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KDM2A lysine demethylase 2A [ Homo sapiens (human) ]

Gene ID: 22992, updated on 5-Mar-2024

Summary

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Official Symbol
KDM2Aprovided by HGNC
Official Full Name
lysine demethylase 2Aprovided by HGNC
Primary source
HGNC:HGNC:13606
See related
Ensembl:ENSG00000173120 MIM:605657; AllianceGenome:HGNC:13606
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
FBL7; CXXC8; FBL11; FBXL11; JHDM1A; LILINA
Summary
This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Expression
Ubiquitous expression in testis (RPKM 25.2), bone marrow (RPKM 22.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.2
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (67119263..67258082)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67110939..67252047)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66886734..67025553)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66841392-66841892 Neighboring gene MPRA-validated peak1310 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66845407-66846302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5068 Neighboring gene ras homolog family member D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66867665-66868165 Neighboring gene uncharacterized LOC107984341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3616 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3618 Neighboring gene uncharacterized LOC124902695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66964839-66965339 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:66989729-66990608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5075 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:67020970-67022169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67038522-67039486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67039487-67040451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67044441-67045054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67045055-67045668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67057124-67058048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67058049-67058971 Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene ankyrin repeat domain 13D

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance. Li F, et al. Nat Commun, 2023 Mar 29. PMID 36991019, Free PMC Article
  2. KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma. Wang J, et al. Biochem Biophys Res Commun, 2022 Oct 8. PMID 35932580
  3. Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3. Lu B, et al. Cell Death Dis, 2022 Jun 13. PMID 35697678, Free PMC Article
  4. Expression pattern and regulatory effect of lysine-specific demethylase 2A gene in clear cell renal cell carcinoma. Wang J, et al. BMC Urol, 2021 Aug 14. PMID 34391411, Free PMC Article
  5. Production of ROS by Gallic Acid Activates KDM2A to Reduce rRNA Transcription. Tanaka Y, et al. Cells, 2020 Oct 10. PMID 33050392, Free PMC Article

See all (112) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Biological Functions of the KDM2 Family of Histone Demethylases.
    Title: Biological Functions of the KDM2 Family of Histone Demethylases.
  2. Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
    Title: Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
  3. Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
    Title: Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
  4. Stabilization of nuclear beta-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
    Title: Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
  5. Histone demethylase KDM2A suppresses EGF-TSPAN8 pathway to inhibit breast cancer cell migration and invasion in vitro.
    Title: Histone demethylase KDM2A suppresses EGF-TSPAN8 pathway to inhibit breast cancer cell migration and invasion in vitro.
  6. KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.
    Title: KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.
  7. NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition.
    Title: NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition.
  8. Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3.
    Title: Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3.
  9. Up-regulation of miR-663a inhibits the cancer stem cell-like properties of glioma via repressing the KDM2A-mediated TGF-beta/SMAD signaling pathway.
    Title: Up-regulation of miR-663a inhibits the cancer stem cell-like properties of glioma via repressing the KDM2A-mediated TGF-β/SMAD signaling pathway.
  10. Nuclear receptor binding SET domain protein 1 promotes epithelial-mesenchymal transition in paclitaxel-resistant breast cancer cells via regulating nuclear factor kappa B and F-box and leucine-rich repeat protein 11.
    Title: Nuclear receptor binding SET domain protein 1 promotes epithelial-mesenchymal transition in paclitaxel-resistant breast cancer cells via regulating nuclear factor kappa B and F-box and leucine-rich repeat protein 11.
Submit: New GeneRIF Correction See all GeneRIFs (46)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ00115, FLJ46431, KIAA1004, DKFZp434M1735

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone H3K36 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K36me/H3K36me2 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone demethylase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables unmethylated CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by competitive promoter binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein demethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of circadian rhythm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
lysine-specific demethylase 2A
Names
CXXC-type zinc finger protein 8
F-box and leucine-rich repeat protein 11
F-box/LRR-repeat protein 11
[Histone-H3]-lysine-36 demethylase 1A
jmjC domain-containing histone demethylation protein 1A
jumonji C domain-containing histone demethylase 1A
lysine (K)-specific demethylase 2A
NP_001243334.1
NP_036440.1
XP_006718543.1
XP_011543163.1
XP_016872880.1
XP_016872881.1
XP_047282579.1
XP_054224095.1
XP_054224096.1
XP_054224097.1
XP_054224098.1
XP_054224099.1

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.

mRNA and Protein(s)

  1. NM_001256405.2 → NP_001243334.1  lysine-specific demethylase 2A isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several 5' exons but contains an alternate 5' exon, uses an internal downstream promoter, and differs in its 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b, also known as SF-KDM2A or short-form KDM2A) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AB490246, AI185920, AL117517, AP001885, DR001963
    Consensus CDS
    CCDS58148.1
    UniProtKB/Swiss-Prot
    Q9Y2K7
    Related
    ENSP00000435776.1, ENST00000530342.2
    Conserved Domains (5) summary
    cd09293
    Location:493 → 699
    AMN1; Antagonist of mitotic exit network protein 1
    pfam02008
    Location:137 → 170
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:491 → 515
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:180 → 236
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam12937
    Location:457 → 497
    F-box-like; F-box-like

