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ICOS

gene
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Also known as AILIMCD278

Summary

ICOS (inducible T cell costimulator, HGNC:5351) is a protein-coding gene on chromosome 2q33.2, encoding Inducible T-cell costimulator (Q9Y6W8). Stimulatory receptor expressed in activated or antigen-experienced T-cells that plays an important role in the immune response.

The protein encoded by this gene belongs to the CD28 and CTLA-4 cell-surface receptor family. It forms homodimers and plays an important role in cell-cell signaling, immune responses, and regulation of cell proliferation.

Source: NCBI Gene 29851 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): common variable immunodeficiency (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 17
  • Clinical variants (ClinVar): 208 total — 9 pathogenic, 5 likely-pathogenic
  • GTEx eGene: eQTL in 3 tissues, sQTL in 0 (q < 0.05)
  • Phenotypes (HPO): 32
  • Drug target: yes — 4 curated mechanism-of-action drugs
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.27 (unconstrained)
  • MANE Select transcript: NM_012092
  • Interaction hub: 2,132 STRING partners (top 6% of genes corpus-wide)

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5351
Approved symbolICOS
Nameinducible T cell costimulator
Location2q33.2
Locus typegene with protein product
StatusApproved
AliasesAILIM, CD278
Ensembl geneENSG00000163600
Ensembl biotypeprotein_coding
OMIM604558
Entrez29851

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

MANE Select: ENST00000316386

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2

ENST00000316386, ENST00000435193, ENST00000897354, ENST00001138099

RefSeq mRNA: 1 — MANE Select: NM_012092 NM_012092

CCDS: CCDS2363

Canonical transcript exons

ENST00000316386 — 5 exons

ExonStartEnd
ENSE00001076433203957799203957883
ENSE00001076434203936763203936872
ENSE00001076436203955636203955971
ENSE00001076437203956659203956765
ENSE00003507544203959586203961577

Expression profiles

Bgee: expression breadth ubiquitous, 110 present calls, max score 79.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 7.1984 / max 718.3986, expressed in 181 samples.

Highest expression (Bgee): lymph node, vermiform appendix, thymus, granulocyte, epithelium of nasopharynx.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ICOS is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 3 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

3 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Thyroideqtl3.9e-03-0.382:203633118:C:G
Artery Aortaeqtl3.0e-02-0.362:204197738:A:G
Skin Sun Exposed Lower legeqtl3.9e-02+0.312:203761998:T:C

FANTOM5 promoters

3 alternative TSS:

