Seroatlas · Human Serome Atlas

KDM1B

Lysine-specific histone demethylase 2

Also known as: AOF1, bA204B7.3, C6orf193, dJ298J15.2, FLJ33898, FLJ34109, FLJ43328, KDM1B_HUMAN, LSD2

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

Protein identityUniProt · HPA

UniProt accession: Q8NB78
Gene: KDM1B
Ensembl: ENSG00000165097
Chromosome: 6
Canonical length: 822 aa
Protein class: Enzymes, Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]

Canonical amino-acid sequenceUniProt

822 residues, UniProt reviewed canonical sequence.

>Q8NB78|KDM1B
     1  MATPRGRTKK KASFDHSPDS LPLRSSGRQA KKKATETTDE DEDGGSEKKY RKCEKAGCTA
    61  TCPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY RSHKDGYDKY TTWKKIWTSN
   121  GKTEPSPKAF MADQQLPYWV QCTKPECRKW RQLTKEIQLT PQIAKTYRCG MKPNTAIKPE
   181  TSDHCSLPED LRVLEVSNHW WYSMLILPPL LKDSVAAPLL SAYYPDCVGM SPSCTSTNRA
   241  AATGNASPGK LEHSKAALSV HVPGMNRYFQ PFYQPNECGK ALCVRPDVME LDELYEFPEY
   301  SRDPTMYLAL RNLILALWYT NCKEALTPQK CIPHIIVRGL VRIRCVQEVE RILYFMTRKG
   361  LINTGVLSVG ADQYLLPKDY HNKSVIIIGA GPAGLAAARQ LHNFGIKVTV LEAKDRIGGR
   421  VWDDKSFKGV TVGRGAQIVN GCINNPVALM CEQLGISMHK FGERCDLIQE GGRITDPTID
   481  KRMDFHFNAL LDVVSEWRKD KTQLQDVPLG EKIEEIYKAF IKESGIQFSE LEGQVLQFHL
   541  SNLEYACGSN LHQVSARSWD HNEFFAQFAG DHTLLTPGYS VIIEKLAEGL DIQLKSPVQC
   601  IDYSGDEVQV TTTDGTGYSA QKVLVTVPLA LLQKGAIQFN PPLSEKKMKA INSLGAGIIE
   661  KIALQFPYRF WDSKVQGADF FGHVPPSASK RGLFAVFYDM DPQKKHSVLM SVIAGEAVAS
   721  VRTLDDKQVL QQCMATLREL FKEQEVPDPT KYFVTRWSTD PWIQMAYSFV KTGGSGEAYD
   781  IIAEDIQGTV FFAGEATNRH FPQTVTGAYL SGVREASKIA AF

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM1B 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): 0.27
Highest tissue expression: 26 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 26 nTPM
thyroid gland: 26 nTPM
testis: 15 nTPM
colon: 13 nTPM
fallopian tube: 13 nTPM
cerebral cortex: 12 nTPM

Single-cell type

neutrophil progenitors: 290 nCPM
neutrophils: 250 nCPM
respiratory ciliated cells: 106 nCPM
fallopian tube ciliated cells: 99 nCPM
kupffer cells: 96 nCPM
thyrotrophs: 87 nCPM

Immune cell

intermediate monocyte: 8.6 nTPM
eosinophil: 7.2 nTPM
non-classical monocyte: 6.9 nTPM
neutrophil: 4.9 nTPM
classical monocyte: 4.6 nTPM
myeloid DC: 3.7 nTPM

Brain region

white matter: 22 nTPM
choroid plexus: 20 nTPM
cerebral cortex: 19 nTPM
medulla oblongata: 18 nTPM
midbrain: 18 nTPM
hippocampal formation: 17 nTPM

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): 0.53
gnomAD pLI: 0
gnomAD missense Z: 1.67
DepMap mean gene effect: 0.05
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% 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 KDM1B in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

GLYR1

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads KDM1B as an antibody target. Whether an autoantibody or antibody against KDM1B could matter depends on whether native KDM1B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM1B 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 KDM1B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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