KDM6B lysine demethylase 6B [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM6Bprovided by HGNC
Official Full Name: lysine demethylase 6Bprovided by HGNC
Primary source: HGNC:HGNC:29012
See related: Ensembl:ENSG00000132510 MIM:611577; AllianceGenome:HGNC:29012
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: JMJD3; NEDSST; NEDCFSA
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 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]
Expression: Ubiquitous expression in bone marrow (RPKM 9.0), appendix (RPKM 7.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7834217..7854796)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (7738322..7760122)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (7737535..7758114)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

YAP represses intestinal inflammation through epigenetic silencing of JMJD3.
Title: YAP represses intestinal inflammation through epigenetic silencing of JMJD3.
MicroRNA-93-5p regulates odontogenic differentiation and dentin formation via KDM6B.
Title: MicroRNA-93-5p regulates odontogenic differentiation and dentin formation via KDM6B.
Targeting lysine demethylase 6B ameliorates ASXL1 truncation-mediated myeloid malignancies in preclinical models.
Title: Targeting lysine demethylase 6B ameliorates ASXL1 truncation-mediated myeloid malignancies in preclinical models.
The ATF4-regulated LncRNA MALAT1 promotes odontoblastic differentiation of human dental pulp stem cells via histone demethylase JMJD3: An in vitro study.
Title: The ATF4-regulated LncRNA MALAT1 promotes odontoblastic differentiation of human dental pulp stem cells via histone demethylase JMJD3: An in vitro study.
KDM6B drives epigenetic reprogramming associated with lymphoid stromal cell early commitment and immune properties.
Title: KDM6B drives epigenetic reprogramming associated with lymphoid stromal cell early commitment and immune properties.
Echinococcus granulosus cyst fluid inhibits KDM6B-mediated demethylation of trimethylated histone H3 lysine 27 and interleukin-1beta production in macrophages.
Title: Echinococcus granulosus cyst fluid inhibits KDM6B-mediated demethylation of trimethylated histone H3 lysine 27 and interleukin-1β production in macrophages.
Myeloid-specific KDM6B inhibition sensitizes glioblastoma to PD1 blockade.
Title: Myeloid-specific KDM6B inhibition sensitizes glioblastoma to PD1 blockade.
NOTCH4 potentiates the IL-13 induced genetic program in M2 alternative macrophages through the AP1 and IRF4-JMJD3 axis.
Title: NOTCH4 potentiates the IL-13 induced genetic program in M2 alternative macrophages through the AP1 and IRF4-JMJD3 axis.
Loss of KDM6B epigenetically confers resistance to lipotoxicity in nonalcoholic fatty liver disease-related HCC.
Title: Loss of KDM6B epigenetically confers resistance to lipotoxicity in nonalcoholic fatty liver disease-related HCC.
JMJD3 is Involved in Intracranial Aneurysm Development by Regulating DLX2 Expression through H3K27me3 Modification.
Title: JMJD3 is Involved in Intracranial Aneurysm Development by Regulating DLX2 Expression through H3K27me3 Modification.

Submit: New GeneRIF Correction See all GeneRIFs (136)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities MedGen: C5193134 OMIM: 618505 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2024-10-23) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2024-10-23) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 upregulates the expression of lysine-specific demethylase 6B (KDM6B) in human B cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-catenin binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K27me2/H3K27me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K27me2/H3K27me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cardiac muscle cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in cell fate commitment	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in endothelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in hippocampus development	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response to antigenic stimulus	IEA Inferred from Electronic Annotation more info
involved_in mesodermal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to activity	IEA Inferred from Electronic Annotation more info
involved_in response to fungicide	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of MLL3/4 complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: lysine-specific demethylase 6B

Names: [histone H3]-trimethyl-L-lysine(27) demethylase 6B; jmjC domain-containing protein 3; jumonji domain containing 3, histone lysine demethylase; jumonji domain-containing protein 3; lysine (K)-specific demethylase 6B

NP_001073893.1

EC 1.14.11.68

NP_001335645.1

EC 1.14.11.68

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_053032.1 RefSeqGene

Range

5018..25597

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001080424.2 → NP_001073893.1 lysine-specific demethylase 6B isoform 1

See identical proteins and their annotated locations for NP_001073893.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) retains an intron in the 3' coding region, compared to variant 2, and encodes a longer protein (isoform 1), compared to isoform 2.

Source sequence(s)

AB002344, AC104581, BC035897

Consensus CDS

CCDS32552.1

Related

ENSP00000254846.5, ENST00000254846.9

Conserved Domains (3) summary

pfam02373
Location:1377 → 1485

JmjC; JmjC domain, hydroxylase

smart00558
Location:1343 → 1407

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

pfam05308
Location:566 → 640

Mito_fiss_reg; Mitochondrial fission regulator
NM_001348716.2 → NP_001335645.1 lysine-specific demethylase 6B isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes the shorter isoform (2).

Source sequence(s)

AC025335, AC104581

Consensus CDS

CCDS86569.1

UniProtKB/Swiss-Prot

C9IZ40, O15054, Q96G33

Related

ENSP00000412513.2, ENST00000448097.7

Conserved Domains (3) summary

pfam02373
Location:1377 → 1485

JmjC; JmjC domain, hydroxylase

smart00558
Location:1343 → 1407

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cl26247
Location:572 → 718

DNA_pol3_delta2; DNA polymerase III, delta subunit