Seroatlas · Human Serome Atlas

KDM2A

Lysine-specific demethylase 2A

Also known as: CXXC8, DKFZP434M1735, FBL11, FBL7, FBXL11, FLJ00115, JHDM1A, KDM2A_HUMAN, KIAA1004, LILINA

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9Y2K7
Gene: KDM2A
Ensembl: ENSG00000173120
Chromosome: 11
Canonical length: 1162 aa
Protein class: Enzymes, Plasma proteins, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

1162 residues, UniProt reviewed canonical sequence.

>Q9Y2K7|KDM2A
     1  MEPEEERIRY SQRLRGTMRR RYEDDGISDD EIEGKRTFDL EEKLHTNKYN ANFVTFMEGK
    61  DFNVEYIQRG GLRDPLIFKN SDGLGIKMPD PDFTVNDVKM CVGSRRMVDV MDVNTQKGIE
   121  MTMAQWTRYY ETPEEEREKL YNVISLEFSH TRLENMVQRP STVDFIDWVD NMWPRHLKES
   181  QTESTNAILE MQYPKVQKYC LMSVRGCYTD FHVDFGGTSV WYHIHQGGKV FWLIPPTAHN
   241  LELYENWLLS GKQGDIFLGD RVSDCQRIEL KQGYTFVIPS GWIHAVYTPT DTLVFGGNFL
   301  HSFNIPMQLK IYNIEDRTRV PNKFRYPFYY EMCWYVLERY VYCITNRSHL TKEFQKESLS
   361  MDLELNGLES GNGDEEAVDR EPRRLSSRRS VLTSPVANGV NLDYDGLGKT CRSLPSLKKT
   421  LAGDSSSDCS RGSHNGQVWD PQCAPRKDRQ VHLTHFELEG LRCLVDKLES LPLHKKCVPT
   481  GIEDEDALIA DVKILLEELA NSDPKLALTG VPIVQWPKRD KLKFPTRPKV RVPTIPITKP
   541  HTMKPAPRLT PVRPAAASPI VSGARRRRVR CRKCKACVQG ECGVCHYCRD MKKFGGPGRM
   601  KQSCVLRQCL APRLPHSVTC SLCGEVDQNE ETQDFEKKLM ECCICNEIVH PGCLQMDGEG
   661  LLNEELPNCW ECPKCYQEDS SEKAQKRKME ESDEEAVQAK VLRPLRSCDE PLTPPPHSPT
   721  SMLQLIHDPV SPRGMVTRSS PGAGPSDHHS ASRDERFKRR QLLRLQATER TMVREKENNP
   781  SGKKELSEVE KAKIRGSYLT VTLQRPTKEL HGTSIVPKLQ AITASSANLR HSPRVLVQHC
   841  PARTPQRGDE EGLGGEEEEE EEEEEEDDSA EEGGAARLNG RGSWAQDGDE SWMQREVWMS
   901  VFRYLSRREL CECMRVCKTW YKWCCDKRLW TKIDLSRCKA IVPQALSGII KRQPVSLDLS
   961  WTNISKKQLT WLVNRLPGLK DLLLAGCSWS AVSALSTSSC PLLRTLDLRW AVGIKDPQIR
  1021  DLLTPPADKP GQDNRSKLRN MTDFRLAGLD ITDATLRLII RHMPLLSRLD LSHCSHLTDQ
  1081  SSNLLTAVGS STRYSLTELN MAGCNKLTDQ TLIYLRRIAN VTLIDLRGCK QITRKACEHF
  1141  ISDLSINSLY CLSDEKLIQK IS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM2A can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.39
Highest tissue expression: 45 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 45 nTPM
testis: 27 nTPM
tonsil: 27 nTPM
cerebellum: 27 nTPM
skeletal muscle: 26 nTPM
thymus: 26 nTPM

Single-cell type

neutrophils: 1,465 nCPM
neutrophil progenitors: 574 nCPM
ocular epithelial cells: 543 nCPM
esophageal apical cells: 522 nCPM
monocyte progenitors: 462 nCPM
cone photoreceptor cells: 416 nCPM

Immune cell

memory B-cell: 3.6 nTPM
naive B-cell: 3.6 nTPM
MAIT T-cell: 2.7 nTPM
neutrophil: 2.7 nTPM
NK-cell: 2.7 nTPM
T-reg: 2.6 nTPM

Brain region

cerebellum: 47 nTPM
choroid plexus: 40 nTPM
medulla oblongata: 37 nTPM
hypothalamus: 35 nTPM
cerebral cortex: 34 nTPM
thalamus: 34 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM2A.

Disease | GeneticClinVar

16 pathogenic / likely-pathogenic of 130 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

KDM2A-related neurodevelopmental disorder
Neurodevelopmental disorder
KDM2A related condition

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.05
gnomAD pLI: 1
gnomAD missense Z: 5.31
DepMap mean gene effect: -0.6
DepMap dependency class: common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of KDM2A in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads KDM2A as an antibody target. Whether an autoantibody or antibody against KDM2A could matter depends on whether native KDM2A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM2A is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label KDM2A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...