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Aliases for CLEC3A Gene

Aliases for CLEC3A Gene

  • C-Type Lectin Domain Family 3 Member A 2 3 3 5
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 1 (Cartilage-Derived) 2 3
  • CLECSF1 3 4
  • C-Type Lectin Domain Family 3, Member A 2
  • C-Type Lectin Superfamily Member 1 4
  • Cartilage-Derived C-Type Lectin 4

External Ids for CLEC3A Gene

Previous HGNC Symbols for CLEC3A Gene


Previous GeneCards Identifiers for CLEC3A Gene

  • GC16P076614
  • GC16P063813

Summaries for CLEC3A Gene

GeneCards Summary for CLEC3A Gene

CLEC3A (C-Type Lectin Domain Family 3 Member A) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include carbohydrate binding. An important paralog of this gene is CLEC3B.

UniProtKB/Swiss-Prot for CLEC3A Gene

  • Promotes cell adhesion to laminin-332 and fibronectin.

Additional gene information for CLEC3A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC3A Gene

Genomics for CLEC3A Gene

GeneHancer (GH) Regulatory Elements for CLEC3A Gene

Promoters and enhancers for CLEC3A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J078022 Promoter 0.5 EPDnew 650.7 +0.0 14 0.1 CLEC3A KRT8P22 ENSG00000261540
GH16J078098 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 17.8 +77.2 77170 2.1 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 WWOX CLEC3A GC16M078111
GH16J077990 Enhancer 0.8 Ensembl ENCODE 23.1 -29.5 -29462 4.6 SMARCE1 NANOG ZNF133 GATA3 JUND POLR2A POU5F1 FOS FOSL2 SETDB1 CLEC3A VAT1L WWOX LOC105371351
GH16J078002 Enhancer 1 Ensembl ENCODE 13.5 -19.3 -19314 0.8 PKNOX1 NFIB FEZF1 GLI4 ZNF2 IRF4 RAD21 RFX5 YY1 HSF1 CLEC3A WWOX LOC105371351
GH16J077961 Enhancer 0.7 ENCODE 15.9 -59.7 -59691 3.6 PKNOX1 EBF1 BATF GATA3 EED ETV6 FOS RUNX3 CREM RXRA CLEC3A NUDT7 VAT1L WWOX LOC105371351
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLEC3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLEC3A gene promoter:

Genomic Locations for CLEC3A Gene

Genomic Locations for CLEC3A Gene
44,247 bases
Plus strand

Genomic View for CLEC3A Gene

Genes around CLEC3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC3A Gene

Proteins for CLEC3A Gene

  • Protein details for CLEC3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    C-type lectin domain family 3 member A
    Protein Accession:
    Secondary Accessions:
    • B2R8C4
    • Q3SX91
    • Q6UXF5

    Protein attributes for CLEC3A Gene

    197 amino acids
    Molecular mass:
    22233 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAQ88742.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for CLEC3A Gene

Post-translational modifications for CLEC3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLEC3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLEC3A Gene

Domains & Families for CLEC3A Gene

Gene Families for CLEC3A Gene

Protein Domains for CLEC3A Gene

Suggested Antigen Peptide Sequences for CLEC3A Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CLEC3A: view

No data available for UniProtKB/Swiss-Prot for CLEC3A Gene

Function for CLEC3A Gene

Molecular function for CLEC3A Gene

UniProtKB/Swiss-Prot Function:
Promotes cell adhesion to laminin-332 and fibronectin.

Phenotypes From GWAS Catalog for CLEC3A Gene

Gene Ontology (GO) - Molecular Function for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with CLEC3A: view
genes like me logo Genes that share phenotypes with CLEC3A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLEC3A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLEC3A Gene

Localization for CLEC3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC3A Gene


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 CLEC3A gene
Compartment Confidence
extracellular 5
cytosol 1

Gene Ontology (GO) - Cellular Components for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA --
genes like me logo Genes that share ontologies with CLEC3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLEC3A Gene

Pathways & Interactions for CLEC3A Gene

SuperPathways for CLEC3A Gene

No Data Available

Interacting Proteins for CLEC3A Gene

Gene Ontology (GO) - Biological Process for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 10524194
GO:0001503 ossification IBA --
genes like me logo Genes that share ontologies with CLEC3A: view

No data available for Pathways by source and SIGNOR curated interactions for CLEC3A Gene

Drugs & Compounds for CLEC3A Gene

No Compound Related Data Available

Transcripts for CLEC3A Gene

mRNA/cDNA for CLEC3A Gene

(15) Selected AceView cDNA sequences:
(4) Additional mRNA sequences :
(2) REFSEQ mRNAs :
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLEC3A Gene

C-type lectin domain family 3, member A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC3A Gene

No ASD Table

Relevant External Links for CLEC3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLEC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLEC3A Gene

mRNA differential expression in normal tissues according to GTEx for CLEC3A Gene

This gene is overexpressed in Bladder (x23.8).

