Seroatlas · Human Serome Atlas

SOX2

Transcription factor SOX-2

Also known as: SOX2_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
P48431
Gene
SOX2
Ensembl
ENSG00000181449
Chromosome
3
Canonical length
317 aa
Protein class
Cancer-related genes, Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors
Subcellular location
Nucleoplasm

OverviewNCBI Gene

This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT). [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

317 residues, UniProt reviewed canonical sequence.

>P48431|SOX2
     1  MYNMMETELK PPGPQQTSGG GGGNSTAAAA GGNQKNSPDR VKRPMNAFMV WSRGQRRKMA
    61  QENPKMHNSE ISKRLGAEWK LLSETEKRPF IDEAKRLRAL HMKEHPDYKY RPRRKTKTLM
   121  KKDKYTLPGG LLAPGGNSMA SGVGVGAGLG AGVNQRMDSY AHMNGWSNGS YSMMQDQLGY
   181  PQHPGLNAHG AAQMQPMHRY DVSALQYNSM TSSQTYMNGS PTYSMSYSQQ GTPGMALGSM
   241  GSVVKSEASS SPPVVTSSSH SRAPCQAGDL RDMISMYLPG AEVPEPAAPS RLHMSQHYQS
   301  GPVPGTAING TLPLSHM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SOX2 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)
0.64
Highest tissue expression
72 nTPM

Expression across tissuesHPA

Tissue

  • amygdala: 72 nTPM
  • basal ganglia: 64 nTPM
  • cerebral cortex: 64 nTPM
  • midbrain: 51 nTPM
  • hippocampal formation: 48 nTPM
  • hypothalamus: 46 nTPM

Single-cell type

  • podocytes: 4.1 nCPM
  • schwann cells: 2.8 nCPM
  • astrocytes: 2.1 nCPM
  • bergmann glia: 1.6 nCPM
  • gastric chief cells: 1.1 nCPM
  • respiratory deuterosomal cells: 1 nCPM

Immune cell

  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM
  • MAIT T-cell: 0 nTPM

Brain region

  • hypothalamus: 139 nTPM
  • spinal cord: 138 nTPM
  • midbrain: 138 nTPM
  • thalamus: 137 nTPM
  • white matter: 136 nTPM
  • amygdala: 134 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SOX2.

Disease | AllUniProt

Conditions SOX2 is implicated in, by any mechanism.

Disease | GeneticClinVar

101 pathogenic / likely-pathogenic of 276 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Disease | ImmuneIEDB

Conditions an epitope on SOX2 was assayed in.

Disease | AutoantibodyPubMed

Conditions in which antibodies against SOX2 are reported. Each links to that disease's full target list.

ReferencesPubMed · IEDB

Publications for SOX2 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

7 publications

Show 2 more

Reference: B cellIEDB

2 publications

Reference: T cellIEDB

1 publication

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)
0.57
gnomAD pLI
0.71
gnomAD missense Z
2.12
DepMap mean gene effect
-0.08
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 9% 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 SOX2 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 SOX2 as an antibody target. Whether an autoantibody or antibody against SOX2 could matter depends on whether native SOX2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SOX2 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 SOX2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/SOX2. 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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