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KDM5A lysine demethylase 5A [ Homo sapiens (human) ]

Gene ID: 5927, updated on 25-Nov-2025
Official Symbol
KDM5Aprovided by HGNC
Official Full Name
lysine demethylase 5Aprovided by HGNC
Primary source
HGNC:HGNC:9886
See related
Ensembl:ENSG00000073614 MIM:180202; AllianceGenome:HGNC:9886
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
RBP2; RBBP2; NEDEHC; RBBP-2
Summary
This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
Annotation information
Note: RBP2 (Gene ID: 5948) and KDM5A (Gene ID: 5927) share the RBP2 symbol/alias in common. RBP2 is a widely used alternative name for lysine demethylase 5A (KDM5A), which can be confused with the official symbol for retinol binding protein 2 (RBP2). [03 Jul 2018]
Expression
Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 8.6) and 25 other tissues See more
Orthologs
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See KDM5A in Genome Data Viewer
Location:
12p13.33
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (280057..389320, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (276885..386174, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (389223..498486, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:320888-321660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:322433-323204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:329915-330870 Neighboring gene solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 Neighboring gene Sharpr-MPRA regulatory region 4015 Neighboring gene uncharacterized LOC105369594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:511068-511620 Neighboring gene Sharpr-MPRA regulatory region 4380 Neighboring gene coiled-coil domain containing 77 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:568273-569256 Neighboring gene uncharacterized LOC124902853 Neighboring gene beta-1,4-N-acetyl-galactosaminyltransferase 3

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistance. Gale M, et al. Oncotarget, 2016 Jun 28. PMID 27224921, Free PMC Article
  2. KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer. Liu H, et al. Cancer Immunol Res, 2022 Aug 3. PMID 35726891, Free PMC Article
  3. Histone demethylase RBP2 induced by Helicobactor Pylori CagA participates in the malignant transformation of gastric epithelial cells. Liang X, et al. Oncotarget, 2014 Jul 30. PMID 25015565, Free PMC Article
  4. TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2. Wei M, et al. J Healthc Eng, 2022. PMID 35126937, Free PMC Article
  5. Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference. Hoekstra M, et al. Anal Biochem, 2021 Nov 15. PMID 34678252

See all (137) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Mechanism of KDM5A-mediated H3K4me3 modification in the osteogenic differentiation of mesenchymal stem cells in steroid-induced osteonecrosis of the femoral head.
    Title: Mechanism of KDM5A-mediated H3K4me3 modification in the osteogenic differentiation of mesenchymal stem cells in steroid-induced osteonecrosis of the femoral head.
  3. KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
    Title: KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
  4. Fbxo22 inhibits metastasis in triple-negative breast cancer through ubiquitin modification of KDM5A and regulation of H3K4me3 demethylation.
    Title: Fbxo22 inhibits metastasis in triple-negative breast cancer through ubiquitin modification of KDM5A and regulation of H3K4me3 demethylation.
  5. Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
    Title: Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
  6. Long non-coding RNA tumor protein 73 antisense RNA 1 influences an interaction between lysine demethylase 5A and promoter of tumor protein 73 to enhance the malignancy of colorectal cancer.
    Title: Long non-coding RNA tumor protein 73 antisense RNA 1 influences an interaction between lysine demethylase 5A and promoter of tumor protein 73 to enhance the malignancy of colorectal cancer.
  7. KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer.
    Title: KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer.
  8. TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2.
    Title: TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2.
  9. Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma.
    Title: Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma.
  10. KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
    Title: KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
Submit: New GeneRIF Correction See all GeneRIFs (69)

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
El Hayek-Chahrour neurodevelopmental disorder
MedGen: C5935620 OMIM: 620820 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
New loci associated with kidney function and chronic kidney disease.
EBI GWAS Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

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 chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables enzyme inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables enzyme inhibitor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K4 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
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 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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription cis-regulatory region binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables transcription coactivator activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in circadian regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in facultative heterochromatin formation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive 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 rhythmic process IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
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 protein-DNA complex IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
lysine-specific demethylase 5A
Names
Jumonji, AT rich interactive domain 1A (RBP2-like)
[histone H3]-trimethyl-L-lysine(4) demethylase 5A
histone demethylase JARID1A
jumonji/ARID domain-containing protein 1A
lysine (K)-specific demethylase 5A
retinoblastoma binding protein 2
NP_001036068.1

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_046993.1 RefSeqGene

    Range
    5136..114399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042603.3 → NP_001036068.1  lysine-specific demethylase 5A

    See identical proteins and their annotated locations for NP_001036068.1

    Status: REVIEWED

    Source sequence(s)
    AB209999, AC007406, BU182136, DA211439
    Consensus CDS
    CCDS41736.1
    UniProtKB/Swiss-Prot
    A8MV76, P29375, Q4LE72, Q86XZ1
    Related
    ENSP00000382688.2, ENST00000399788.7
    Conserved Domains (8) summary
    smart00545
    Location:18 → 59
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:85 → 170
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:470 → 586
    JmjC; JmjC domain, hydroxylase
    cd15602
    Location:295 → 343
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:1163 → 1215
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:1608 → 1659
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    pfam02928
    Location:676 → 728
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:741 → 1070
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    280057..389320 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    276885..386174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005056.2: Suppressed sequence

    Description
    NM_005056.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P29375.3 GenPept UniProtKB/Swiss-Prot:P29375

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