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Aliases for CLEC2D Gene

Aliases for CLEC2D Gene

  • C-Type Lectin Domain Family 2 Member D 2 3 5
  • Lectin-Like Transcript 1 2 3 4
  • C-Type Lectin Superfamily 2, Member D 2 3
  • Lectin-Like NK Cell Receptor 3 4
  • Osteoclast Inhibitory Lectin 3 4
  • C-Type Lectin Related F 2 3
  • LLT-1 3 4
  • CLAX 3 4
  • LLT1 3 4
  • OCIL 3 4
  • C-Type Lectin Domain Family 2, Member D 2

External Ids for CLEC2D Gene

Previous GeneCards Identifiers for CLEC2D Gene

  • GC12P009715
  • GC12P009809
  • GC12P009565
  • GC12P009817

Summaries for CLEC2D Gene

Entrez Gene Summary for CLEC2D Gene

  • This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]

GeneCards Summary for CLEC2D Gene

CLEC2D (C-Type Lectin Domain Family 2 Member D) is a Protein Coding gene. Among its related pathways are Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell and Immune System. GO annotations related to this gene include transmembrane signaling receptor activity and carbohydrate binding. An important paralog of this gene is CLEC2A.

UniProtKB/Swiss-Prot for CLEC2D Gene

  • Receptor for KLRB1 that protects target cells against natural killer cell-mediated lysis. Inhibits osteoclast formation. Inhibits bone resorption. Modulates the release of interferon-gamma. Binds high molecular weight sulfated glycosaminoglycans.

Gene Wiki entry for CLEC2D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC2D Gene

Genomics for CLEC2D Gene

Regulatory Elements for CLEC2D Gene

Enhancers for CLEC2D 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
GH12F009646 1.5 FANTOM5 ENCODE 39.3 -13.2 -13236 10.0 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 SLC30A9 CBX5 SP3 SP5 CLEC2D LOC374443 KLRB1 CLECL1 CLEC12A ENSG00000214776 PHC1 CD69 CLEC7A DDX12P
GH12F009614 1.1 FANTOM5 Ensembl ENCODE 39.3 -48.5 -48461 3.3 PKNOX1 MTA2 SCRT2 NBN TBX21 MAFK SPI1 CLEC2D KLRB1 KLRF1 ENSG00000214776 ENSG00000257027 CD69 CLECL1 LOC374443 CLEC2B
GH12F009666 1.2 Ensembl ENCODE 25.7 +6.1 6078 9.4 HDGF PKNOX1 GLIS2 GATA2 CBX5 FOS ZNF263 JUNB REST TBX21 CLEC2D ENSG00000213443 CLECL1 ENSG00000257027 ENSG00000214776 LOC374443 LOC728715 ENSG00000255753 GC12M011542
GH12F009736 1.6 FANTOM5 Ensembl ENCODE 17.3 +75.1 75054 7.6 PKNOX1 GATA2 CBX5 ZNF143 JUNB TBX21 MEF2D SMARCA4 HMBOX1 STAT3 CLECL1 CLEC2D KLRB1 ENSG00000213443 ENSG00000214776 CD69 CLEC7A ENSG00000257027 CLEC2B KLRF1
GH12F009605 1.1 FANTOM5 ENCODE 24.7 -58.1 -58070 3.2 HDAC1 PKNOX1 TBL1XR1 BMI1 ZNF143 ETV6 CREM SMAD5 CBFB CEBPB CLEC2D ENSG00000214776 LOC642846 KLRF2 DDX12P LOC374443 LOC101930452 KLRB1 KLRF1 PIR60914
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLEC2D on UCSC Golden Path with GeneCards custom track

Genomic Location for CLEC2D Gene

9,664,969 bp from pter
9,699,555 bp from pter
34,587 bases
Plus strand

Genomic View for CLEC2D Gene

Genes around CLEC2D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC2D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC2D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC2D Gene

Proteins for CLEC2D Gene

  • Protein details for CLEC2D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    C-type lectin domain family 2 member D
    Protein Accession:
    Secondary Accessions:
    • D6CI39
    • D6CI40
    • D6CI41
    • Q6YID5
    • Q8WUP7
    • Q9HD37
    • Q9HD38

    Protein attributes for CLEC2D Gene

    191 amino acids
    Molecular mass:
    21849 Da
    Quaternary structure:
    • Homodimer or heterodimer; disulfide-linked.