  2. NM_012308.3 → NP_036440.1  lysine-specific demethylase 2A isoform a

    See identical proteins and their annotated locations for NP_036440.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AF179221, AP000729, AP001885, BC047486, BC064360, BE675843
    Consensus CDS
    CCDS44657.1
    UniProtKB/Swiss-Prot
    D4QA03, E9PIL6, I3VM55, Q49A21, Q4G0M3, Q69YY8, Q9BVH5, Q9H7H5, Q9UK66, Q9Y2K7
    UniProtKB/TrEMBL
    I3VM53
    Related
    ENSP00000432786.1, ENST00000529006.7
    Conserved Domains (6) summary
    pfam02008
    Location:576 → 609
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:930 → 954
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:619 → 675
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam12937
    Location:896 → 934
    F-box-like; F-box-like
    cl21464
    Location:199 → 299
    cupin_like; Conserved domain found in cupin and related proteins
    cl28166
    Location:932 → 1138
    AMN1; Antagonist of mitotic exit network protein 1

RNA

  1. NR_027473.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AP000729, AP001885, BC047486, BE675843
    Related
    ENST00000398645.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    67119263..67258082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017017391.2 → XP_016872880.1  lysine-specific demethylase 2A isoform X1

    UniProtKB/TrEMBL
    I3VM54
    Related
    ENSP00000309302.6, ENST00000308783.9
    Conserved Domains (8) summary
    cd09293
    Location:915 → 1121
    AMN1; Antagonist of mitotic exit network protein 1
    sd00034
    Location:913 → 937
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:602 → 658
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam02008
    Location:559 → 592
    zf-CXXC; CXXC zinc finger domain
    pfam12937
    Location:879 → 917
    F-box-like
    pfam17811
    Location:287 → 322
    JHD; Jumonji helical domain
    cd21784
    Location:433 → 500
    CTD_KDM2A; C-terminal domain found in Lysine-specific demethylase 2A
    cl40423
    Location:182 → 282
    cupin_RmlC-like; RmlC-like cupin superfamily

  2. XM_017017392.2 → XP_016872881.1  lysine-specific demethylase 2A isoform X1

    UniProtKB/TrEMBL
    I3VM54
    Conserved Domains (8) summary
    cd09293
    Location:915 → 1121
    AMN1; Antagonist of mitotic exit network protein 1
    sd00034
    Location:913 → 937
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:602 → 658
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam02008
    Location:559 → 592
    zf-CXXC; CXXC zinc finger domain
    pfam12937
    Location:879 → 917
    F-box-like
    pfam17811
    Location:287 → 322
    JHD; Jumonji helical domain
    cd21784
    Location:433 → 500
    CTD_KDM2A; C-terminal domain found in Lysine-specific demethylase 2A
    cl40423
    Location:182 → 282
    cupin_RmlC-like; RmlC-like cupin superfamily

  3. XM_047426623.1 → XP_047282579.1  lysine-specific demethylase 2A isoform X2

  4. XM_006718480.4 → XP_006718543.1  lysine-specific demethylase 2A isoform X3

    Conserved Domains (6) summary
    cd09293
    Location:837 → 1043
    AMN1; Antagonist of mitotic exit network protein 1
    pfam02008
    Location:481 → 514
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:835 → 859
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:524 → 580
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam12937
    Location:801 → 841
    F-box-like; F-box-like
    cl21464
    Location:104 → 204
    cupin_like; Conserved domain found in cupin and related proteins

  5. XM_011544861.2 → XP_011543163.1  lysine-specific demethylase 2A isoform X4

    UniProtKB/Swiss-Prot
    Q9Y2K7
    Related
    ENST00000526258.5
    Conserved Domains (5) summary
    cd09293
    Location:626 → 832
    AMN1; Antagonist of mitotic exit network protein 1
    pfam02008
    Location:270 → 303
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:624 → 648
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:313 → 369
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam12937
    Location:590 → 630
    F-box-like; F-box-like

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    67110939..67252047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368120.1 → XP_054224095.1  lysine-specific demethylase 2A isoform X1

    UniProtKB/TrEMBL
    I3VM54

  2. XM_054368121.1 → XP_054224096.1  lysine-specific demethylase 2A isoform X1

    UniProtKB/TrEMBL
    I3VM54

  3. XM_054368122.1 → XP_054224097.1  lysine-specific demethylase 2A isoform X2

  4. XM_054368123.1 → XP_054224098.1  lysine-specific demethylase 2A isoform X3

  5. XM_054368124.1 → XP_054224099.1  lysine-specific demethylase 2A isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2K7.3 GenPept UniProtKB/Swiss-Prot:Q9Y2K7

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