Seroatlas · Human Serome Atlas

KDM6B

Lysine-specific demethylase 6B

Also known as: JMJD3, KDM6B_HUMAN, KIAA0346

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

Protein identityUniProt · HPA

UniProt accession: O15054
Gene: KDM6B
Ensembl: ENSG00000132510
Chromosome: 17
Canonical length: 1643 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nuclear speckles

OverviewNCBI Gene

The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

Canonical amino-acid sequenceUniProt

1643 residues, UniProt reviewed canonical sequence.

>O15054|KDM6B
     1  MHRAVDPPGA RAAREAFALG GLSCAGAWSS CPPHPPPRSA WLPGGRCSAS IGQPPLPAPL
    61  PPSHGSSSGH PSKPYYAPGA PTPRPLHGKL ESLHGCVQAL LREPAQPGLW EQLGQLYESE
   121  HDSEEATRCY HSALRYGGSF AELGPRIGRL QQAQLWNFHT GSCQHRAKVL PPLEQVWNLL
   181  HLEHKRNYGA KRGGPPVKRA AEPPVVQPVP PAALSGPSGE EGLSPGGKRR RGCNSEQTGL
   241  PPGLPLPPPP LPPPPPPPPP PPPPLPGLAT SPPFQLTKPG LWSTLHGDAW GPERKGSAPP
   301  ERQEQRHSLP HPYPYPAPAY TAHPPGHRLV PAAPPGPGPR PPGAESHGCL PATRPPGSDL
   361  RESRVQRSRM DSSVSPAATT ACVPYAPSRP PGLPGTTTSS SSSSSSNTGL RGVEPNPGIP
   421  GADHYQTPAL EVSHHGRLGP SAHSSRKPFL GAPAATPHLS LPPGPSSPPP PPCPRLLRPP
   481  PPPAWLKGPA CRAAREDGEI LEELFFGTEG PPRPAPPPLP HREGFLGPPA SRFSVGTQDS
   541  HTPPTPPTPT TSSSNSNSGS HSSSPAGPVS FPPPPYLARS IDPLPRPPSP AQNPQDPPLV
   601  PLTLALPPAP PSSCHQNTSG SFRRPESPRP RVSFPKTPEV GPGPPPGPLS KAPQPVPPGV
   661  GELPARGPRL FDFPPTPLED QFEEPAEFKI LPDGLANIMK MLDESIRKEE EQQQHEAGVA
   721  PQPPLKEPFA SLQSPFPTDT APTTTAPAVA VTTTTTTTTT TTATQEEEKK PPPALPPPPP
   781  LAKFPPPSQP QPPPPPPPSP ASLLKSLASV LEGQKYCYRG TGAAVSTRPG PLPTTQYSPG
   841  PPSGATALPP TSAAPSAQGS PQPSASSSSQ FSTSGGPWAR ERRAGEEPVP GPMTPTQPPP
   901  PLSLPPARSE SEVLEEISRA CETLVERVGR SATDPADPVD TAEPADSGTE RLLPPAQAKE
   961  EAGGVAAVSG SCKRRQKEHQ KEHRRHRRAC KDSVGRRPRE GRAKAKAKVP KEKSRRVLGN
  1021  LDLQSEEIQG REKSRPDLGG ASKAKPPTAP APPSAPAPSA QPTPPSASVP GKKAREEAPG
  1081  PPGVSRADML KLRSLSEGPP KELKIRLIKV ESGDKETFIA SEVEERRLRM ADLTISHCAA
  1141  DVVRASRNAK VKGKFRESYL SPAQSVKPKI NTEEKLPREK LNPPTPSIYL ESKRDAFSPV
  1201  LLQFCTDPRN PITVIRGLAG SLRLNLGLFS TKTLVEASGE HTVEVRTQVQ QPSDENWDLT
  1261  GTRQIWPCES SRSHTTIAKY AQYQASSFQE SLQEEKESED EESEEPDSTT GTPPSSAPDP
  1321  KNHHIIKFGT NIDLSDAKRW KPQLQELLKL PAFMRVTSTG NMLSHVGHTI LGMNTVQLYM
  1381  KVPGSRTPGH QENNNFCSVN INIGPGDCEW FAVHEHYWET ISAFCDRHGV DYLTGSWWPI
  1441  LDDLYASNIP VYRFVQRPGD LVWINAGTVH WVQATGWCNN IAWNVGPLTA YQYQLALERY
  1501  EWNEVKNVKS IVPMIHVSWN VARTVKISDP DLFKMIKFCL LQSMKHCQVQ RESLVRAGKK
  1561  IAYQGRVKDE PAYYCNECDV EVFNILFVTS ENGSRNTYLV HCEGCARRRS AGLQGVVVLE
  1621  QYRTEELAQA YDAFTLAPAS TSR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM6B 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): 0.54
Highest tissue expression: 34 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 34 nTPM
adipose tissue: 31 nTPM
ovary: 28 nTPM
lung: 26 nTPM
pituitary gland: 21 nTPM
cerebellum: 20 nTPM

Single-cell type

neutrophils: 858 nCPM
epicardial cells: 600 nCPM
epididymal basal cells: 398 nCPM
monocytes: 350 nCPM
mast cells: 322 nCPM
ocular epithelial cells: 283 nCPM

Immune cell

neutrophil: 8.9 nTPM
basophil: 3.6 nTPM
eosinophil: 1.1 nTPM
plasmacytoid DC: 0.7 nTPM
classical monocyte: 0.6 nTPM
naive B-cell: 0.5 nTPM

Brain region

cerebral cortex: 61 nTPM
cerebellum: 37 nTPM
white matter: 24 nTPM
hypothalamus: 22 nTPM
medulla oblongata: 21 nTPM
thalamus: 19 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM6B.

Disease | AllUniProt

Conditions KDM6B is implicated in, by any mechanism.

Stolerman neurodevelopmental syndrome (NEDSST) MIM:618505

Disease | GeneticClinVar

116 pathogenic / likely-pathogenic of 838 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
Inborn genetic diseases
KDM6B-related disorder
Neurodevelopmental abnormality
See cases

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): 0.14
gnomAD pLI: 1
gnomAD missense Z: 1.32
DepMap mean gene effect: 0
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% 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 KDM6B 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 KDM6B as an antibody target. Whether an autoantibody or antibody against KDM6B could matter depends on whether native KDM6B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM6B 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 KDM6B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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