Seroatlas · Human Serome Atlas

KDM1A

Lysine-specific histone demethylase 1A

Also known as: AOF2, BHC110, KDM1, KDM1A_HUMAN, KIAA0601, LSD1

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

Protein identityUniProt · HPA

UniProt accession
O60341
Gene
KDM1A
Ensembl
ENSG00000004487
Chromosome
1
Canonical length
852 aa
Protein class
Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location
Nucleoplasm,Cytosol

OverviewNCBI Gene

This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

Canonical amino-acid sequenceUniProt

852 residues, UniProt reviewed canonical sequence.

>O60341|KDM1A
     1  MLSGKKAAAA AAAAAAAATG TEAGPGTAGG SENGSEVAAQ PAGLSGPAEV GPGAVGERTP
    61  RKKEPPRASP PGGLAEPPGS AGPQAGPTVV PGSATPMETG IAETPEGRRT SRRKRAKVEY
   121  REMDESLANL SEDEYYSEEE RNAKAEKEKK LPPPPPQAPP EEENESEPEE PSGVEGAAFQ
   181  SRLPHDRMTS QEAACFPDII SGPQQTQKVF LFIRNRTLQL WLDNPKIQLT FEATLQQLEA
   241  PYNSDTVLVH RVHSYLERHG LINFGIYKRI KPLPTKKTGK VIIIGSGVSG LAAARQLQSF
   301  GMDVTLLEAR DRVGGRVATF RKGNYVADLG AMVVTGLGGN PMAVVSKQVN MELAKIKQKC
   361  PLYEANGQAV PKEKDEMVEQ EFNRLLEATS YLSHQLDFNV LNNKPVSLGQ ALEVVIQLQE
   421  KHVKDEQIEH WKKIVKTQEE LKELLNKMVN LKEKIKELHQ QYKEASEVKP PRDITAEFLV
   481  KSKHRDLTAL CKEYDELAET QGKLEEKLQE LEANPPSDVY LSSRDRQILD WHFANLEFAN
   541  ATPLSTLSLK HWDQDDDFEF TGSHLTVRNG YSCVPVALAE GLDIKLNTAV RQVRYTASGC
   601  EVIAVNTRST SQTFIYKCDA VLCTLPLGVL KQQPPAVQFV PPLPEWKTSA VQRMGFGNLN
   661  KVVLCFDRVF WDPSVNLFGH VGSTTASRGE LFLFWNLYKA PILLALVAGE AAGIMENISD
   721  DVIVGRCLAI LKGIFGSSAV PQPKETVVSR WRADPWARGS YSYVAAGSSG NDYDLMAQPI
   781  TPGPSIPGAP QPIPRLFFAG EHTIRNYPAT VHGALLSGLR EAGRIADQFL GAMYTLPRQA
   841  TPGVPAQQSP SM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM1A 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)
0.34
Highest tissue expression
68 nTPM

Expression across tissuesHPA

Tissue

  • testis: 68 nTPM
  • thymus: 41 nTPM
  • parathyroid gland: 37 nTPM
  • tongue: 30 nTPM
  • skeletal muscle: 29 nTPM
  • ovary: 29 nTPM

Single-cell type

  • early primary spermatocytes: 152 nCPM
  • erythrocyte progenitors: 151 nCPM
  • megakaryocyte-erythroid progenitors: 141 nCPM
  • urothelial cells: 140 nCPM
  • thyrotrophs: 125 nCPM
  • endometrial luminal cells: 119 nCPM

Immune cell

  • plasmacytoid DC: 6.8 nTPM
  • memory B-cell: 6.2 nTPM
  • non-classical monocyte: 4.7 nTPM
  • naive CD8 T-cell: 4.5 nTPM
  • intermediate monocyte: 4 nTPM
  • T-reg: 3.8 nTPM

Brain region

  • hypothalamus: 17 nTPM
  • cerebral cortex: 17 nTPM
  • cerebellum: 15 nTPM
  • basal ganglia: 15 nTPM
  • hippocampal formation: 14 nTPM
  • midbrain: 14 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM1A.

Disease | AllUniProt

Conditions KDM1A is implicated in, by any mechanism.

  • Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) MIM:616728
  • ACTH-independent macronodular adrenal hyperplasia 3 (AIMAH3) MIM:620990

Disease | GeneticClinVar

16 pathogenic / likely-pathogenic of 1,161 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
0.28
gnomAD pLI
1
gnomAD missense Z
4.68
DepMap mean gene effect
-0.1
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% 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 KDM1A 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 KDM1A as an antibody target. Whether an autoantibody or antibody against KDM1A could matter depends on whether native KDM1A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM1A 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 KDM1A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/KDM1A. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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