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. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in... See more...

Aliases for CLEC4D Gene

Aliases for CLEC4D Gene

  • C-Type Lectin Domain Family 4 Member D 2 3 4 5
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 8 2 3
  • C-Type Lectin Superfamily Member 8 3 4
  • C-Type Lectin-Like Receptor 6 3 4
  • Dectin 3 2 3
  • CLECSF8 3 4
  • CLEC-6 3 4
  • MCL 3 4
  • C-Type Lectin Domain Family 4, Member D 2
  • Macrophage C-Type Lectin 3
  • C-Type Lectin Receptor 3
  • CD368 Antigen 4
  • Dectin-3 3
  • CD368 3
  • CLEC6 3
  • MPCL 3

External Ids for CLEC4D Gene

Previous HGNC Symbols for CLEC4D Gene

  • CLECSF8

Previous GeneCards Identifiers for CLEC4D Gene

  • GC12P008559
  • GC12P008666
  • GC12P008448

Summaries for CLEC4D Gene

Entrez Gene Summary for CLEC4D 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. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLEC4D Gene

CLEC4D (C-Type Lectin Domain Family 4 Member D) is a Protein Coding gene. Diseases associated with CLEC4D include Subcutaneous Mycosis and Chromoblastomycosis. Among its related pathways are Innate Immune System and CLEC7A (Dectin-1) signaling. Gene Ontology (GO) annotations related to this gene include carbohydrate binding. An important paralog of this gene is CLEC6A.

UniProtKB/Swiss-Prot Summary for CLEC4D Gene

  • A calcium-dependent lectin involved in innate recognition of pathogen-associated molecular patterns (PAMPs). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells (By similarity). Binding of mycobacterial trehalose 6,6'-dimycolate (TDM) to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T-helper 1 and T-helper 17 cell subtypes (PubMed:23602766). Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T cells (PubMed:14971047).

Additional gene information for CLEC4D Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLEC4D Gene

Genomics for CLEC4D Gene

GeneHancer (GH) Regulatory Elements for CLEC4D Gene

Promoters and enhancers for CLEC4D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J008513 Promoter 0.7 EPDnew Ensembl 517.2 +4.7 4726 1.6 CLEC4D SUPT4H1P2 lnc-CLEC4E-3 CLEC4E lnc-CLEC4D-2
GH12J008492 Enhancer 0.9 FANTOM5 ENCODE 24.3 -16.2 -16243 1.3 BCL11A RELA TCF12 CBFB MEF2B SPI1 BATF IRF4 POU2F2 EBF1 piR-30188-039 CLEC4E CLEC4D CLEC6A CLEC4A NECAP1 C3AR1 M6PR FOXJ2 RNU6-275P
GH12J008527 Enhancer 0.3 Ensembl 18.1 +18.1 18126 1.2 TEAD4 SPI1 CLEC4D RNU6-275P CLEC6A lnc-CLEC4D-2 lnc-CLEC4E-3 SUPT4H1P2
GH12J008519 Enhancer 0.3 Ensembl 16.9 +9.3 9325 2.4 NFE2 EZH2 CLEC4D RNU6-275P lnc-CLEC4E-3 SUPT4H1P2 lnc-CLEC4D-2
GH12J008475 Enhancer 0.6 Ensembl ENCODE 6.7 -33.8 -33849 1.2 USF1 SP1 POU5F1 NANOG CLEC4E CLEC4D RNU6-275P RF00026-217 piR-50852-034 CLEC6A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC4D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLEC4D

Top Transcription factor binding sites by QIAGEN in the CLEC4D gene promoter:
  • C/EBPalpha
  • FAC1
  • FOXF2
  • GR
  • GR-alpha
  • GR-beta
  • HEN1
  • Nkx3-1 v3
  • Nkx3-1 v4
  • STAT5B

