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KDM5B lysine demethylase 5B [ Homo sapiens (human) ]

Gene ID: 10765, updated on 5-Aug-2026
Official Symbol
KDM5Bprovided by HGNC
Official Full Name
lysine demethylase 5Bprovided by HGNC
Primary source
HGNC:HGNC:18039
See related
Ensembl:ENSG00000117139 MIM:605393; AllianceGenome:HGNC:18039
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
CT31; PLU1; PUT1; MRT65; PLU-1; JARID1B; PPP1R98; RBP2-H1; RBBP2H1A
Summary
This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Expression
Broad expression in testis (RPKM 55.0), skin (RPKM 8.8) and 18 other tissues See more
Orthologs
all
Try the new Gene page
Try the new Transcripts and proteins table
See KDM5B in Genome Data Viewer
Location:
1q32.1
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202724495..202808421, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201986695..202071080, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202693623..202777549, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene small nucleolar RNA SNORA70 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202536800-202537472 Neighboring gene Sharpr-MPRA regulatory region 13308 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:202557917-202559116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202560242-202561068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202591842-202592466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202606743-202607308 Neighboring gene synaptotagmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202611908-202612840 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202626482-202626641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202627175-202627676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202640443-202640943 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202645972-202646140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202671295-202671794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202764986-202765486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202765487-202765987 Neighboring gene COX7C pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1706 Neighboring gene solute carrier family 25 member 39 pseudogene 1 Neighboring gene uncharacterized LOC124904583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1707 Neighboring gene MGAT4 family member E, pseudogene Neighboring gene prostate cancer associated transcript 6

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2'-Deoxycytidine. Leadem BR, et al. Cancer Res, 2018 Mar 1. PMID 29282222, Free PMC Article
  2. The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers. Klein BJ, et al. Cell Rep, 2014 Jan 30. PMID 24412361, Free PMC Article
  3. KDM5B demethylates H3K4 to recruit XRCC1 and promote chemoresistance. Xu W, et al. Int J Biol Sci, 2018. PMID 29989047, Free PMC Article
  4. Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor. Kristensen LH, et al. FEBS J, 2012 Jun. PMID 22420752
  5. KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. Kidder BL, et al. Genome Biol, 2014 Feb 4. PMID 24495580, Free PMC Article

See all (252) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LncRNA HOXC-AS3 accelerates malignant proliferation of cervical cancer cells via stabilizing KDM5B.
    Title: LncRNA HOXC-AS3 accelerates malignant proliferation of cervical cancer cells via stabilizing KDM5B.
  2. AUP1 transcriptionally activated by KDM5B reprograms lipid metabolism to promote the malignant progression of cervical cancer.
    Title: AUP1 transcriptionally activated by KDM5B reprograms lipid metabolism to promote the malignant progression of cervical cancer.
  3. A Genotype/Phenotype Study of KDM5B-Associated Disorders Suggests a Pathogenic Effect of Dominantly Inherited Missense Variants.
    Title: A Genotype/Phenotype Study of KDM5B-Associated Disorders Suggests a Pathogenic Effect of Dominantly Inherited Missense Variants.
  4. ETS homologous factor, controlled by lysine-specific demethylase 5B, suppresses clear cell renal cell carcinoma by inducing Filamin-B.
    Title: ETS homologous factor, controlled by lysine-specific demethylase 5B, suppresses clear cell renal cell carcinoma by inducing Filamin-B.
  5. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
    Title: Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
  6. KDM5B promotes metastasis and epithelial-mesenchymal transition via Wnt/beta-catenin pathway in squamous cell carcinoma of the head and neck.
    Title: KDM5B promotes metastasis and epithelial-mesenchymal transition via Wnt/β-catenin pathway in squamous cell carcinoma of the head and neck.
  7. Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis.
    Title: Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis.
  8. Deubiquitinase USP7 stabilizes KDM5B and promotes tumor progression and cisplatin resistance in nasopharyngeal carcinoma through the ZBTB16/TOP2A axis.
    Title: Deubiquitinase USP7 stabilizes KDM5B and promotes tumor progression and cisplatin resistance in nasopharyngeal carcinoma through the ZBTB16/TOP2A axis.
  9. Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
    Title: Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
  10. Long Noncoding RNA HOXA-AS2 Facilitates Prostate Cancer Progression by Inhibiting miR-885-5p to Upregulate KDM5B.
    Title: Long Noncoding RNA HOXA-AS2 Facilitates Prostate Cancer Progression by Inhibiting miR-885-5p to Upregulate KDM5B.
Submit: New GeneRIF Correction See all GeneRIFs (109)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal recessive 65
MedGen: C4748219 OMIM: 618109 GeneReviews: Not available
Compare labs

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Replication interactions

Interaction Pubs
Knockdown of lysine (K)-specific demethylase 5B (KDM5B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ10538, FLJ12459, FLJ12491, FLJ16281, FLJ23670

