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    ICOS inducible T cell costimulator [ Homo sapiens (human) ]

    Gene ID: 29851, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ICOSprovided by HGNC
    Official Full Name
    inducible T cell costimulatorprovided by HGNC
    Primary source
    HGNC:HGNC:5351
    See related
    Ensembl:ENSG00000163600 MIM:604558; AllianceGenome:HGNC:5351
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AILIM; CD278; CVID1
    Summary
    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. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in lymph node (RPKM 7.8), bone marrow (RPKM 6.5) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ICOS in Genome Data Viewer
    Location:
    2q33.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (203936763..203961577)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (204418652..204443466)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (204801486..204826300)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 474, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17015 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:204675919-204677118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12259 Neighboring gene cytotoxic T-lymphocyte associated protein 4 Neighboring gene uncharacterized LOC101927840 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:204808046-204809245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17017 Neighboring gene zinc finger protein 555 pseudogene Neighboring gene uncharacterized LOC124907966

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. ICOS-gene variants are not associated with atopic disease susceptibility in European children. Beier KC, et al. Pediatr Allergy Immunol, 2009 May. PMID 19175887
    2. The Effect of ICOS Polymorphism Interactions with HBV Mutations on HBV Subtype Infection Outcomes. Song XM, et al. Ann Hepatol, 2018 Oct 16. PMID 30600290
    3. Cutting edge: polymorphisms in the ICOS promoter region are associated with allergic sensitization and Th2 cytokine production. Shilling RA, et al. J Immunol, 2005 Aug 15. PMID 16081771
    4. Expression and function of inducible co-stimulator in patients with systemic lupus erythematosus: possible involvement in excessive interferon-gamma and anti-double-stranded DNA antibody production. Kawamoto M, et al. Arthritis Res Ther, 2006. PMID 16563187, Free PMC Article
    5. Circulating follicular helper T cells exhibit reduced ICOS expression and impaired function in narcolepsy type 1 patients. Nguyen XH, et al. J Autoimmun, 2018 Nov. PMID 30104107

    See all (189) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Joint effects of CD8A and ICOS in Long QT Syndrome (LQTS) and Beckwith-Wiedemann Syndrome (BWS).
      Title: Joint effects of CD8A and ICOS in Long QT Syndrome (LQTS) and Beckwith-Wiedemann Syndrome (BWS).
    2. ICOS-ICOSL pathway enhances NKT-like cell antiviral function in pregnant women with COVID-19.
      Title: ICOS-ICOSL pathway enhances NKT-like cell antiviral function in pregnant women with COVID-19.
    3. The Expression and Prognostic Significance of ICOS in NSCLC Integrated Pan-Cancer and Multi-Omics Analyses.
      Title: The Expression and Prognostic Significance of ICOS in NSCLC Integrated Pan-Cancer and Multi-Omics Analyses.
    4. Transcriptional profile and immune infiltration in colorectal cancer reveal the significance of inducible T-cell costimulator as a crucial immune checkpoint molecule.
      Title: Transcriptional profile and immune infiltration in colorectal cancer reveal the significance of inducible T-cell costimulator as a crucial immune checkpoint molecule.
    5. Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development.
      Title: Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development.
    6. Synovial inducible costimulator is correlated with severity in knee osteoarthritis.
      Title: Synovial inducible costimulator is correlated with severity in knee osteoarthritis.
    7. Molecular and clinical characterization of ICOS expression in breast cancer through large-scale transcriptome data.
      Title: Molecular and clinical characterization of ICOS expression in breast cancer through large-scale transcriptome data.
    8. Expression and prognosis of inducible T-cell co-stimulator and its ligand in Chinese stage I-III lung adenocarcinoma patients.
      Title: Expression and prognosis of inducible T-cell co-stimulator and its ligand in Chinese stage I-III lung adenocarcinoma patients.
    9. ICOS gene polymorphisms in systemic lupus erythematosus: A case-control study.
      Title: ICOS gene polymorphisms in systemic lupus erythematosus: A case-control study.
    10. CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjogren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.
      Title: CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjögren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.
    Submit: New GeneRIF Correction See all GeneRIFs (148)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Immunodeficiency, common variable, 1
    MedGen: C3149378 OMIM: 607594 GeneReviews: Not available
    		Compare labs
    Immunodeficiency, common variable, 2
    MedGen: C3150354 OMIM: 240500 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study in alopecia areata implicates both innate and adaptive immunity.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC39850

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell costimulation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in T cell tolerance induction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in immune response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    inducible T-cell costimulator
    Names
    activation-inducible lymphocyte immunomediatory molecule
    inducible T-cell co-stimulator
    inducible costimulator

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011586.1 RefSeqGene

      Range
      4969..29798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_65

    mRNA and Protein(s)

    1. NM_012092.4 → NP_036224.1  inducible T-cell costimulator precursor

      See identical proteins and their annotated locations for NP_036224.1

      Status: REVIEWED

      Source sequence(s)
      AJ277832, CB528580
      Consensus CDS
      CCDS2363.1
      UniProtKB/Swiss-Prot
      Q8N6W8, Q9Y6W8
      UniProtKB/TrEMBL
      Q53QY6
      Related
      ENSP00000319476.6, ENST00000316386.11
      Conserved Domains (1) summary
      pfam15910
      Location:23 → 134
      V-set_2; ICOS V-set domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      203936763..203961577
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444022.1 → XP_047299978.1  inducible T-cell costimulator isoform X1

    RNA

    1. XR_007073112.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      204418652..204443466
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341553.1 → XP_054197528.1  inducible T-cell costimulator isoform X1

    RNA

    1. XR_008486351.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6W8.1 GenPept UniProtKB/Swiss-Prot:Q9Y6W8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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