Seroatlas · Human Serome Atlas

CD9

CD9 antigen

Also known as: BA2, CD9_HUMAN, MIC3, MRP-1, P24, TSPAN29

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

Protein identityUniProt · HPA

UniProt accession: P21926
Gene: CD9
Ensembl: ENSG00000010278
Chromosome: 12
Canonical length: 228 aa
Protein class: Cancer-related genes, CD markers, Plasma proteins, Predicted membrane proteins, Transporters
Subcellular location: Plasma membrane
Secretome location: Intracellular and membrane
Quaternary structure: Homodimer

OverviewNCBI Gene

This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011]

Canonical amino-acid sequenceUniProt

228 residues, UniProt reviewed canonical sequence.

>P21926|CD9
     1  MPVKGGTKCI KYLLFGFNFI FWLAGIAVLA IGLWLRFDSQ TKSIFEQETN NNNSSFYTGV
    61  YILIGAGALM MLVGFLGCCG AVQESQCMLG LFFGFLLVIF AIEIAAAIWG YSHKDEVIKE
   121  VQEFYKDTYN KLKTKDEPQR ETLKAIHYAL NCCGLAGGVE QFISDICPKK DVLETFTVKS
   181  CPDAIKEVFD NKFHIIGAVG IGIAVVMIFG MIFSMILCCA IRRNREMV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CD9 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: 4
Mean surface accessibility (rSASA): 0.32
Highest tissue expression: 828 nTPM

Expression across tissuesHPA

Tissue

parathyroid gland: 828 nTPM
esophagus: 811 nTPM
salivary gland: 528 nTPM
vagina: 460 nTPM
prostate: 459 nTPM
rectum: 438 nTPM

Single-cell type

esophageal apical cells: 6,752 nCPM
esophageal suprabasal cells: 3,292 nCPM
respiratory ionocytes: 2,532 nCPM
esophageal basal cells: 1,958 nCPM
respiratory secretory cells: 1,893 nCPM
respiratory basal cells: 1,483 nCPM

Immune cell

basophil: 1,962 nTPM
eosinophil: 1,159 nTPM
total PBMC: 72 nTPM
classical monocyte: 61 nTPM
neutrophil: 31 nTPM
intermediate monocyte: 24 nTPM

Brain region

white matter: 266 nTPM
medulla oblongata: 194 nTPM
basal ganglia: 178 nTPM
choroid plexus: 171 nTPM
thalamus: 154 nTPM
cerebral cortex: 135 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CD9.

Disease | ImmuneIEDB

Conditions an epitope on CD9 was assayed in.

skin melanoma T cell

ReferencesPubMed · IEDB

Publications for CD9 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

5 publications

Thrombosis and shock induced by activating antiplatelet antibodies in human Fc gamma RIIA transgenic mice: the interplay among antibody, spleen, and Fc receptor.
2000 · Blood · RCR 0.8 · 42 citations
Relationship of antibodies against CD4+ T cells in HIV-infected patients to markers of activation and progression: autoantibodies are closely associated with CD4 cell depletion.
1993 · Immunology · RCR 0.7 · 28 citations
Platelet activation induced by an antiplatelet autoantibody against CD9 antigen and its inhibition by another autoantibody in immune thrombocytopenic purpura.
1993 · Br J Haematol · RCR 0.6 · 23 citations
Antibodies reactive with HIV-1 antigens in systemic lupus erythematosus.
1996 · Lupus · RCR 0.6 · 16 citations
Antibodies against linear epitopes on Goodpasture autoantigen in patients with anti-neutrophil cytoplasmic antibody-associated vasculitis.
2017 · Clin Rheumatol · RCR 0.2 · 3 citations

Reference: T cellIEDB

1 publication

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.
2019 · Mol Ther · RCR 1.5 · 50 citations

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): 0.86
gnomAD pLI: 0
gnomAD missense Z: 0.87
DepMap mean gene effect: -0.07
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

integrin binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CD9 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 CD9 as an antibody target. Whether an autoantibody or antibody against CD9 could matter depends on whether native CD9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CD9 is annotated at the cell surface, where native CD9 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 CD9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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