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone binding IEA
Inferred from Electronic Annotation
more info
  
enables histone demethylase activity TAS
Traceable Author Statement
more info
  
enables nucleic acid binding EXP
Inferred from Experiment
more info
 PubMed 
enables nucleic acid binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to fibroblast growth factor stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in lens fiber cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to fungicide IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
lysine-specific demethylase 5B
Names
[histone H3]-trimethyl-L-lysine(4) demethylase 5B
cancer/testis antigen 31
histone demethylase JARID1B
jumonji, AT rich interactive domain 1B
jumonji/ARID domain-containing protein 1B
lysine (K)-specific demethylase 5B
protein phosphatase 1, regulatory subunit 98
putative DNA/chromatin binding motif
retinoblastoma-binding protein 2 homolog 1
retinoblastoma-binding protein 2, homolog 1A
NP_001300971.1
NP_001334520.1
NP_001386746.1
NP_006609.3
XP_011507392.1
XP_011507393.1
XP_054189910.1
XP_054189911.1

NEW Try the new Transcript table

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

  1. NG_050659.1 RefSeqGene

    Range
    5987..89913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001314042.2 → NP_001300971.1  lysine-specific demethylase 5B isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC098934, AC104463
    Consensus CDS
    CCDS81417.1
    UniProtKB/TrEMBL
    A0ACI8U4T1
    Related
    ENSP00000356233.2, ENST00000367264.8
    Conserved Domains (8) summary
    smart00501
    Location:98 → 188
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:31 → 72
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:522 → 638
    JmjC; JmjC domain, hydroxylase
    cd15603
    Location:347 → 392
    PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
    cd15607
    Location:1214 → 1257
    PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
    cd15687
    Location:1522 → 1571
    PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
    pfam02928
    Location:728 → 780
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:793 → 1122
    PLU-1; PLU-1-like protein

  2. NM_001347591.2 → NP_001334520.1  lysine-specific demethylase 5B isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two exons in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    AC098934, AC104463
    Consensus CDS
    CCDS91143.1
    UniProtKB/TrEMBL
    A0A3B3ITA8, A0ACI8U484
    Related
    ENSP00000497671.1, ENST00000650569.2

  3. NM_001399817.1 → NP_001386746.1  lysine-specific demethylase 5B isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site for exon 1 compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC098934, AC104463
    Consensus CDS
    CCDS91144.1
    UniProtKB/TrEMBL
    A0A3B3IS40, A0ACI8U4T1
    Related
    ENSP00000497113.1, ENST00000648056.2

  4. NM_006618.5 → NP_006609.3  lysine-specific demethylase 5B isoform 2

    See identical proteins and their annotated locations for NP_006609.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC098934, AC104463
    Consensus CDS
    CCDS30974.1
    UniProtKB/Swiss-Prot
    O95811, Q15752, Q9UGL1, Q9Y3Q5
    UniProtKB/TrEMBL
    A0ACI8U4T1
    Related
    ENSP00000356234.3, ENST00000367265.9
    Conserved Domains (8) summary
    smart00501
    Location:98 → 188
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:31 → 72
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:486 → 602
    JmjC; JmjC domain, hydroxylase
    cd15603
    Location:311 → 356
    PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
    cd15607
    Location:1178 → 1221
    PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
    cd15687
    Location:1486 → 1535
    PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
    pfam02928
    Location:692 → 744
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:757 → 1086
    PLU-1; PLU-1-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    202724495..202808421 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509091.3 → XP_011507393.1  lysine-specific demethylase 5B isoform X1

    See identical proteins and their annotated locations for XP_011507393.1

    UniProtKB/TrEMBL
    Q9UFD3
    Conserved Domains (6) summary
    pfam02373
    Location:364 → 480
    JmjC; JmjC domain, hydroxylase
    cd15603
    Location:189 → 234
    PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
    cd15607
    Location:1056 → 1099
    PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
    cd15687
    Location:1364 → 1413
    PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
    pfam02928
    Location:570 → 622
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:635 → 964
    PLU-1; PLU-1-like protein

  2. XM_011509090.4 → XP_011507392.1  lysine-specific demethylase 5B isoform X1

    See identical proteins and their annotated locations for XP_011507392.1

    UniProtKB/TrEMBL
    Q9UFD3
    Related
    ENSP00000235790.4, ENST00000235790.9
    Conserved Domains (6) summary
    pfam02373
    Location:364 → 480
    JmjC; JmjC domain, hydroxylase
    cd15603
    Location:189 → 234
    PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
    cd15607
    Location:1056 → 1099
    PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
    cd15687
    Location:1364 → 1413
    PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
    pfam02928
    Location:570 → 622
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:635 → 964
    PLU-1; PLU-1-like protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201986695..202071080 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333935.1 → XP_054189910.1  lysine-specific demethylase 5B isoform X1

    UniProtKB/TrEMBL
    Q9UFD3

  2. XM_054333936.1 → XP_054189911.1  lysine-specific demethylase 5B isoform X1

    UniProtKB/TrEMBL
    Q9UFD3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UGL1.3 GenPept UniProtKB/Swiss-Prot:Q9UGL1

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