    Three dimensional structures from OCA and Proteopedia for CLEC2D Gene

    Alternative splice isoforms for CLEC2D Gene

neXtProt entry for CLEC2D Gene

Post-translational modifications for CLEC2D Gene

  • Glycosylation at Asn 95
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLEC2D Gene

Domains & Families for CLEC2D Gene

Gene Families for CLEC2D Gene

Protein Domains for CLEC2D Gene

Suggested Antigen Peptide Sequences for CLEC2D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 C-type lectin domain.
  • Contains 1 C-type lectin domain.
genes like me logo Genes that share domains with CLEC2D: view

Function for CLEC2D Gene

Molecular function for CLEC2D Gene

UniProtKB/Swiss-Prot Function:
Receptor for KLRB1 that protects target cells against natural killer cell-mediated lysis. Inhibits osteoclast formation. Inhibits bone resorption. Modulates the release of interferon-gamma. Binds high molecular weight sulfated glycosaminoglycans.
UniProtKB/Swiss-Prot Induction:
Up-regulated by IL1A/interleukin-1 alpha and prostaglandin E2 in cultured osteogenic sarcoma cells.

Gene Ontology (GO) - Molecular Function for CLEC2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity TAS 10541800
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with CLEC2D: view
genes like me logo Genes that share phenotypes with CLEC2D: view

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLEC2D Gene

Localization for CLEC2D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC2D Gene

Cell membrane; Single-pass type II membrane protein. Cell surface.
Isoform 2: Endoplasmic reticulum.
Isoform 4: Endoplasmic reticulum.

Subcellular locations from

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 CLEC2D gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
nucleus 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for CLEC2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 20843815
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 10541800
GO:0009986 cell surface IEA,IDA 20843815
GO:0016020 membrane IEA,TAS 10541800
genes like me logo Genes that share ontologies with CLEC2D: view

Pathways & Interactions for CLEC2D Gene

genes like me logo Genes that share pathways with CLEC2D: view

Interacting Proteins for CLEC2D Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
Selected Interacting proteins: Q9UHP7-CLC2D_HUMAN ENSP00000261340 for CLEC2D Gene via IID STRING

Gene Ontology (GO) - Biological Process for CLEC2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007166 cell surface receptor signaling pathway TAS 10541800
GO:0050776 regulation of immune response TAS --
genes like me logo Genes that share ontologies with CLEC2D: view

No data available for SIGNOR curated interactions for CLEC2D Gene

Drugs & Compounds for CLEC2D Gene

(1) Drugs for CLEC2D Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with CLEC2D: view

Transcripts for CLEC2D Gene

Unigene Clusters for CLEC2D Gene

C-type lectin domain family 2, member D:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC2D Gene

No ASD Table

Relevant External Links for CLEC2D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLEC2D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLEC2D Gene

mRNA differential expression in normal tissues according to GTEx for CLEC2D Gene

This gene is overexpressed in Whole Blood (x4.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC2D Gene

Protein tissue co-expression partners for CLEC2D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLEC2D Gene:


SOURCE GeneReport for Unigene cluster for CLEC2D Gene:


mRNA Expression by UniProt/SwissProt for CLEC2D Gene:

