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    CLEC4C C-type lectin domain family 4 member C [ Homo sapiens (human) ]

    Gene ID: 170482, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLEC4Cprovided by HGNC
    Official Full Name
    C-type lectin domain family 4 member Cprovided by HGNC
    Primary source
    HGNC:HGNC:13258
    See related
    Ensembl:ENSG00000198178 MIM:606677; AllianceGenome:HGNC:13258
    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
    DLEC; HECL; BDCA2; CD303; BDCA-2; CLECSF7; CLECSF11; PRO34150
    Summary
    This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in dendritic cell function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in lymph node (RPKM 1.5), spleen (RPKM 0.9) and 6 other tissues See more
    Orthologs
    all
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    Genomic context

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    See CLEC4C in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7729383..7749541, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7744033..7766234, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7881979..7902137, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7846215-7846852 Neighboring gene growth differentiation factor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7856907-7857580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7860307-7860932 Neighboring gene developmental pluripotency associated 3 Neighboring gene MPRA-validated peak1561 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7918923-7919522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7919523-7920122 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:7924892-7925059 Neighboring gene NANOG neighbor homeobox Neighboring gene NANOG 5' regulatory region Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:7950942-7951507 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7951508-7952074 Neighboring gene Nanog homeobox

    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. Identification and characterization of the gene for a novel C-type lectin (CLECSF7) that maps near the natural killer gene complex on human chromosome 12. Fernandes MJ, et al. Genomics, 2000 Oct 15. PMID 11031109
    2. Engagement of BDCA-2 blocks TRAIL-mediated cytotoxic activity of plasmacytoid dendritic cells. Riboldi E, et al. Immunobiology, 2009. PMID 19577819
    3. Human C-type lectin domain family 4, member C (CLEC4C/BDCA-2/CD303) is a receptor for asialo-galactosyl-oligosaccharides. Riboldi E, et al. J Biol Chem, 2011 Oct 14. PMID 21880719, Free PMC Article
    4. TLR9/TLR7-triggered downregulation of BDCA2 expression on human plasmacytoid dendritic cells from healthy individuals and lupus patients. Wu P, et al. Clin Immunol, 2008 Oct. PMID 18684674
    5. Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer. Nagae M, et al. Proteins, 2014 Jul. PMID 24425442

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The differentiation of new human CD303(+) Plasmacytoid dendritic cell subpopulations expressing CD205 and/or CD103 regulated by Non-Small-Cell lung cancer cells.
      Title: The differentiation of new human CD303(+) Plasmacytoid dendritic cell subpopulations expressing CD205 and/or CD103 regulated by Non-Small-Cell lung cancer cells.
    2. Zika Virus Inhibits IFN-alpha Response by Human Plasmacytoid Dendritic Cells and Induces NS1-Dependent Triggering of CD303 (BDCA-2) Signaling.
      Title: Zika Virus Inhibits IFN-α Response by Human Plasmacytoid Dendritic Cells and Induces NS1-Dependent Triggering of CD303 (BDCA-2) Signaling.
    3. Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.
      Title: Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.
    4. 24F4A (BIIB059) is an antibody targeting BDCA2.
      Title: Effect of in vivo Hydroxychloroquine and ex vivo Anti-BDCA2 mAb Treatment on pDC IFNα Production From Patients Affected With Cutaneous Lupus Erythematosus.
    5. Identification of serum glycoprotein ligands for the immunomodulatory receptor blood dendritic cell antigen 2.
      Title: Identification of serum glycoprotein ligands for the immunomodulatory receptor blood dendritic cell antigen 2.
    6. decrease in the surface expression of CLEC4C and the endoplasmic reticulum localization of the mutant construct were observed
      Title: CLEC4C p.K210del variant causes impaired cell surface transport in plasmacytoid dendritic cells of amyotrophic lateral sclerosis.
    7. Human BDCA2+CD123+CD56+ dendritic cells (DCs) related to blastic plasmacytoid dendritic cell neoplasm represent a unique myeloid DC subset.
      Title: Human BDCA2+CD123+CD56+ dendritic cells (DCs) related to blastic plasmacytoid dendritic cell neoplasm represent a unique myeloid DC subset.
    8. BDCA-2 binds selectively to glycans containing the epitope Galbeta1-3/4GlcNAcbeta1-2Man.
      Title: A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2.
    9. We show the crystal structures of a carbohydrate recognition domain (CRD) of human C-type lectin receptor blood dendritic cell antigen-2 (BDCA2).
      Title: Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
    10. Reduction in Treg numbers following Ag delivery to BDCA2 restored both CD4(+) T cell activation and Ab responses, demonstrating that Tregs were required for the observed tolerance.
      Title: Targeting antigens through blood dendritic cell antigen 2 on plasmacytoid dendritic cells promotes immunologic tolerance.
    Submit: New GeneRIF Correction See all GeneRIFs (20)