Promoter IDTPM avgSamples expressed
247856.5113177
247860.478869
247840.208265

Top tissues by expression

showing 100 of 266 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lymph nodeUBERON:000002979.37gold quality
vermiform appendixUBERON:000115476.97gold quality
thymusUBERON:000237075.66silver quality
granulocyteCL:000009475.36gold quality
epithelium of nasopharynxUBERON:000195173.47gold quality
bloodUBERON:000017872.48gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047371.18gold quality
caecumUBERON:000115370.66gold quality
superficial temporal arteryUBERON:000161467.54gold quality
bone marrowUBERON:000237166.27gold quality
tonsilUBERON:000237265.23gold quality
spleenUBERON:000210665.17gold quality
gall bladderUBERON:000211064.88gold quality
palpebral conjunctivaUBERON:000181263.07gold quality
rectumUBERON:000105262.64gold quality
colonic epitheliumUBERON:000039760.97silver quality
right lungUBERON:000216760.58gold quality
small intestine Peyer’s patchUBERON:000345459.07gold quality
upper lobe of left lungUBERON:000895259.06gold quality
upper lobe of lungUBERON:000894858.63gold quality
bone marrow cellCL:000209258.40silver quality
small intestineUBERON:000210857.34gold quality
epithelial cell of pancreasCL:000008357.33gold quality
gluteal muscleUBERON:000200057.26gold quality
lungUBERON:000204856.92gold quality
tendon of biceps brachiiUBERON:000818856.68gold quality
visceral pleuraUBERON:000240156.57silver quality
oral cavityUBERON:000016756.41silver quality
triceps brachiiUBERON:000150956.16gold quality
esophagus squamous epitheliumUBERON:000692054.95silver quality
duodenumUBERON:000211454.60gold quality
myocardiumUBERON:000234954.25gold quality
lower lobe of lungUBERON:000894953.05silver quality
nasal cavity mucosaUBERON:000182652.98gold quality
smooth muscle tissueUBERON:000113552.96gold quality
mucosa of transverse colonUBERON:000499152.94gold quality
omental fat padUBERON:001041452.89gold quality
peritoneumUBERON:000235852.85gold quality
adipose tissue of abdominal regionUBERON:000780852.21gold quality
mucosa of sigmoid colonUBERON:000499352.00gold quality
left uterine tubeUBERON:000130351.71gold quality
cervix squamous epitheliumUBERON:000692250.96gold quality
mucosa of urinary bladderUBERON:000125950.75silver quality
olfactory segment of nasal mucosaUBERON:000538650.67gold quality
frontal poleUBERON:000279550.41gold quality
male germ cellCL:000001550.33gold quality
middle frontal gyrusUBERON:000270250.30gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
right coronary arteryUBERON:000162550.15gold quality
spermCL:000001950.00gold quality
quadriceps femorisUBERON:000137749.98gold quality
cardia of stomachUBERON:000116249.95gold quality
urinary bladderUBERON:000125549.62gold quality
vastus lateralisUBERON:000137949.61gold quality
buccal mucosa cellCL:000233649.49gold quality
cervix epitheliumUBERON:000480149.34gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
blood vessel layerUBERON:000479749.29gold quality
cerebellar vermisUBERON:000472049.25gold quality
hair follicleUBERON:000207349.18gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
oviduct epitheliumUBERON:000480448.88gold quality
penisUBERON:000098948.85gold quality
type B pancreatic cellCL:000016948.83gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
nasal cavity epitheliumUBERON:000538448.45gold quality
layer of synovial tissueUBERON:000761648.43gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
intestineUBERON:000016048.16gold quality
upper arm skinUBERON:000426348.06gold quality
tongue squamous epitheliumUBERON:000691947.92gold quality
metanephric glomerulusUBERON:000473647.74gold quality
renal glomerulusUBERON:000007447.60gold quality
cranial nerve IIUBERON:000094147.57silver quality
fallopian tubeUBERON:000388947.51gold quality
superior surface of tongueUBERON:000737147.48gold quality
transverse colonUBERON:000115747.46gold quality
kidney epitheliumUBERON:000481947.32gold quality
periodontal ligamentUBERON:000826647.14gold quality
diaphragmUBERON:000110347.05gold quality
nephron tubuleUBERON:000123146.88gold quality
endometrium epitheliumUBERON:000481146.85gold quality
amniotic fluidUBERON:000017346.78silver quality
deltoidUBERON:000147646.38gold quality
muscle tissueUBERON:000238546.31gold quality
esophagus mucosaUBERON:000246946.12gold quality
body of stomachUBERON:000116146.09gold quality
liverUBERON:000210745.93silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099145.46silver quality
metanephrosUBERON:000008145.42gold quality
stomachUBERON:000094545.40gold quality
pylorusUBERON:000116645.35gold quality
dorsal motor nucleus of vagus nerveUBERON:000287045.35gold quality
large intestineUBERON:000005945.33gold quality
inferior olivary complexUBERON:000212745.14gold quality
endometriumUBERON:000129545.12gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-CURD-89yes1677.44
E-CURD-122yes40.30
E-CURD-88yes36.73
E-CURD-46yes16.04
E-ANND-3yes7.92

HPA expression

RNA tissue specificity: Group enriched

50 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Thymustissue18.8
Bone marrowtissue15.6not detected
Tonsiltissue15.2medium
Lymph nodetissue13.4medium
Appendixtissue7.2low
Spleentissue3.1not detected
Urinary bladdertissue2.5not detected
Lungtissue2.5not detected
Gallbladdertissue1.3not detected
Stomach 1tissue1.2not detected
Rectumtissue1.2not detected
Small intestinetissue1.0not detected
Colontissue0.7not detected
Duodenumtissue0.7not detected
Esophagustissue0.5not detected
Spinal cordtissue0.5
Prostatetissue0.5not detected
Adipose tissuetissue0.4not detected
Salivary glandtissue0.4not detected
Livertissue0.4not detected
Breasttissue0.3not detected
Smooth muscletissue0.3not detected
Cervixtissue0.2not detected
Skin 1tissue0.2not detected
Testistissue0.2not detected
Vaginatissue0.2not detected
Endometrium 1tissue0.2not detected
Thalamustissue0.2
Superior colliculitissue0.2
Substantia nigratissue0.2
Thyroid glandtissue0.2not detected
Heart muscletissue0.1not detected
Ponstissue0.1
Epididymistissue0.1not detected
Basal gangliatissue0.1not detected
Putamentissue0.1
Amygdalatissue0.1
Medulla oblongatatissue0.1
Hypothalamustissue0.1
Placentatissue0.1not detected
Kidneytissue0.1not detected
Corpus callosumtissue0.1
Adrenal glandtissue0.1not detected
Hippocampal formationtissue0.1
Entorhinal cortextissue0.1
Periaqueductal graytissue0.1
Olfactory bulbtissue0.1
Fallopian tubetissue0.1not detected
Septumtissue0.1
Caudate putamentissue0.1

Brain sub-regions (HPA Brain Atlas): detected in 27; highest nTPM — Ventral spinal cord (0.5), Dorsal spinal cord (0.3), Motor hypoglossal nucleus (0.3), Nucleus gracilis (0.3), Nucleus tractus solitarii (0.3).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, GATA3, HAND1, NFATC2, STAT3, STAT6, TBX21

miRNA regulators (miRDB)

