Seroatlas · Human Serome Atlas

HMGB1

High mobility group protein B1

Also known as: DKFZp686A04236, HMG1, HMG3, HMGB1_HUMAN, SBP-1

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

Protein identityUniProt · HPA

UniProt accession
P09429
Gene
HMGB1
Ensembl
ENSG00000189403
Chromosome
13
Canonical length
215 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins
Subcellular location
Nucleoplasm
Secretome location
Secreted to blood

OverviewNCBI Gene

This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription, and is involved in organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]

Canonical amino-acid sequenceUniProt

215 residues, UniProt reviewed canonical sequence.

>P09429|HMGB1
     1  MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK TMSAKEKGKF
    61  EDMAKADKAR YEREMKTYIP PKGETKKKFK DPNAPKRPPS AFFLFCSEYR PKIKGEHPGL
   121  SIGDVAKKLG EMWNNTAADD KQPYEKKAAK LKEKYEKDIA AYRAKGKPDA AKKGVVKAEK
   181  SKKKKEEEED EEDEEDEEEE EDEEDEDEEE DDDDE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against HMGB1 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
Cell surface
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.48
Highest tissue expression
801 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 801 nTPM
  • thymus: 702 nTPM
  • tonsil: 588 nTPM
  • lymph node: 494 nTPM
  • spinal cord: 374 nTPM
  • skeletal muscle: 312 nTPM

Single-cell type

  • erythrocyte progenitors: 1,881 nCPM
  • platelets: 1,550 nCPM
  • megakaryocyte progenitors: 1,467 nCPM
  • megakaryocytes: 1,403 nCPM
  • monocyte progenitors: 1,272 nCPM
  • extravillous trophoblasts: 1,164 nCPM

Immune cell

  • total PBMC: 759 nTPM
  • basophil: 757 nTPM
  • eosinophil: 660 nTPM
  • T-reg: 497 nTPM
  • neutrophil: 453 nTPM
  • NK-cell: 447 nTPM

Brain region

  • white matter: 259 nTPM
  • medulla oblongata: 224 nTPM
  • spinal cord: 215 nTPM
  • hypothalamus: 215 nTPM
  • basal ganglia: 214 nTPM
  • midbrain: 202 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about HMGB1.

Disease | GeneticClinVar

6 pathogenic / likely-pathogenic of 37 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Disease | ImmuneIEDB

Conditions an epitope on HMGB1 was assayed in.

Disease | AutoantibodyPubMed

Conditions in which antibodies against HMGB1 are reported. Each links to that disease's full target list.

ReferencesPubMed · IEDB

Publications for HMGB1 from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.

Reference: AutoantibodyPubMed

25 publications

Show 20 more

Reference: B cellIEDB

2 publications

Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. IEDB — curated epitope assays from the Immune Epitope Database (Vita et al., Nucleic Acids Research 2019). Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.

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)
0.47
gnomAD pLI
0.82
gnomAD missense Z
2.69
DepMap mean gene effect
-0.5
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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 HMGB1 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 HMGB1 as an antibody target. Whether an autoantibody or antibody against HMGB1 could matter depends on whether native HMGB1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

HMGB1 is annotated at the cell surface, where native HMGB1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label HMGB1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/HMGB1. 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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