Seroatlas · Human Serome Atlas

KDM5B

Lysine-specific demethylase 5B

Also known as: CT31, JARID1B, KDM5B_HUMAN, PLU-1, PPP1R98, RBBP2H1A

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

Protein identityUniProt · HPA

UniProt accession: Q9UGL1
Gene: KDM5B
Ensembl: ENSG00000117139
Chromosome: 1
Canonical length: 1544 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm,Cytosol

OverviewNCBI Gene

This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

Canonical amino-acid sequenceUniProt

1544 residues, UniProt reviewed canonical sequence.

>Q9UGL1|KDM5B
     1  MEAATTLHPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG
    61  ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK LNFLDQIAKY WELQGSTLKI
   121  PHVERKILDL FQLNKLVAEE GGFAVVCKDR KWTKIATKMG FAPGKAVGSH IRGHYERILN
   181  PYNLFLSGDS LRCLQKPNLT TDTKDKEYKP HDIPQRQSVQ PSETCPPARR AKRMRAEAMN
   241  IKIEPEETTE ARTHNLRRRM GCPTPKCENE KEMKSSIKQE PIERKDYIVE NEKEKPKSRS
   301  KKATNAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLI PPLHDVPKGD WRCPKCLAQE
   361  CSKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM VPTELVEKEF WRLVSTIEED
   421  VTVEYGADIA SKEFGSGFPV RDGKIKLSPE EEEYLDSGWN LNNMPVMEQS VLAHITADIC
   481  GMKLPWLYVG MCFSSFCWHI EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE
   541  LFVSQPDLLH QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV
   601  NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST VQKDMAIMIE
   661  DEKALRETVR KLGVIDSERM DFELLPDDER QCVKCKTTCF MSAISCSCKP GLLVCLHHVK
   721  ELCSCPPYKY KLRYRYTLDD LYPMMNALKL RAESYNEWAL NVNEALEAKI NKKKSLVSFK
   781  ALIEESEMKK FPDNDLLRHL RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN
   841  ELRQFVTQLY ALPCVLSQTP LLKDLLNRVE DFQQHSQKLL SEETPSAAEL QDLLDVSFEF
   901  DVELPQLAEM RIRLEQARWL EEVQQACLDP SSLTLDDMRR LIDLGVGLAP YSAVEKAMAR
   961  LQELLTVSEH WDDKAKSLLK ARPRHSLNSL ATAVKEIEEI PAYLPNGAAL KDSVQRARDW
  1021  LQDVEGLQAG GRVPVLDTLI ELVTRGRSIP VHLNSLPRLE TLVAEVQAWK ECAVNTFLTE
  1081  NSPYSLLEVL CPRCDIGLLG LKRKQRKLKE PLPNGKKKST KLESLSDLER ALTESKETAS
  1141  AMATLGEARL REMEALQSLR LANEGKLLSP LQDVDIKICL CQKAPAAPMI QCELCRDAFH
  1201  TSCVAVPSIS QGLRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD ALRYMIERTV
  1261  NWQHRAQQLL SSGNLKFVQD RVGSGLLYSR WQASAGQVSD TNKVSQPPGT TSFSLPDDWD
  1321  NRTSYLHSPF STGRSCIPLH GVSPEVNELL MEAQLLQVSL PEIQELYQTL LAKPSPAQQT
  1381  DRSSPVRPSS EKNDCCRGKR DGINSLERKL KRRLEREGLS SERWERVKKM RTPKKKKIKL
  1441  SHPKDMNNFK LERERSYELV RSAETHSLPS DTSYSEQEDS EDEDAICPAV SCLQPEGDEV
  1501  DWVQCDGSCN QWFHQVCVGV SPEMAEKEDY ICVRCTVKDA PSRK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM5B 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): 0.37
Highest tissue expression: 35 nTPM

Expression across tissuesHPA

Tissue

testis: 35 nTPM
retina: 16 nTPM
bone marrow: 13 nTPM
skin: 6.8 nTPM
esophagus: 6.1 nTPM
vagina: 4.9 nTPM

Single-cell type

rod photoreceptor cells: 844 nCPM
early primary spermatocytes: 380 nCPM
late spermatids: 369 nCPM
neutrophils: 315 nCPM
late primary spermatocytes: 312 nCPM
sertoli cells: 308 nCPM

Immune cell

basophil: 45 nTPM
neutrophil: 35 nTPM
eosinophil: 20 nTPM
naive B-cell: 18 nTPM
NK-cell: 13 nTPM
memory B-cell: 11 nTPM

Brain region

choroid plexus: 34 nTPM
cerebellum: 29 nTPM
cerebral cortex: 27 nTPM
hippocampal formation: 27 nTPM
white matter: 22 nTPM
basal ganglia: 21 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM5B.

Disease | AllUniProt

Conditions KDM5B is implicated in, by any mechanism.

Intellectual developmental disorder, autosomal recessive 65 (MRT65) MIM:618109

Disease | GeneticClinVar

98 pathogenic / likely-pathogenic of 549 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Intellectual disability, autosomal recessive 65
Inborn genetic diseases
KDM5B-related disorder
Neurodevelopmental disorder
See cases

Disease | ImmuneIEDB

Conditions an epitope on KDM5B was assayed in.

breast cancer T 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): 0.57
gnomAD pLI: 0
gnomAD missense Z: 1.78
DepMap mean gene effect: -0.16
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 11% 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

ARID DNA-binding domain
Zinc finger, PHD-type
JmjC domain
JmjN domain
Zinc finger, C5HC2-type
Zinc finger, FYVE/PHD-type
Zinc finger, RING/FYVE/PHD-type
Lysine-specific demethylase-like domain
Zinc finger, PHD-type, conserved site
Zinc finger, PHD-finger
ARID DNA-binding domain superfamily
Lysine-specific demethylase 5, C-terminal helical domain
PHD-finger
ARID/BRIGHT DNA binding domain
JmjC domain, hydroxylase
jmjN domain
C5HC2 zinc finger
PLU-1-like protein
Lysine-specific demethylase 5, C-terminal helical domain
Lysine-specific demethylase 5B, first PHD-finger
Lysine-specific demethylase 5B, third PHD-finger
Lysine-specific demethylase 5B, ARID domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of KDM5B 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 KDM5B as an antibody target. Whether an autoantibody or antibody against KDM5B could matter depends on whether native KDM5B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM5B 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 KDM5B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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