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Aliases for CLEC4C Gene

Aliases for CLEC4C Gene

  • C-Type Lectin Domain Family 4 Member C 2 3 5
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 7 2 3
  • C-Type Lectin Domain Family 4, Member C 2 3
  • C-Type Lectin Superfamily Member 7 3 4
  • Dendritic Lectin 3 4
  • CLECSF11 3 4
  • CLECSF7 3 4
  • BDCA-2 3 4
  • BDCA2 3 4
  • DLEC 3 4
  • HECL 3 4
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 11 3
  • Blood Dendritic Cell Antigen 2 Protein 3
  • Blood Dendritic Cell Antigen 2 4
  • Dendritic Cell Lectin B 3
  • CD303 Antigen 4
  • PRO34150 3
  • CD303 3

External Ids for CLEC4C Gene

Previous HGNC Symbols for CLEC4C Gene

  • CLECSF11
  • CLECSF7

Previous GeneCards Identifiers for CLEC4C Gene

  • GC12M007776
  • GC12M007882

Summaries for CLEC4C Gene

Entrez Gene Summary for CLEC4C Gene

  • 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]

GeneCards Summary for CLEC4C Gene

CLEC4C (C-Type Lectin Domain Family 4 Member C) is a Protein Coding gene. Diseases associated with CLEC4C include Ovary Serous Adenocarcinoma and Blastic Plasmacytoid Dendritic Cell. Among its related pathways are Defective C1GALT1C1 causes Tn polyagglutination syndrome (TNPS) and Toll-Like receptor Signaling Pathways. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is CLEC6A.

UniProtKB/Swiss-Prot for CLEC4C Gene

  • Lectin-type cell surface receptor which may play a role in antigen capturing by dendritic cells (PubMed:11748283, PubMed:21880719, PubMed:25995448). Specifically recognizes non-sialylated galactose-terminated biantennary glycans containing the trisaccharide epitope Gal(beta1-3/4)GlcNAc(beta1-2)Man (PubMed:21880719, PubMed:25995448). Binds to serum IgG (PubMed:25995448). Efficiently targets ligand into antigen-processing and peptide-loading compartments for presentation to T-cells (PubMed:11748283). May mediate potent inhibition of induction of IFN-alpha/beta expression in plasmacytoid dendritic cells (PubMed:11748283, PubMed:21880719). May act as a signaling receptor that activates protein-tyrosine kinases and mobilizes intracellular calcium (PubMed:11748283).

Additional gene information for CLEC4C Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC4C Gene

Genomics for CLEC4C Gene

Regulatory Elements for CLEC4C Gene

Enhancers for CLEC4C Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H007757 0.6 Ensembl ENCODE 9.8 -7.0 -6957 1 POU5F1 CLEC4C NANOGNB
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLEC4C on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the CLEC4C gene promoter:

Genomic Location for CLEC4C Gene

Chromosome:
12
Start:
7,729,415 bp from pter
End:
7,751,605 bp from pter
Size:
22,191 bases
Orientation:
Minus strand

Genomic View for CLEC4C Gene

Genes around CLEC4C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC4C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC4C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC4C Gene

Proteins for CLEC4C Gene

  • Protein details for CLEC4C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WTT0-CLC4C_HUMAN
    Recommended name:
    C-type lectin domain family 4 member C
    Protein Accession:
    Q8WTT0
    Secondary Accessions:
    • D3DUU3
    • Q3T1C3
    • Q6UXS8
    • Q8WXX8

    Protein attributes for CLEC4C Gene

    Size:
    213 amino acids
    Molecular mass:
    25038 Da
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for CLEC4C Gene

    Alternative splice isoforms for CLEC4C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLEC4C Gene

Post-translational modifications for CLEC4C Gene

  • Glycosylation at posLast=110110, Asn137, and posLast=164164

Other Protein References for CLEC4C Gene

No data available for DME Specific Peptides for CLEC4C Gene

Domains & Families for CLEC4C Gene

Gene Families for CLEC4C Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CLEC4C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CLEC4C: view

No data available for UniProtKB/Swiss-Prot for CLEC4C Gene

Function for CLEC4C Gene

Molecular function for CLEC4C Gene

UniProtKB/Swiss-Prot Function:
Lectin-type cell surface receptor which may play a role in antigen capturing by dendritic cells (PubMed:11748283, PubMed:21880719, PubMed:25995448). Specifically recognizes non-sialylated galactose-terminated biantennary glycans containing the trisaccharide epitope Gal(beta1-3/4)GlcNAc(beta1-2)Man (PubMed:21880719, PubMed:25995448). Binds to serum IgG (PubMed:25995448). Efficiently targets ligand into antigen-processing and peptide-loading compartments for presentation to T-cells (PubMed:11748283). May mediate potent inhibition of induction of IFN-alpha/beta expression in plasmacytoid dendritic cells (PubMed:11748283, PubMed:21880719). May act as a signaling receptor that activates protein-tyrosine kinases and mobilizes intracellular calcium (PubMed:11748283).

