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    ICAM3 intercellular adhesion molecule 3 [ Homo sapiens (human) ]

    Gene ID: 3385, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ICAM3provided by HGNC
    Official Full Name
    intercellular adhesion molecule 3provided by HGNC
    Primary source
    HGNC:HGNC:5346
    See related
    Ensembl:ENSG00000076662 MIM:146631; AllianceGenome:HGNC:5346
    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
    CD50; CDW50; ICAM-R
    Summary
    The protein encoded by this gene is a member of the intercellular adhesion molecule (ICAM) family. All ICAM proteins are type I transmembrane glycoproteins, contain 2-9 immunoglobulin-like C2-type domains, and bind to the leukocyte adhesion LFA-1 protein. This protein is constitutively and abundantly expressed by all leucocytes and may be the most important ligand for LFA-1 in the initiation of the immune response. It functions not only as an adhesion molecule, but also as a potent signalling molecule. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
    Expression
    Biased expression in bone marrow (RPKM 55.9), spleen (RPKM 28.5) and 12 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ICAM3 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10333776..10339624, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10459888..10465751, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10444452..10450300, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene FDX2-ZGLP1 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10064 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10427579-10427770 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10430834-10431047 Neighboring gene ferredoxin 2 Neighboring gene ribonucleoprotein, PTB binding 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10442682-10443598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10443599-10444515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10445230-10445848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10448906-10449654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10450403-10451150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10451151-10451898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10463923-10464686 Neighboring gene tyrosine kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10474734-10475234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10491214-10491877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10499431-10499931 Neighboring gene cell division cycle 37, HSP90 cochaperone Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10066 Neighboring gene microRNA 1181

    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. The human intercellular adhesion molecule 3 (ICAM3) gene is located in the 19p13.2-p13.3 region, close to the ICAM1 gene. Bossy D, et al. Genomics, 1994 Oct. PMID 7851905
    2. Vascular endothelium of human dental pulp expresses diverse adhesion molecules for leukocyte emigration. Sawa Y, et al. Tissue Cell, 1998 Apr. PMID 9661300
    3. Functional role of ICAM-3 polymorphism in genetic susceptibility to SARS infection. Khoo US, et al. Hong Kong Med J, 2009 Oct. PMID 19801714
    4. Intercellular adhesion molecule-3 binding of integrin alphaL beta2 requires both extension and opening of the integrin headpiece. Tang XY, et al. J Immunol, 2008 Apr 1. PMID 18354203
    5. CD20 positive mycosis fungoides: a case report. Sen F, et al. J Cutan Pathol, 2008 Apr. PMID 18261116

    See all (98) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Functional evaluation of various ICAM3 transcript variants in diffuse large B-Cell lymphoma.
      Title: Functional evaluation of various ICAM3 transcript variants in diffuse large B-Cell lymphoma.
    2. Association of Circulating ICAM3 Concentrations with Severity and Short-term Outcomes of Acute Ischemic Stroke.
      Title: Association of Circulating ICAM3 Concentrations with Severity and Short-term Outcomes of Acute Ischemic Stroke.
    3. Changes in the Surface Expression of Intercellular Adhesion Molecule 3, the Induction of Apoptosis, and the Inhibition of Cell-Cycle Progression of Human Multidrug-Resistant Jurkat/A4 Cells Exposed to a Random Positioning Machine.
      Title: Changes in the Surface Expression of Intercellular Adhesion Molecule 3, the Induction of Apoptosis, and the Inhibition of Cell-Cycle Progression of Human Multidrug-Resistant Jurkat/A4 Cells Exposed to a Random Positioning Machine.
    4. Vascular injury biomarkers and stroke risk: A population-based study.
      Title: Vascular injury biomarkers and stroke risk: A population-based study.
    5. we identify a potential CSC regulator and suggest a novel mechanism by which ICAM3 governs cancer cell stemness and inflammation.
      Title: ICAM3 mediates inflammatory signaling to promote cancer cell stemness.
    6. Lewis-antigen-containing ICAM-2/3 on Jurkat leukemia cells interact with DC-SIGN to regulate DC functions.
      Title: Lewis-antigen-containing ICAM-2/3 on Jurkat leukemia cells interact with DC-SIGN to regulate DC functions.
    7. exploration of the underlying mechanism demonstrated that ICAM3 not only binds to LFA-1 with its extracellular domain and structure protein ERM but also to lamellipodia with its intracellular domain which causes a tension that pulls cells apart (metastasis).
      Title: ICAM3 mediates tumor metastasis via a LFA-1-ICAM3-ERM dependent manner.
    8. Increased expression of PECAM-1, ICAM-3, and VCAM-1 in colonic biopsies from patients with inflammatory bowel disease (IBD) in clinical remission is associated with subsequent flares; this suggests that increases in the expression of these proteins may be early events that lead to flares in patients with IBD
      Title: Increased Cell Adhesion Molecules, PECAM-1, ICAM-3, or VCAM-1, Predict Increased Risk for Flare in Patients With Quiescent Inflammatory Bowel Disease.
    9. with larger patient groups and preferably detailed histopathological and clinical evaluations, are needed to explain the severity of ICAM-1, ICAM-2, and ICAM-3 molecules in Barrett's esophagus
      Title: Investigation of intercellular adhesion molecules (ICAMs) gene expressions in patients with Barrett's esophagus.
    10. ICAM3 acts as recognition receptors in the phagocytosis portals of macrophages for engulfment of apoptotic neutrophils.
      Title: Novel role of ICAM3 and LFA-1 in the clearance of apoptotic neutrophils by human macrophages.
    Submit: New GeneRIF Correction See all GeneRIFs (44)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env AM3 inhibits the interaction of DC-SIGN with ICAM3 and HIV-1 gp120 protein and blocks the DC-SIGN-dependent capture of HIV virions and the HIV trans-infection capability of DC-SIGN transfectants PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with ICAM3; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables integrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables integrin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phagocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    intercellular adhesion molecule 3
    Names
    ICAM-3