Protein differential expression in normal tissues from HIPED for CLEC3A Gene

This gene is overexpressed in Kidney (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC3A Gene

Protein tissue co-expression partners for CLEC3A Gene

NURSA nuclear receptor signaling pathways regulating expression of CLEC3A Gene:


SOURCE GeneReport for Unigene cluster for CLEC3A Gene:


mRNA Expression by UniProt/SwissProt for CLEC3A Gene:

Tissue specificity: Restricted to cartilage and breast. Also expressed in breast cancers.
genes like me logo Genes that share expression patterns with CLEC3A: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC3A Gene

Orthologs for CLEC3A Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLEC3A 34 33
  • 99.32 (n)
(Canis familiaris)
Mammalia CLEC3A 34 33
  • 91.16 (n)
(Bos Taurus)
Mammalia CLEC3A 34 33
  • 89.51 (n)
(Rattus norvegicus)
Mammalia Clec3a 33
  • 87.41 (n)
(Mus musculus)
Mammalia Clec3a 16 34 33
  • 86.05 (n)
(Monodelphis domestica)
Mammalia CLEC3A 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia CLEC3A 34
  • 79 (a)
(Gallus gallus)
Aves CLEC3A 34 33
  • 74.27 (n)
(Anolis carolinensis)
Reptilia CLEC3A 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clec3a 33
  • 69.43 (n)
(Danio rerio)
Actinopterygii LOC100330122 33
  • 62.15 (n)
  • 57 (a)
Species where no ortholog for CLEC3A 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLEC3A Gene

Gene Tree for CLEC3A (if available)
Gene Tree for CLEC3A (if available)
Evolutionary constrained regions (ECRs) for CLEC3A: view image

Paralogs for CLEC3A Gene

Paralogs for CLEC3A Gene

(2) SIMAP similar genes for CLEC3A Gene using alignment to 4 proteins:

  • Q3SX92_HUMAN
genes like me logo Genes that share paralogs with CLEC3A: view

Variants for CLEC3A Gene

Sequence variations from dbSNP and Humsavar for CLEC3A Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000055292 -- 78,025,309(+) C/G genic_upstream_transcript_variant, intron_variant
rs1000415948 -- 78,022,176(+) A/G upstream_transcript_variant
rs1000488111 -- 78,022,317(+) A/G/T upstream_transcript_variant
rs1000716427 -- 78,027,396(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000751192 -- 78,023,065(+) G/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC3A Gene

Variant ID Type Subtype PubMed ID
dgv3031n100 CNV gain 25217958
dgv3032n100 CNV loss 25217958
dgv5216n54 CNV loss 21841781
esv2760418 CNV gain+loss 21179565
esv3582336 CNV loss 25503493
esv3582337 CNV loss 25503493
esv3639185 CNV loss 21293372
esv3639186 CNV loss 21293372
esv3639187 CNV gain 21293372
nsv1056016 CNV loss 25217958
nsv1056561 CNV gain 25217958
nsv1058985 CNV loss 25217958
nsv817742 CNV gain 17921354
nsv833293 CNV gain 17160897

Variation tolerance for CLEC3A Gene

Residual Variation Intolerance Score: 55% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.05; 68.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC3A 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 CLEC3A Gene

Disorders for CLEC3A Gene

Additional Disease Information for CLEC3A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CLEC3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLEC3A Gene

Publications for CLEC3A Gene

  1. The cartilage-derived, C-type lectin (CLECSF1): structure of the gene and chromosomal location. (PMID: 10524194) Neame PJ … Grimm DR (Biochimica et biophysica acta 1999) 2 3 4 22 58
  2. Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity. (PMID: 19173304) Tsunezumi J … Miyazaki K (Journal of cellular biochemistry 2009) 3 4 22 58
  3. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. (PMID: 19844255) Dastani Z … Genest J (European journal of human genetics : EJHG 2010) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58

Products for CLEC3A Gene

Sources for CLEC3A Gene

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