Gene Ontology (GO) - Molecular Function for CLEC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030246 carbohydrate binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CLEC4C: view
genes like me logo Genes that share phenotypes with CLEC4C: view

Animal Models for CLEC4C Gene

MGI Knock Outs for CLEC4C:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLEC4C
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for CLEC4C (DLEC/CLEC4C/BDCA-2)

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for CLEC4C Gene

Localization for CLEC4C Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC4C Gene

Cell membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLEC4C gene
Compartment Confidence
plasma membrane 5
extracellular 3
cytosol 1
endosome 1

Gene Ontology (GO) - Cellular Components for CLEC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030667 secretory granule membrane TAS --
GO:0070821 tertiary granule membrane TAS --
genes like me logo Genes that share ontologies with CLEC4C: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLEC4C Gene

Pathways & Interactions for CLEC4C Gene

genes like me logo Genes that share pathways with CLEC4C: view

Interacting Proteins for CLEC4C Gene

Gene Ontology (GO) - Biological Process for CLEC4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS --
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0043312 neutrophil degranulation TAS --
GO:0045087 innate immune response IEA --
genes like me logo Genes that share ontologies with CLEC4C: view

No data available for SIGNOR curated interactions for CLEC4C Gene

Drugs & Compounds for CLEC4C Gene

(1) Drugs for CLEC4C Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with CLEC4C: view

Transcripts for CLEC4C Gene

mRNA/cDNA for CLEC4C Gene

Unigene Clusters for CLEC4C Gene

C-type lectin domain family 4, member C:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CLEC4C
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for CLEC4C (DLEC/CLEC4C/BDCA-2)

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC4C Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7
SP1: -
SP2:
SP3: -

Relevant External Links for CLEC4C Gene

GeneLoc Exon Structure for
CLEC4C
ECgene alternative splicing isoforms for
CLEC4C

Expression for CLEC4C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLEC4C Gene

mRNA differential expression in normal tissues according to GTEx for CLEC4C Gene

This gene is overexpressed in Whole Blood (x36.4) and Testis (x7.8).

NURSA nuclear receptor signaling pathways regulating expression of CLEC4C Gene:

CLEC4C

SOURCE GeneReport for Unigene cluster for CLEC4C Gene:

Hs.351812

mRNA Expression by UniProt/SwissProt for CLEC4C Gene:

Q8WTT0-CLC4C_HUMAN
Tissue specificity: Expressed in plasmacytoid dendritic cells (PDCs). Constitutively expressed in immature monocyte-derived dendritic cells (iMDDC) and is significantly down-regulated upon maturation with LPS but not with TNF-alpha.

Evidence on tissue expression from TISSUES for CLEC4C Gene

  • Lymph node(3.2)
  • Spleen(2.8)
  • Blood(2.1)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with CLEC4C: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC4C Gene

Orthologs for CLEC4C Gene

This gene was present in the common ancestor of mammals.

Orthologs for CLEC4C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLEC4C 33 34
  • 99.69 (n)
mouse
(Mus musculus)
Mammalia Clec4b1 33 16
  • 63.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 48 (a)
OneToMany
Species where no ortholog for CLEC4C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CLEC4C Gene

ENSEMBL:
Gene Tree for CLEC4C (if available)
TreeFam:
Gene Tree for CLEC4C (if available)

Paralogs for CLEC4C Gene

(19) SIMAP similar genes for CLEC4C Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CLEC4C: view

Variants for CLEC4C Gene

Sequence variations from dbSNP and Humsavar for CLEC4C Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000275741 -- 7,736,738(+) CCCAT(C/T)TCTAC intron-variant
rs1000513576 -- 7,745,208(+) ATGAG(C/G)GGGGG intron-variant
rs1000529117 -- 7,729,010(+) CCGGG(C/T)GCAGT downstream-variant-500B
rs1000689936 -- 7,736,982(+) TCCCA(A/G)CACTT intron-variant
rs1000770035 -- 7,730,610(+) ACTCT(A/C)GCCTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC4C Gene

Variant ID Type Subtype PubMed ID
dgv57e55 CNV gain 17911159
dgv5e196 CNV duplication 17116639
dgv6e196 CNV duplication 17116639
esv2422393 CNV duplication 17116639
esv2662383 CNV deletion 23128226
esv2759877 CNV gain+loss 17122850
esv3628437 CNV loss 21293372
esv3628438 CNV loss 21293372
esv3628439 CNV loss 21293372
esv3892131 CNV gain 25118596
nsv1113455 CNV deletion 24896259
nsv1122691 CNV deletion 24896259
nsv428270 CNV gain 18775914
nsv557273 CNV loss 21841781

Variation tolerance for CLEC4C Gene

Residual Variation Intolerance Score: 69.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.59; 44.94% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLEC4C Gene

Human Gene Mutation Database (HGMD)
CLEC4C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC4C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC4C Gene

Disorders for CLEC4C Gene

MalaCards: The human disease database

(3) MalaCards diseases for CLEC4C Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ovary serous adenocarcinoma
  • malignant ovarian serous tumor
blastic plasmacytoid dendritic cell
  • blastic nk-cell lymphoma
ovarian cystadenocarcinoma
  • cystadenocarcinoma of ovary
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for CLEC4C

Genetic Association Database (GAD)
CLEC4C
Human Genome Epidemiology (HuGE) Navigator
CLEC4C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLEC4C
genes like me logo Genes that share disorders with CLEC4C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLEC4C Gene

Publications for CLEC4C Gene

  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. (PMID: 11031109) Fernandes MJ … Calabretta B (Genomics 2000) 2 3 4 22 60
  2. Molecular and genomic characterization of human DLEC, a novel member of the C-type lectin receptor gene family preferentially expressed on monocyte-derived dendritic cells. (PMID: 11536172) Arce I … Fernández-Ruiz E (European journal of immunology 2001) 2 3 4 60
  3. A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2. (PMID: 25995448) Jégouzo SA … Taylor ME (The Journal of biological chemistry 2015) 3 4 60
  4. Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer. (PMID: 24425442) Nagae M … Yamaguchi Y (Proteins 2014) 3 4 60
  5. Human C-type lectin domain family 4, member C (CLEC4C/BDCA-2/CD303) is a receptor for asialo-galactosyl-oligosaccharides. (PMID: 21880719) Riboldi E … Sozzani S (The Journal of biological chemistry 2011) 3 4 60

Products for CLEC4C Gene

Sources for CLEC4C Gene

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