    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.

    mRNA and Protein(s)

    1. NM_001320605.2 → NP_001307534.1  intercellular adhesion molecule 3 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate internal exon, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AC114271, AK226023, BC040123, CR982084
      UniProtKB/TrEMBL
      B2R736
      Conserved Domains (3) summary
      pfam03921
      Location:32 → 114
      ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
      pfam13895
      Location:221 → 300
      Ig_2; Immunoglobulin domain
      cl11960
      Location:117 → 211
      Ig; Immunoglobulin domain

    2. NM_001320606.2 → NP_001307535.1  intercellular adhesion molecule 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
      Source sequence(s)
      AK309643, BC040123, CR982084
      Consensus CDS
      CCDS82290.1
      UniProtKB/TrEMBL
      Q5NKU1
      Related
      ENST00000589261.5
      Conserved Domains (4) summary
      smart00410
      Location:343 → 399
      IG_like; Immunoglobulin like
      pfam03921
      Location:1 → 37
      ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
      pfam13895
      Location:240 → 319
      Ig_2; Immunoglobulin domain
      cl11960
      Location:40 → 134
      Ig; Immunoglobulin domain

    3. NM_001320608.2 → NP_001307537.1  intercellular adhesion molecule 3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) retains an intron and initiates translation at a downstream start site, compared to variant 1. It encodes isoform 4 which is shorter than isoform 1.
      Source sequence(s)
      AC114271, BC034409, BC046121, CR982084
      Related
      ENST00000589900.5
      Conserved Domains (3) summary
      smart00410
      Location:159 → 215
      IG_like; Immunoglobulin like
      pfam13895
      Location:56 → 135
      Ig_2; Immunoglobulin domain
      cl11960
      Location:160 → 208
      Ig; Immunoglobulin domain

    4. NM_001395374.1 → NP_001382303.1  intercellular adhesion molecule 3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC114271
      Conserved Domains (1) summary
      cl11960
      Location:225 → 274
      Ig; Immunoglobulin domain

    5. NM_001395375.1 → NP_001382304.1  intercellular adhesion molecule 3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC114271
      Related
      ENST00000706692.1
      Conserved Domains (1) summary
      cl11960
      Location:129 → 178
      Ig; Immunoglobulin domain

    6. NM_001395376.1 → NP_001382305.1  intercellular adhesion molecule 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC114271
      UniProtKB/TrEMBL
      A0A9L9PXS1
      Related
      ENSP00000516505.1, ENST00000706691.1
      Conserved Domains (1) summary
      cl11960
      Location:84 → 133
      Ig; Immunoglobulin domain

    7. NM_002162.5 → NP_002153.2  intercellular adhesion molecule 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_002153.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC114271, AK226023, BC040123, CR982084
      Consensus CDS
      CCDS12235.1
      UniProtKB/Swiss-Prot
      P32942, Q6PD68
      UniProtKB/TrEMBL
      B2R736
      Related
      ENSP00000160262.3, ENST00000160262.10
      Conserved Domains (4) summary
      pfam03921
      Location:32 → 114
      ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
      pfam13895
      Location:317 → 396
      Ig_2; Immunoglobulin domain
      cd00096
      Location:420 → 476
      Ig; Immunoglobulin domain
      cl11960
      Location:117 → 211
      Ig; Immunoglobulin 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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      10333776..10339624 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      10459888..10465751 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P32942.2 GenPept UniProtKB/Swiss-Prot:P32942

    Gene LinkOut

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

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