Tissue specificity: Detected in peripheral blood leukocytes, osteoblasts, lymph node, thymus and spleen. Isoform 1, isoform 2 and isoform 4 are expressed in T- and B-lymphocytes, and at lower levels in NK cells. They are also expressed in B-cell lines and LPS-matured monocyte-derived dendritic cells.
genes like me logo Genes that share expression patterns with CLEC2D: view

Primer Products

No data available for Protein differential expression in normal tissues for CLEC2D Gene

Orthologs for CLEC2D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC2D Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLEC2D 35
  • 99 (a)
(Canis familiaris)
Mammalia CLEC2D 34 35
  • 77.31 (n)
(Rattus norvegicus)
Mammalia Clec2h 34
  • 63.64 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 39 (a)
(Mus musculus)
Mammalia Clec2j 35
  • 33 (a)
Clec2d 35
  • 29 (a)
Clec2e 35
  • 29 (a)
Clec2h 35
  • 26 (a)
Clec2g 35
  • 22 (a)
(Bos Taurus)
Mammalia -- 35
  • 32 (a)
-- 35
  • 30 (a)
(Gallus gallus)
Aves -- 35
  • 32 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 23 (a)
-- 35
  • 22 (a)
-- 35
  • 18 (a)
Species where no ortholog for CLEC2D 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)
  • 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)
  • 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 CLEC2D Gene

Gene Tree for CLEC2D (if available)
Gene Tree for CLEC2D (if available)

Paralogs for CLEC2D Gene

Paralogs for CLEC2D Gene Pseudogenes for CLEC2D Gene

genes like me logo Genes that share paralogs with CLEC2D: view

Variants for CLEC2D Gene

Sequence variations from dbSNP and Humsavar for CLEC2D Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1044771 -- 9,699,333(+) ttatt(A/C)ttaat nc-transcript-variant, utr-variant-3-prime
rs10492164 -- 9,694,537(+) ACAGA(C/T)ATGAA intron-variant
rs1056151 -- 9,698,427(+) aaaaa(A/T)agtct nc-transcript-variant, utr-variant-3-prime
rs1059858 -- 9,698,090(+) AAAGG(A/C/G)TATTT nc-transcript-variant, utr-variant-3-prime
rs10734807 -- 9,690,817(+) AAAAA(A/T)GTCAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC2D Gene

Variant ID Type Subtype PubMed ID
nsv975446 CNV duplication 23825009
nsv428271 CNV gain 18775914
nsv1051530 CNV gain 25217958
esv2759878 CNV gain+loss 17122850

Variation tolerance for CLEC2D Gene

Residual Variation Intolerance Score: 82.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.42; 63.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLEC2D Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC2D Gene

Disorders for CLEC2D Gene

Relevant External Links for CLEC2D

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CLEC2D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLEC2D Gene

Publications for CLEC2D Gene

  1. The Asn19Lys substitution in the osteoclast inhibitory lectin (OCIL) gene is associated with a reduction of bone mineral density in postmenopausal women. (PMID: 18465072) Pineda B. … GarcA-a-PAcrez M.A. (Calcif. Tissue Int. 2008) 3 22 46 64
  2. Lectin-like transcript-1 is a ligand for the inhibitory human NKR-P1A receptor. (PMID: 16339513) Rosen D.B. … Lanier L.L. (J. Immunol. 2005) 3 4 22 64
  3. Characterization of sugar binding by osteoclast inhibitory lectin. (PMID: 15123656) Gange C.T. … Ng K.W. (J. Biol. Chem. 2004) 3 4 22 64
  4. Isolation of a human homolog of osteoclast inhibitory lectin that inhibits the formation and function of osteoclasts. (PMID: 14753741) Hu Y.S. … Ng K.W. (J. Bone Miner. Res. 2004) 3 4 22 64
  5. The LLT1 receptor induces IFN-gamma production by human natural killer cells. (PMID: 15104121) Mathew P.A. … Pham H.T. (Mol. Immunol. 2004) 3 4 22 64

Products for CLEC2D Gene

Sources for CLEC2D Gene

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