    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

    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 HIV-1 gp120-mediated inhibition of IFN-alpha production involves CD4 and BDCA2 in plasmacytoid dendritic cells PubMed
    env HIV-1 gp120 monomers and trimers bind to BDCA2 in transfected cells 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

    Clone Names

    • MGC125789, MGC125791, MGC125792, MGC125793

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pattern recognition receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in antifungal innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in tertiary granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 4 member C
    Names
    C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 11
    C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7
    C-type lectin superfamily member 7
    blood dendritic cell antigen 2 protein
    dendritic cell lectin b
    dendritic lectin

    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_001371390.1 → NP_001358319.1  C-type lectin domain family 4 member C isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC006517, AY358223
      Consensus CDS
      CCDS8583.1
      UniProtKB/Swiss-Prot
      D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8
      UniProtKB/TrEMBL
      B3KV04
      Related
      ENSP00000353500.3, ENST00000360345.8
      Conserved Domains (1) summary
      cd03590
      Location:83 → 208
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    2. NM_001371391.1 → NP_001358320.1  C-type lectin domain family 4 member C isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC006517
      UniProtKB/TrEMBL
      B3KV04
      Conserved Domains (1) summary
      cd03590
      Location:46 → 171
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    3. NM_130441.3 → NP_569708.1  C-type lectin domain family 4 member C isoform 1

      See identical proteins and their annotated locations for NP_569708.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1).
      Source sequence(s)
      AC006517, AF293615
      Consensus CDS
      CCDS8583.1
      UniProtKB/Swiss-Prot
      D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8
      UniProtKB/TrEMBL
      B3KV04
      Related
      ENSP00000440428.1, ENST00000542353.5
      Conserved Domains (1) summary
      cd03590
      Location:83 → 208
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    4. NM_203503.2 → NP_987099.1  C-type lectin domain family 4 member C isoform 2

      See identical proteins and their annotated locations for NP_987099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as DLEC-beta, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), compared to isoform 1.
      Source sequence(s)
      AC006517, AF293615, AF325460
      Consensus CDS
      CCDS8584.1
      UniProtKB/TrEMBL
      B3KV04
      Related
      ENSP00000445338.1, ENST00000540085.5
      Conserved Domains (1) summary
      cd03590
      Location:52 → 177
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      7729383..7749541 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024448873.2 → XP_024304641.1  C-type lectin domain family 4 member C isoform X1

      UniProtKB/Swiss-Prot
      D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8
      UniProtKB/TrEMBL
      B3KV04
      Conserved Domains (1) summary
      cd03590
      Location:83 → 208
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      7744033..7766234 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371339.1 → XP_054227314.1  C-type lectin domain family 4 member C isoform X2

    2. XM_054371337.1 → XP_054227312.1  C-type lectin domain family 4 member C isoform X1

      UniProtKB/Swiss-Prot
      D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8

    3. XM_054371338.1 → XP_054227313.1  C-type lectin domain family 4 member C isoform X1

      UniProtKB/Swiss-Prot
      D3DUU3, Q3T1C3, Q6UXS8, Q8WTT0, Q8WXX8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WTT0.1 GenPept UniProtKB/Swiss-Prot:Q8WTT0

    Gene LinkOut

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