCBI Gene)
JMJD3NEDCFSANEDSST
Chromosome 17
Chromosome location 17p13.1
Summary 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
SNPs SNP information provided by dbSNP.
2
SNP ID Visualize variation Clinical significance Consequence
rs769566928 AGAG>- Uncertain-significance, pathogenic Frameshift variant, coding sequence variant
rs1597850788 AG>- Uncertain-significance, pathogenic Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
506
miRTarBase ID miRNA Experiments Reference
MIRT017568 hsa-miR-335-5p Microarray 18185580
MIRT021179 hsa-miR-186-5p Sequencing 20371350
MIRT027296 hsa-miR-101-3p Sequencing 20371350
MIRT052574 hsa-let-7a-5p CLASH 23622248
MIRT049017 hsa-miR-92a-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
41
GO ID Ontology Definition Evidence Reference
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0002437 Process Inflammatory response to antigenic stimulus IEA
GO:0003682 Function Chromatin binding IEA
GO:0005515 Function Protein binding IPI 21841772
GO:0005634 Component Nucleus IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
611577 29012 ENSG00000132510
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O15054
Protein name Lysine-specific demethylase 6B (EC 1.14.11.68) (JmjC domain-containing protein 3) (Jumonji domain-containing protein 3) (Lysine demethylase 6B) ([histone H3]-trimethyl-L-lysine(27) demethylase 6B)
Protein function Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17713478, PubMed:17825402, PubMed:17851529, PubMed:18003914). Demethylates trimethylated and dimethylated H3 'Lys-2
PDB 2XUE , 2XXZ , 4ASK , 5FP3 , 5OY3 , 6F6D
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02373 JmjC 1377 1485 JmjC domain, hydroxylase Domain
Sequence
MHRAVDPPGARAAREAFALGGLSCAGAWSSCPPHPPPRSAWLPGGRCSASIGQPPLPAPL
PPSHGSSSGHPSKPYYAPGAPTPRPLHGKLESLHGCVQALLREPAQPGLWEQLGQLYESE
HDSEEATRCYHSALRYGGSFAELGPRIGRLQQAQLWNFHTGSCQHRAKVLPPLEQVWNLL
HLEHKRNYGAKRGGPPVKRAAEPPVVQPVPPAALSGPSGEEGLSPGGKRRRGCNSEQTGL
PPGLPLPPPPLPPPPPPPPPPPPPLPGLATSPPFQLTKPGLWSTLHGDAWGPERKGSAPP
ERQEQRHSLPHPYPYPAPAYTAHPPGHRLVPAAPPGPGPRPPGAESHGCLPATRPPGSDL
RESRVQRSRMDSSVSPAATTACVPYAPSRPPGLPGTTTSSSSSSSSNTGLRGVEPNPGIP
GADHYQTPALEVSHHGRLGPSAHSSRKPFLGAPAATPHLSLPPGPSSPPPPPCPRLLRPP
PPPAWLKGPACRAAREDGEILEELFFGTEGPPRPAPPPLPHREGFLGPPASRFSVGTQDS
HTPPTPPTPTTSSSNSNSGSHSSSPAGPVSFPPPPYLARSIDPLPRPPSPAQNPQDPPLV
PLTLALPPAPPSSCHQNTSGSFRRPESPRPRVSFPKTPEVGPGPPPGPLSKAPQPVPPGV
GELPARGPRLFDFPPTPLEDQFEEPAEFKILPDGLANIMKMLDESIRKEEEQQQHEAGVA
PQPPLKEPFASLQSPFPTDTAPTTTAPAVAVTTTTTTTTTTTATQEEEKKPPPALPPPPP
LAKFPPPSQPQPPPPPPPSPASLLKSLASVLEGQKYCYRGTGAAVSTRPGPLPTTQYSPG
PPSGATALPPTSAAPSAQGSPQPSASSSSQFSTSGGPWARERRAGEEPVPGPMTPTQPPP
PLSLPPARSESEVLEEISRACETLVERVGRSATDPADPVDTAEPADSGTERLLPPAQAKE
EAGGVAAVSGSCKRRQKEHQKEHRRHRRACKDSVGRRPREGRAKAKAKVPKEKSRRVLGN
LDLQSEEIQGREKSRPDLGGASKAKPPTAPAPPSAPAPSAQPTPPSASVPGKKAREEAPG
PPGVSRADMLKLRSLSEGPPKELKIRLIKVESGDKETFIASEVEERRLRMADLTISHCAA
DVVRASRNAKVKGKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPV
LLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLT
GTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDP
KNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYM
KVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPI
LDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNV
GPLTAYQYQLALERY
EWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKK
IAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLE
QYRTEELAQAYDAFTLAPASTSR
Sequence length 1643
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Oxidative Stress Induced Senescence
HDMs demethylate histones
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
281
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual disability Likely pathogenic; Pathogenic rs2544521866 RCV005626626
KDM6B-related disorder Likely pathogenic rs1294523865, rs2544524865, rs988670906, rs2544526628 RCV004749834
RCV005250241
RCV003403022
RCV003894683
Malignant tumor of urinary bladder Likely pathogenic rs2078522713 RCV005930259
Neurodevelopmental abnormality Pathogenic rs957520585 RCV001264704
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Conflicting classifications of pathogenicity rs148641957 RCV005893878
Colon adenocarcinoma Conflicting classifications of pathogenicity rs148641957 RCV005893877
Developmental disorder Uncertain significance rs2151379708, rs2544534873 RCV001843808
RCV003764472
KDM6B-related neurodevelopmental disorder Uncertain significance rs1378460812 RCV001563620
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Anti Neutrophil Cytoplasmic Antibody Associated Vasculitis Stimulate 27755585
Attention Deficit Disorder with Hyperactivity Associate 33155823, 36251081
Autism Spectrum Disorder Associate 36251081
Breast Neoplasms Associate 21841772, 33962648, 37223020
Carcinogenesis Associate 35254477, 36564369
Carcinoma Hepatocellular Associate 25049231, 35254477
Carcinoma Merkel Cell Associate 34399838
Carcinoma Non Small Cell Lung Associate 26303949, 31210309
Carcinoma Non Small Cell Lung Inhibit 31155967
Carcinoma Renal Cell Associate 23057811, 26261509, 28177890