Targeting ICOS by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 117 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3163100.0077.238605
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-450099.9972.722367
HSA-MIR-806899.9873.852376
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-3692-3P99.9870.272139
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-570-3P99.9672.414910
HSA-MIR-590-3P99.9674.346478
HSA-MIR-426799.9666.532368
HSA-MIR-548AT-5P99.9670.832666
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-767-5P99.9570.85993
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-568299.8972.561005
HSA-MIR-548AR-3P99.8571.263889

Functional genomics

gnomAD constraint: pLI 0.00324, LOEUF 1.27, missense Z 0.851 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000316386 — one region, missense o/e 0.86.

Literature-anchored findings (GeneRIF, showing 40)

  • its polymorphism may contributes to the pathogenesis of spondyloarthropathy (PMID:11771526)
  • Genetic polymorphism of the human ICOS gene. (PMID:11904679)
  • role of ligation in modulating TCR-induced transcriptional profiles (PMID:12195015)
  • ICOS reversely regulates IL-10 on re-activation of human effector T cells with mature dendritic cells. Interaction of ICOS with ICOS-L strongly promoted IL-10 secretion. (PMID:12207353)
  • ICOS provides co-stimulation to memory t-cells [review] (PMID:12456021)
  • Analysis of the upstream region of ICOS revealed an additional eight single nucleotide polymorphism (PMID:12753665)
  • local immune responses may be modulated by H4/ICOS expressed on T cells in the joints of patients with rheumatoid arthritis, and thus it may be involved in the pathogenetic mechanism of rheumatoid arthritis. (PMID:12784384)
  • ICOS is upregulated on human T cells after stimulation and can modulate both Th1 and Th2 cytokine production in the absence and presence of B7-1 (CD80) and B7-2 (CD86)costimulation. (PMID:12864987)
  • Targeting of specific chemokine and chemokine receptor pathways and/or ICOS may have clinical application in the prevention and treatment of chronic allograft nephropathy. (PMID:12919091)
  • AILIM has a role in regulating the signaling cascades for T-cell proliferation and IL-10 production (PMID:14550257)
  • ICOS does not belong to the group of genes that, if mutated, present clinically as the hyper-IgM syndrome. (PMID:14610488)
  • Highly expressed ICOS in activated CD4(+) lamina propria T cells of inflammatory bowel (IBD) contributes to dysregulated immune responses. Hyperexpression limited to inflammatory sites in IBD. Feasible therapeutic target for treatment of IBD. (PMID:14988837)
  • A subtype of regulatory T cells in human blood can be identified by expression of ICOS after activation; these ICOS-expressing cells block the capacity of reciprocal ICOS-negative cells to proliferate and to produce cytokines. (PMID:15100277)
  • ICOS expression on activated Th cells may provide a powerful means to amplify effector T cell responses in peripheral tissues, independently of the polarized state of the Th cells (PMID:15265908)
  • AILIM/ICOS-B7h interactions play an important role in the endothelium in controlling the entry of memory/effector T-cells into inflamed tissues in the periphery. (PMID:15339883)
  • The incidence of ICOS deficiency among patients with Common variable immunodeficiency is less than 5% (PMID:15507387)
  • invariant NKT cell activation is regulated by CD28 and IOCS independently (PMID:15629449)
  • A predominant effect of ICOS-mediated costimulation on T helper type 2 (Th2) cell differentiation in transgenic ICOS-deficient mice may be achieved by the enhancement of IL-4 receptor-mediated signaling. (PMID:15699127)
  • ICOS is an influential costimulatory pathway in atherosclerosis & may play a protective role. It localizes with T cells in human aortic plaque. (PMID:15941568)
  • This study could not confirm association with the CD28/CTLA4/ICOS gene region in multiple sclerosis. (PMID:16005527)
  • Two variants in the ICOS promoter region are significantly associated with allergic sensitization and production of type 2 T helper (Th2) cell cytokines (PMID:16081771)
  • ICOS is involved in abnormal T cell activation in systsemic lupus erythematosus (SLE) and blockade of the interaction between ICOS and its receptor may have therapeutic value in the treatment of this intractable disease. (PMID:16563187)
  • There are no major effects of the CD28/CTLA4/ICOS gene region on susceptibility to primary sclerosing cholangitis but minor contributions cannot be excluded. (PMID:16638702)
  • ICOS activation is associated with T helper type 1 (Th1) cell responses in human intracellular tuberculosis infection and may contribute to the amplification of those responses. (PMID:16670305)
  • This review summarizes the evidence that ICOS expression regulates T-cell-dependent B cell responses and proposes a model for the role of ICOS in diseases characterized by dysregulated humoral immunity. (PMID:16790364)
  • genetic variation in ICOS gene regulates the expression of both CTLA4 and ICOS and not only the splicing of sCTLA4 as suggested earlier. (PMID:16996590)
  • Both the PI3-kinase/Akt and Rho family cascades operate coordinately to induce the forward migration of activated T cells by AILIM/ICOS signaling. (PMID:17077177)
  • With multiethnic DNA panels that represent a wide spectrum of ethnic groups, we demonstrate long-range linkage disequilibrium among CD28, CTLA4, and ICOS costimulatory genes. (PMID:17197413)
  • ICOS may be relevant in inducing an acute immune response and may be critically involved in perpetuating inflammation in chronically immune-mediated disorders of the peripheral nervous system. (PMID:17242332)
  • These results define elevated populations of memory T-lymphocytes expressing B7 molecules in rheumatoid arthritis (RA) synovial fluid that either stimulate T cells through ICOS, or down-regulate RA synovial tissue T-lymphocytes through B7H1 and B7H2. (PMID:17323353)
  • The whole blood gene expression quantities of costimulatory molecules CD154 and ICOS reasonably robustly differentiated rejection patients from control patients. (PMID:17414714)
  • ICOS gene haplotypes correlate with IL10 secretion and multiple sclerosis. (PMID:17481737)
  • Of 9 CVID patients…No mutations of SAP, ICOS, TACI, BAFFR, and CD19 were identified (PMID:18051214)
  • definition of a newly discovered pathway that prevents autoimmunity by limiting the levels on T lymphocytes of aco-stimulatory receptor, the inducible T-cell co-stimulator(ICOS) (PMID:18172933)
  • Modulation of immune responses by ICOS-expressing naturally occurring T regulatory cells present in melanoma tissue depends upon costimulatory signals delivered to the CD4-positive CD25-negative responder cells and the cytokine milieu. (PMID:18292519)
  • p50alpha is likely a determining factor in ICOS-mediated PI3K activity in T cells (PMID:18641334)
  • Children with type 1 diabetes show decreased inducrion of ICOS in T cells. (PMID:18973208)
  • The shared CTLA4-ICOS risk locus in celiac disease, IgA deficiency and common variable immunodeficiency. (PMID:19020530)
  • ICOS-induced T cell spreading and filopodia/microspike formation may promote antigen recognition by enhancing a T cell’s scanning potential of an adherent APC surface. (PMID:19095735)
  • ICOS variants do not play a major role in the development of atopy in European children. (PMID:19175887)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusIcosENSMUSG00000026009
rattus_norvegicusIcosENSRNOG00000046196

