Seroatlas · Human Serome Atlas

KDM2B

Lysine-specific demethylase 2B

Also known as: CXXC2, Fbl10, FBXL10, JHDM1B, KDM2B_HUMAN, PCCX2

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

Protein identityUniProt · HPA

UniProt accession: Q8NHM5
Gene: KDM2B
Ensembl: ENSG00000089094
Chromosome: 12
Canonical length: 1336 aa
Protein class: Enzymes, Predicted intracellular proteins
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. Multiple alternatively spliced transcript variants have been found for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1336 residues, UniProt reviewed canonical sequence.

>Q8NHM5|KDM2B
     1  MAGPQMGGSA EDHPPRKRHA AEKQKKKTVI YTKCFEFESA TQRPIDRQRY DENEDLSDVE
    61  EIVSVRGFSL EEKLRSQLYQ GDFVHAMEGK DFNYEYVQRE ALRVPLIFRE KDGLGIKMPD
   121  PDFTVRDVKL LVGSRRLVDV MDVNTQKGTE MSMSQFVRYY ETPEAQRDKL YNVISLEFSH
   181  TKLEHLVKRP TVVDLVDWVD NMWPQHLKEK QTEATNAIAE MKYPKVKKYC LMSVKGCFTD
   241  FHIDFGGTSV WYHVFRGGKI FWLIPPTLHN LALYEEWVLS GKQSDIFLGD RVERCQRIEL
   301  KQGYTFFIPS GWIHAVYTPV DSLVFGGNIL HSFNVPMQLR IYEIEDRTRV QPKFRYPFYY
   361  EMCWYVLERY VYCVTQRSHL TQEYQRESML IDAPRKPSID GFSSDSWLEM EEEACDQQPQ
   421  EEEEKDEEGE GRDRAPKPPT DGSTSPTSTP SEDQEALGKK PKAPALRFLK RTLSNESEES
   481  VKSTTLAVDY PKTPTGSPAT EVSAKWTHLT EFELKGLKAL VEKLESLPEN KKCVPEGIED
   541  PQALLEGVKN VLKEHADDDP SLAITGVPVV TWPKKTPKNR AVGRPKGKLG PASAVKLAAN
   601  RTTAGARRRR TRCRKCEACL RTECGECHFC KDMKKFGGPG RMKQSCIMRQ CIAPVLPHTA
   661  VCLVCGEAGK EDTVEEEEGK FNLMLMECSI CNEIIHPGCL KIKESEGVVN DELPNCWECP
   721  KCNHAGKTGK QKRGPGFKYA SNLPGSLLKE QKMNRDNKEG QEPAKRRSEC EEAPRRRSDE
   781  HSKKVPPDGL LRRKSDDVHL RKKRKYEKPQ ELSGRKRASS LQTSPGSSSH LSPRPPLGSS
   841  LSPWWRSSLT YFQQQLKPGK EDKLFRKKRR SWKNAEDRMA LANKPLRRFK QEPEDELPEA
   901  PPKTRESDHS RSSSPTAGPS TEGAEGPEEK KKVKMRRKRR LPNKELSREL SKELNHEIQR
   961  TENSLANENQ QPIKSEPESE GEEPKRPPGI CERPHRFSKG LNGTPRELRH QLGPSLRSPP
  1021  RVISRPPPSV SPPKCIQMER HVIRPPPISP PPDSLPLDDG AAHVMHREVW MAVFSYLSHQ
  1081  DLCVCMRVCR TWNRWCCDKR LWTRIDLNHC KSITPLMLSG IIRRQPVSLD LSWTNISKKQ
  1141  LSWLINRLPG LRDLVLSGCS WIAVSALCSS SCPLLRTLDV QWVEGLKDAQ MRDLLSPPTD
  1201  NRPGQMDNRS KLRNIVELRL AGLDITDASL RLIIRHMPLL SKLHLSYCNH VTDQSINLLT
  1261  AVGTTTRDSL TEINLSDCNK VTDQCLSFFK RCGNICHIDL RYCKQVTKEG CEQFIAEMSV
  1321  SVQFGQVEEK LLQKLS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM2B 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): 0.43
Highest tissue expression: 22 nTPM

Expression across tissuesHPA

Tissue

skin: 22 nTPM
thymus: 22 nTPM
lymph node: 21 nTPM
tonsil: 20 nTPM
cerebellum: 19 nTPM
appendix: 18 nTPM

Single-cell type

cdc: 228 nCPM
nk-cells: 148 nCPM
myonuclei: 147 nCPM
b-cells: 143 nCPM
t-cells: 126 nCPM
retinal bipolar cells: 123 nCPM

Immune cell

memory B-cell: 9.5 nTPM
naive B-cell: 9.4 nTPM
gdT-cell: 6.3 nTPM
naive CD8 T-cell: 5.8 nTPM
MAIT T-cell: 4.9 nTPM
memory CD4 T-cell: 4.9 nTPM

Brain region

cerebellum: 36 nTPM
cerebral cortex: 30 nTPM
pons: 28 nTPM
white matter: 27 nTPM
basal ganglia: 27 nTPM
medulla oblongata: 26 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM2B.

Disease | GeneticClinVar

19 pathogenic / likely-pathogenic of 336 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder with congenital cardiac defects and variable renal and ocular abnormalities
KDM2B-related disorder
Inborn genetic diseases
KDM2B-related syndrome

Disease | ImmuneIEDB

Conditions an epitope on KDM2B was assayed in.

narcolepsy B cell
multiple sclerosis B cell
peripheral nervous system disease B cell

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): 0.18
gnomAD pLI: 1
gnomAD missense Z: 3.44
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 KDM2B 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 KDM2B as an antibody target. Whether an autoantibody or antibody against KDM2B could matter depends on whether native KDM2B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM2B 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 KDM2B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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