Genomic Locations for CLEC4D Gene

Genomic Locations for CLEC4D Gene
chr12:8,509,475-8,522,366
(GRCh38/hg38)
Size:
12,892 bases
Orientation:
Plus strand
chr12:8,662,071-8,674,962
(GRCh37/hg19)
Size:
12,892 bases
Orientation:
Plus strand

Genomic View for CLEC4D Gene

Genes around CLEC4D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC4D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC4D Gene

Proteins for CLEC4D Gene

  • Protein details for CLEC4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WXI8-CLC4D_HUMAN
    Recommended name:
    C-type lectin domain family 4 member D
    Protein Accession:
    Q8WXI8
    Secondary Accessions:
    • Q8N5J5

    Protein attributes for CLEC4D Gene

    Size:
    215 amino acids
    Molecular mass:
    24704 Da
    Quaternary structure:
    • Heterodimer with CLEC4E; disulfide-linked. CLEC4E acts as a bridge for interaction between CLEC4D and FCER1G to form a functional complex.

    Three dimensional structures from OCA and Proteopedia for CLEC4D Gene

neXtProt entry for CLEC4D Gene

Post-translational modifications for CLEC4D Gene

  • Glycosylation at Asn45, Asn102, and Asn111
  • Modification sites at PhosphoSitePlus

Other Protein References for CLEC4D Gene

No data available for DME Specific Peptides for CLEC4D Gene

Domains & Families for CLEC4D Gene

Gene Families for CLEC4D Gene

Protein Domains for CLEC4D Gene

Blocks:
  • Type II antifreeze protein signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLEC4D Gene

GenScript: Design optimal peptide antigens:
  • C-type lectin-like receptor 6 (CLC4D_HUMAN)
genes like me logo Genes that share domains with CLEC4D: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CLEC4D Gene

Function for CLEC4D Gene

Molecular function for CLEC4D Gene

UniProtKB/Swiss-Prot Function:
A calcium-dependent lectin involved in innate recognition of pathogen-associated molecular patterns (PAMPs). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells (By similarity). Binding of mycobacterial trehalose 6,6'-dimycolate (TDM) to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T-helper 1 and T-helper 17 cell subtypes (PubMed:23602766). Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T cells (PubMed:14971047).
UniProtKB/Swiss-Prot Induction:
By autocrine inflammatory stimuli.

Phenotypes From GWAS Catalog for CLEC4D Gene

Gene Ontology (GO) - Molecular Function for CLEC4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25910212
GO:0030246 carbohydrate binding IEA --
GO:0034987 immunoglobulin receptor binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CLEC4D: view
genes like me logo Genes that share phenotypes with CLEC4D: view

Animal Models for CLEC4D Gene

MGI Knock Outs for CLEC4D:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLEC4D

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLEC4D Gene

Localization for CLEC4D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC4D Gene

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 CLEC4D gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytosol 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CLEC4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0035579 specific granule membrane TAS --
GO:0070821 tertiary granule membrane TAS --
genes like me logo Genes that share ontologies with CLEC4D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLEC4D Gene

Pathways & Interactions for CLEC4D Gene

genes like me logo Genes that share pathways with CLEC4D: view

Pathways by source for CLEC4D Gene

Gene Ontology (GO) - Biological Process for CLEC4D 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:0002292 T cell differentiation involved in immune response IEA --
GO:0002376 immune system process IEA --
GO:0030887 positive regulation of myeloid dendritic cell activation ISS,IEA --
genes like me logo Genes that share ontologies with CLEC4D: view

No data available for SIGNOR curated interactions for CLEC4D Gene

Drugs & Compounds for CLEC4D Gene

(2) Drugs for CLEC4D Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for CLEC4D Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLEC4D: view

Transcripts for CLEC4D Gene

mRNA/cDNA for CLEC4D Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC4D Gene

No ASD Table

Relevant External Links for CLEC4D Gene

GeneLoc Exon Structure for
CLEC4D

Expression for CLEC4D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLEC4D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLEC4D Gene

This gene is overexpressed in Whole Blood (x45.9).