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1858745) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 53 distinct phenotype terms.

Mouse phenotype (MP)Records
decreased IgG1 level4
abnormal immune system physiology3
decreased IgG level3
decreased IgE level3
abnormal spleen morphology2
abnormal Peyer’s patch germinal center morphology2
abnormal T cell physiology2
abnormal B cell physiology2
abnormal immunoglobulin level2
abnormal class switch recombination2
abnormal CD4-positive, alpha-beta T cell physiology2
small Peyer’s patches2
decreased spleen germinal center number2
decreased interleukin-4 secretion2
abnormal interleukin level2
abnormal leukocyte cell number1
abnormal small intestine morphology1
decreased IgA level1
abnormal T cell differentiation1
small lymph nodes1
abnormal spleen germinal center morphology1
abnormal B cell number1
short tibia1
decreased anti-insulin autoantibody level1
abnormal cytokine secretion1

+28 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusQ58DF973.4%Diamond
Canis lupus familiarisQ7YR7372.7%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
CTLA4protein-coding1493

Protein

Protein identifiers

Inducible T-cell costimulator — Q9Y6W8 (reviewed: Q9Y6W8)

Alternative names: Activation-inducible lymphocyte immunomediatory molecule

All UniProt accessions (2): Q9Y6W8, Q53QY6

UniProt curated annotations — full annotation on UniProt →

Function. Stimulatory receptor expressed in activated or antigen-experienced T-cells that plays an important role in the immune response. Upon binding to its ligand ICOSL expressed on antigen presenting cells (APCs), delivers costimulatory signals that enhances all basic T-cell responses to a foreign antigen, namely proliferation, secretion of lymphokines including IL10, up-regulation of molecules that mediate cell-cell interaction, and effective help for antibody secretion by B-cells. Also acts as a costimulatory receptor critical for the differentiation of T follicular regulatory cells upon immune challenges such as viral infection. Mechanistically, potentiates TCR-induced calcium flux by augmenting PLCG1 activation and actin remodeling. In addition, activates PI3K signaling pathways independently of calcium flux. Essential both for efficient interaction between T and B-cells and for normal antibody responses to T-cell dependent antigens. Prevents the apoptosis of pre-activated T-cells. Plays a critical role in CD40-mediated class switching of immunoglobin isotypes.

Subunit / interactions. Homodimer; disulfide-linked. Interacts with ICOSLG. Interacts with PIK3R1. Interacts with TBK1; this interaction is critical for the maturation of T follicular regulatory cells.

Subcellular location. Cell membrane Secreted.

Tissue specificity. Activated T-cells. Highly expressed on tonsillar T-cells, which are closely associated with B-cells in the apical light zone of germinal centers, the site of terminal B-cell maturation. Expressed at lower levels in thymus, lung, lymph node and peripheral blood leukocytes. Expressed in the medulla of fetal and newborn thymus.

Post-translational modifications. N-glycosylated.

Disease relevance. Immunodeficiency, common variable, 1 (CVID1) [MIM:607594] A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low. The disease is caused by variants affecting the gene represented in this entry.

Induction. By phorbol myristate acetate (PMA) and ionomycin. Up-regulated early on T-cells and continues to be expressed into the later phases of T-cell activation.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y6W8-11yes
Q9Y6W8-22

RefSeq proteins (1): NP_036224* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR039943ICOSFamily

Pfam: PF15910

UniProt features (22 total): strand 9, topological domain 2, glycosylation site 2, disulfide bond 2, signal peptide 1, chain 1, splice variant 1, mutagenesis site 1, helix 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

2 structures by resolution:

PDBTitleMethodResolution (Å)
7JOOCrystal structure of ICOS in complex with antibody STIM003 and anti-kappa VHH domainX-RAY DIFFRACTION2.4
6X4GCrystal structure of ICOS in complex with ICOS-L and an anti ICOS-L VNAR domainX-RAY DIFFRACTION3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y6W8-F174.240.22

Antibody-complex structures (SAbDab)

3 antibodies co-crystallized with this protein: 6X4G, 7JOO, ALOMFILIMAB

Human Protein Atlas

Protein class: CD markers, Predicted membrane proteins, Disease related genes, Human disease related genes, Primary immunodeficiency

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): plasma membrane; actin filaments

Antibody reliability (HPA): IH approved · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2)

TypePositions
Disulfide bond42–109, 63–83

Glycosylation sites (2)

TypePositions
N-linked (glcnac…) asparagine89, 110

Mutagenesis-validated functional residues (1)

PositionPhenotype
110about 4.3-fold improvement in binding affinity to icoslg.

Function

Pathways and Gene Ontology

Reactome pathways

5 curated (TAS) of 10; 6 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

10 pathways:

IDPathwayEvidence
R-HSA-2219530Constitutive Signaling by Aberrant PI3K in Cancer ⚕curated
R-HSA-9725371Nuclear events stimulated by ALK signaling in cancer ⚕curated
R-HSA-9927354Co-stimulation by ICOScurated
R-HSA-6811558PI5P, PP2A and IER3 Regulate PI3K/AKT Signalingcurated
R-HSA-1257604PIP3 activates AKT signalingcurated
R-HSA-1643685Disease ⚕—
R-HSA-5663202Diseases of signal transduction by growth factor receptors and second messengers ⚕—
R-HSA-9725370Signaling by ALK fusions and activated point mutants ⚕—
R-HSA-9700206Signaling by ALK in cancer ⚕—
R-HSA-9938027Affinity selection of immunoglobulinselectronic

MSigDB gene sets: 385 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_TOLERANCE_INDUCTION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GOBP_LYMPHOCYTE_COSTIMULATION, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_CELL_CELL_ADHESION, GOBP_CD4_POSITIVE_ALPHA_BETA_T_CELL_ACTIVATION, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, GOBP_T_CELL_DIFFERENTIATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_CELL_ACTIVATION, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS

GO Biological Process (5): T cell tolerance induction (GO:0002517), immune response (GO:0006955), T cell costimulation (GO:0031295), T follicular helper cell differentiation (GO:0061470), cell-cell adhesion (GO:0098609)

GO Molecular Function (2): signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (3): extracellular region (GO:0005576), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897)

Reactome top-level categories

9 top-level categories:

CategoryPathways
Signaling by ALK fusions and activated point mutants1
Immunoglobulin maturation1
Intracellular signaling by second messengers1
PI3K/AKT Signaling in Cancer1
Negative regulation of the PI3K/AKT network1
Regulation of T cell activation by CD28 family1
Disease1
Diseases of signal transduction by growth factor receptors and second messengers1
Signaling by ALK in cancer1