Protein differential expression in normal tissues from HIPED for CLEC4D Gene

This gene is overexpressed in Monocytes (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC4D Gene



Protein tissue co-expression partners for CLEC4D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLEC4D

SOURCE GeneReport for Unigene cluster for CLEC4D Gene:

Hs.351811

mRNA Expression by UniProt/SwissProt for CLEC4D Gene:

Q8WXI8-CLC4D_HUMAN
Tissue specificity: Expressed weakly in peripheral blood leukocytes, bone marrow and spleen. Expression is confined mostly in monocytes and macrophage and seems to be up-regulated by IL-6, IL-10, TNF-alpha and IFN-gamma.

Evidence on tissue expression from TISSUES for CLEC4D Gene

  • Blood(4.1)
genes like me logo Genes that share expression patterns with CLEC4D: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC4D Gene

Orthologs for CLEC4D Gene

This gene was present in the common ancestor of mammals.

Orthologs for CLEC4D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLEC4D 31 30
  • 99.38 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CLEC4D 31 30
  • 80.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CLEC4D 31 30
  • 79.25 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Clec4d 17 31 30
  • 74.61 (n)
rat
(Rattus norvegicus)
Mammalia Clec4d 30
  • 73.87 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 47 (a)
OneToMany
Species where no ortholog for CLEC4D 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)
  • 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)
  • 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 CLEC4D Gene

ENSEMBL:
Gene Tree for CLEC4D (if available)
TreeFam:
Gene Tree for CLEC4D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLEC4D: view image

Paralogs for CLEC4D Gene

(13) SIMAP similar genes for CLEC4D Gene using alignment to 2 proteins:

  • CLC4D_HUMAN
  • A6NHA5_HUMAN
genes like me logo Genes that share paralogs with CLEC4D: view

Variants for CLEC4D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLEC4D Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs4304840 Benign: not specified. - 8,515,301(+) A/Gp.Ser32Gly MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CLEC4D Gene

Structural Variations from Database of Genomic Variants (DGV) for CLEC4D Gene

Variant ID Type Subtype PubMed ID
dgv1362n100 CNV gain 25217958
nsv1035270 CNV gain 25217958
nsv1051530 CNV gain 25217958
nsv518125 CNV loss 19592680
nsv518772 CNV gain 19592680
nsv526021 CNV loss 19592680
nsv557342 CNV loss 21841781

Variation tolerance for CLEC4D Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.54; 72.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC4D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC4D Gene

Disorders for CLEC4D Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLEC4D Gene - From: DISEASES

Disorder Aliases PubMed IDs
subcutaneous mycosis
  • subcutaneous fungal disease
chromoblastomycosis
  • chromomycosis
phaeohyphomycosis
  • infection by dematiacious fungi
cryptococcosis
  • busse-buschke's disease
blastomycosis
  • blastomyces dermatitidis infection
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLEC4D

genes like me logo Genes that share disorders with CLEC4D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLEC4D Gene

Publications for CLEC4D Gene

  1. The human C-type lectin CLECSF8 is a novel monocyte/macrophage endocytic receptor. (PMID: 14971047) Arce I … Fernández-Ruiz E (European journal of immunology 2004) 3 4 23 54
  2. Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL. (PMID: 24101491) Furukawa A … Maenaka K (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 54
  3. Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex. (PMID: 15368084) Flornes LM … Fossum S (Immunogenetics 2004) 3 4 54
  4. The Syk-Coupled C-Type Lectin Receptors Dectin-2 and Dectin-3 Are Involved in Paracoccidioides brasiliensis Recognition by Human Plasmacytoid Dendritic Cells. (PMID: 29616019) Preite NW … Loures FV (Frontiers in immunology 2018) 3 54
  5. Widespread macromolecular interaction perturbations in human genetic disorders. (PMID: 25910212) Sahni N … Vidal M (Cell 2015) 3 54

Products for CLEC4D Gene

Sources for CLEC4D Gene