GO top-level categories

16 GO namespaces:

CategoryTerms
tolerance induction1
immune system process1
response to stimulus1
lymphocyte costimulation1
positive regulation of T cell activation1
T-helper cell differentiation1
exhausted T cell differentiation1
cell adhesion1
molecular transducer activity1
binding1
cellular anatomical structure1
membrane1
cell periphery1
plasma membrane1
cell surface1
side of membrane1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 10 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO termNSEvidence
T follicular helper cell differentiationBPdirect assay
plasma membraneCCdirect assay
signaling receptor activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 2,132 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
ICOSICOSLGO75144952
ICOSCTLA4P16410952
ICOSA0A087X1L8A0A087X1L8944
ICOSCXCR5P32302936
ICOSCD4P01730919
ICOSPDCD1Q15116892
ICOSCD274Q9NZQ7884
ICOSCD80P33681882
ICOSCD8AP01732866
ICOSCD40LGP29965862
ICOSFOXP3Q9BZS1859
ICOSTNFRSF4P43489857
ICOSIL2P01585849
ICOSPDCD1LG2Q9BQ51841
ICOSCD86P42081836

IntAct

Human interaction partners of ICOS in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

PartnerInteraction typeMIscoreRecords
ICOSLGphysical association0.85010
PIK3R1association0.6206
TBK1physical association0.5003
WIF1physical association0.3701
GAKassociation0.3501
TNFassociation0.3501
TNFSF9association0.3501

BioGRID (20 interactions; top human partners by supporting records): ACY1 (Affinity Capture-MS; 2 records), ICOSLG (Affinity Capture-MS; 2 records), TNF (Affinity Capture-MS; 2 records), CDC20B (Affinity Capture-MS), ITFG3 (Affinity Capture-MS), MFI2 (Affinity Capture-MS), NUFIP2 (Protein-RNA), PCDH1 (Affinity Capture-MS), PGK1 (Cross-Linking-MS (XL-MS)), PIK3R1 (Affinity Capture-Western), RC3H1 (Protein-RNA), TBK1 (Affinity Capture-Western), TNFSF9 (Affinity Capture-MS), TRHDE (Affinity Capture-MS), WIF1 (Two-hybrid)

SIGNOR signaling

4 signaling interactions:

AEffectBMechanism
ICOSLG“up-regulates activity”ICOSbinding
ICOS“up-regulates activity”PIK3R1binding
hsa-mir-146a-5p“down-regulates quantity by repression”ICOS“post transcriptional regulation”
hsa-mir-27a-3p“down-regulates quantity by repression”ICOS“post transcriptional regulation”

Ligand–receptor pairs (CellPhoneDB) (1)

Curated ligand–receptor partners (cell-cell communication), distinct from the protein–protein interactions above.

1 ligand–receptor pairs:

PartnerThis gene’s roleSignaling class
ICOSLGreceptor

Disease & clinical

Genetic variants

Variant evidence for ICOS: 208 ClinVar records (14 pathogenic / likely pathogenic); 17 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

208 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic9
Likely pathogenic5
Uncertain significance84
Likely benign66
Benign24

Top pathogenic / likely-pathogenic (14)

Showing all 14 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
663980NM_012092.4(ICOS):c.58+1G>ALikely pathogeniccriteria provided, multiple submitters, no conflicts2
940397NM_012092.4(ICOS):c.181del (p.Ile61fs)Pathogeniccriteria provided, single submitter1
1359008NM_012092.4(ICOS):c.61G>T (p.Glu21Ter)Pathogeniccriteria provided, single submitter1
1449576NM_012092.4(ICOS):c.318T>G (p.Tyr106Ter)Pathogeniccriteria provided, single submitter1
2002817NM_012092.4(ICOS):c.17G>A (p.Trp6Ter)Pathogeniccriteria provided, single submitter1
2003841NM_012092.4(ICOS):c.357del (p.Phe119fs)Pathogeniccriteria provided, single submitter1
2993769NM_012092.4(ICOS):c.291C>A (p.Tyr97Ter)Pathogeniccriteria provided, single submitter1
4728975NM_012092.4(ICOS):c.272dup (p.Ser91fs)Pathogeniccriteria provided, single submitter1
573877NM_012092.4(ICOS):c.394+2T>CLikely pathogeniccriteria provided, single submitter1
2585218NM_012092.4(ICOS):c.136_139del (p.Asp46fs)Likely pathogeniccriteria provided, single submitter1
4871840NM_012092.4(ICOS):c.285del (p.Leu96fs)Likely pathogeniccriteria provided, single submitter1
4959479NM_012092.4(ICOS):c.501+2T>ALikely pathogeniccriteria provided, single submitter1
871366GRCh37/hg19 2q33.2(chr2:204820359-204821488)x0Pathogeniccriteria provided, single submitter1
5501NM_012092.4(ICOS):c.59-594_501+93delPathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore ICOS’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 285):

Position(s)EffectΔscoreSites
2:203942270donor_gain1.0000
2:203955631acceptor_gain0.9900
2:203955786donor_gain0.9900
2:203956657–203956658acceptor_loss0.99006
2:203956766–203956767donor_loss0.99005
2:203957884–203957885donor_loss0.99005
2:203936873–203936874donor_loss0.98003
2:203955634–203955635acceptor_loss0.98006
2:203955836donor_gain0.9800
2:203955972–203955973donor_loss0.98005

AlphaMissense

123 missense substitutions predicted likely pathogenic (of 1,313 scored), across 43 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
C10970.8510.908
C4270.8140.901
C6370.7210.810
C8370.6960.767
F9450.7920.845
F3150.7860.857
F5150.7810.879
Y10750.6550.780
P11650.6530.731
F11940.8330.899
F11440.7760.817
W14240.6700.756
F9530.8160.816
F3330.7940.794
I4030.7850.877
M5330.7620.832
G14630.6890.696
G15730.6660.692
L9630.6560.702
F18230.6480.648

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA)favorable0.00046
Head and Neck Squamous Cell Carcinoma (TCGA)favorable0.000645

Disease associations

OMIM: gene MIM:604558 | disease phenotypes: MIM:607594

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
immunodeficiency, common variable, 1StrongAutosomal recessive4

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

DiseaseClassificationInheritance
common variable immunodeficiencyDefinitiveAR

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (5 panels, 5 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

5 panels:

PanelRating
COVID-19 researchgreen
Gastrointestinal epithelial barrier disordersgreen
Infantile enterocolitis & monogenic inflammatory bowel diseasegreen
Intestinal failure or congenital diarrhoeagreen
Primary immunodeficiency or monogenic inflammatory bowel diseasegreen

Mondo (1): immunodeficiency, common variable, 1 (MONDO:0011864)

Orphanet (2): OBSOLETE: Common variable immunodeficiency (Orphanet:1572), Late-onset combined immunodeficiency due to ICOS deficiency (Orphanet:695183)

HPO phenotypes

32 phenotypes (HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000403Recurrent otitis media
HP:0000509Conjunctivitis
HP:0001287Meningitis
HP:0001744Splenomegaly
HP:0001904Autoimmune neutropenia
HP:0002014Diarrhea
HP:0002090Pneumonia
HP:0002110Bronchiectasis
HP:0002240Hepatomegaly
HP:0002664Neoplasm
HP:0002665Lymphoma
HP:0002716Lymphadenopathy
HP:0002718Recurrent bacterial infections
HP:0002720Decreased circulating IgA concentration
HP:0002721Immunodeficiency
HP:0002729Follicular hyperplasia
HP:0002837Recurrent bronchitis
HP:0002850Decreased circulating IgM concentration
HP:0002960Autoimmunity
HP:0004315Decreased circulating IgG concentration
HP:0005387Combined immunodeficiency
HP:0006532Recurrent pneumonia
HP:0010976Decreased total B cell count
HP:0011108Recurrent sinusitis
HP:0011462Young adult onset
HP:0011463Childhood onset
HP:0011839Abnormal total T cell number
HP:0011840Abnormal T cell physiology
HP:0030388Decreased class-switched memory B cell proportion
HP:0410301Partial absence of specific antibody response to unconjugated pneumococcus polysaccharide

GWAS associations

17 associations:

StudyTraitp-value
GCST004866_12Alopecia areata2e-20
GCST003988_11Hypothyroidism1e-15
GCST004302_16Primary biliary cholangitis1e-13
GCST000719_1Alopecia areata4e-13
GCST006627_46Diastolic blood pressure3e-12
GCST000612_31Celiac disease6e-9
GCST004904_18Body mass index4e-8
GCST005568_31Rheumatoid arthritis (ACPA-positive)4e-8
GCST003045_68Ulcerative colitis1e-7
GCST002931_2Aluminium levels3e-7
GCST003043_157Inflammatory bowel disease5e-7
GCST005569_4Rheumatoid arthritis5e-7
GCST001762_612Obesity-related traits1e-6
GCST005588_17Idiopathic dilated cardiomyopathy5e-6
GCST009391_779Metabolite levels5e-6
GCST009391_806Metabolite levels5e-6
GCST009391_736Metabolite levels7e-6

EFO canonical traits (from GWAS)

7 canonical traits:

EFO IDTrait name
EFO:0004736aspartate aminotransferase measurement
EFO:0004340body mass index
EFO:0009094idiopathic dilated cardiomyopathy
EFO:0006336diastolic blood pressure
EFO:0010391sphingomyelin 16:0 measurement
EFO:0010396sphingomyelin 22:1 measurement
EFO:0010394sphingomyelin 18:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3712953 (SINGLE PROTEIN), CHEMBL5482971 (PROTEIN-PROTEIN INTERACTION)

Drugs by curated mechanism of action (ChEMBL)

Drugs whose curated ChEMBL mechanism of action targets the ICOS protein itself — single-protein targets only (drugs acting on a protein family or complex that merely includes it are excluded). Includes antibodies and oligonucleotides that bioactivity screening does not capture.

4 curated-mechanism drugs:

DrugModalityMax phase
FELADILIMABAntibody3
ROZIBAFUSP ALFAProtein2
VOPRATELIMABAntibody2
MEDI-570Unknown1

PharmGKB: 1 entry (CPIC guideline: no)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — CD molecules

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
feladilimabBinding8.87pKd

ChEMBL bioactivities

6 potent at pChembl≥5 of 19 total, top 6 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.73IC501870nMCHEMBL5591374
5.43IC503680nMCHEMBL5592269
5.35IC504480nMCHEMBL5591374
5.35Kd4470nMCHEMBL5590462
5.33IC504680nMCHEMBL2171562
5.25IC505650nMCHEMBL5429501

PubChem BioAssay actives

6 with measured affinity, of 28 total; 5 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(2S)-4-amino-2-[[(2S)-2-[[(2S)-2-[[(3S,9S,12S,18S,21S,27S,30R,35R,38S,41S,44S,47S)-30-[[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]amino]-41,44-dibenzyl-9,27-bis[(4-hydroxyphenyl)methyl]-38-(2-methylpropyl)-2,8,11,17,20,26,29,37,40,43,46-undecaoxo-18-propan-2-yl-32,33-dithia-1,7,10,16,19,25,28,36,39,42,45-undecazapentacyclo[45.3.0.03,7.012,16.021,25]pentacontane-35-carbonyl]amino]-4-methylpentanoyl]amino]-3-phenylpropanoyl]amino]-4-oxobutanoic acid2115250: Inhibition of ICOS/ICOSL (unknown origin) interaction by ELISA methodic501.8700uM
(1R,4S,10S,13S,19S,22S,28S,34S,37S,40S,43S,46R,49S,55S,58S,61S)-37,40,58-tribenzyl-4,22,61-tris[(4-hydroxyphenyl)methyl]-43,49-bis(2-methylpropyl)-13-propan-2-yl-65,66-dithia-3,6,12,15,21,24,30,36,39,42,45,48,51,57,60,63-hexadecazaheptacyclo[44.17.4.06,10.015,19.024,28.030,34.051,55]heptahexacontane-2,5,11,14,20,23,29,35,38,41,44,47,50,56,59,62-hexadecone2115249: Inhibition of ICOS/ICOSL (unknown origin) interaction by TR-FRET assayic503.6800uM
2-[3-[(1R,4S,7S,13S,19S,22S,25S,28S,31R,34S,40S,43S,49S)-40-benzyl-19-[(2S)-butan-2-yl]-22-(hydroxymethyl)-25,28-bis[(4-hydroxyphenyl)methyl]-4,49-bis(2-methylpropyl)-3,6,12,18,21,24,27,30,33,36,39,42,48,51-tetradecaoxo-53,54-dithia-2,5,11,17,20,23,26,29,32,35,38,41,47,50-tetradecazapentacyclo[29.20.4.07,11.013,17.043,47]pentapentacontan-34-yl]propyl]guanidine2115251: Binding affinity to ICOS (unknown origin) assessed as dissociation constantkd4.4700uM
N-[3-(benzylamino)-6-chloro-9H-pyrido[3,4-b]indol-8-yl]pyridine-3-carboxamide1977233: Inhibition of C-terminal IgG1 Fc region fused human ICOS extracellular domain (1 to 141 residues)/C-terminal polyhistidine tagged human ICOSL extracellular domain (1 to 258 residues) interaction incubated for 1 hr by TR-FRET assayic504.6800uM
N-(6-chloro-7-methoxy-9H-pyrido[3,4-b]indol-8-yl)-4-methylpyrimidine-5-carboxamide1977233: Inhibition of C-terminal IgG1 Fc region fused human ICOS extracellular domain (1 to 141 residues)/C-terminal polyhistidine tagged human ICOSL extracellular domain (1 to 258 residues) interaction incubated for 1 hr by TR-FRET assayic505.6500uM

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutants, Occupationalaffects expression, increases expression2
Benzo(a)pyrenedecreases expression, increases methylation2
Nickelincreases expression2
(+)-JQ1 compounddecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Dieldrinincreases expression1
Ozoneincreases abundance, increases expression1
Tobacco Smoke Pollutionincreases expression1
Aflatoxin B1increases methylation1
Sodium Seleniteincreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5580017BindingBinding affinity to ICOS (unknown origin) assessed as dissociation constantDesign of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction. — *Bioorg Med Chem Lett*

Cellosaurus cell lines

6 cell lines: 4 cancer cell line, 2 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A7ZZRaji-hICOSCancer cell lineMale
CVCL_B8HQAbcam HCT 116 ICOS KOCancer cell lineMale
CVCL_B8WZAbcam MCF-7 ICOS KOCancer cell lineFemale
CVCL_B9K0Abcam A-549 ICOS KOCancer cell lineMale
CVCL_D7BJAbeomics CHO-K1 ICOSSpontaneously immortalized cell lineFemale
CVCL_E5ISCHO-K1/ICOSSpontaneously immortalized cell lineFemale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for ICOS across ~30M SureChEMBL compounds — explore on Sugi Predict.