Aliases for CLEC3A Gene

Aliases for CLEC3A Gene

  • C-Type Lectin Domain Family 3 Member A 2 3 4 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 Summary for CLEC3A Gene

Additional gene information for CLEC3A Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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/Enhancer 0.6 EPDnew Ensembl 506.1 -0.1 -114 0.8 TEAD4 CLEC3A ENSG00000261540 lnc-VAT1L-1
GH16J078098 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 17.8 +77.4 77386 2.6 ZBTB40 ZNF217 EP300 CTCF SIN3A NRF1 MYC USF1 POLR2G SP1 WWOX NONHSAG020051.2 CLEC3A ENSG00000261707 piR-42370-008
GH16J077961 Enhancer 0.9 Ensembl ENCODE 19.5 -57.4 -57441 8.1 SP1 TEAD4 BCL11A HDAC2 RXRA CREB1 CBFB YY1 NANOG MEF2B CLEC3A WWOX NUDT7 VAT1L lnc-VAT1L-1 LOC105371351 L13712-008
GH16J077990 Enhancer 0.8 Ensembl ENCODE 23.2 -29.5 -29462 4.6 JUND FOS POLR2A NANOG GATA3 ESR1 CHD7 ZNF133 EP300 SETDB1 CLEC3A VAT1L WWOX lnc-VAT1L-1
GH16J078033 Enhancer 0.6 Ensembl 18.9 +12.3 12253 1.3 OSR2 ZNF213 GATA3 ZSCAN16 ZNF18 SALL1 ZNF664 FEZF1 GLIS1 ZBTB12 CLEC3A ENSG00000261540 KRT8P22
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC3A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLEC3A

Top Transcription factor binding sites by QIAGEN in the CLEC3A gene promoter:
  • Evi-1
  • FOXJ2 (long isoform)
  • FOXO1
  • FOXO1a
  • NRSF form 1
  • NRSF form 2
  • p53
  • Pax-6
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for CLEC3A Gene

Genomic Locations for CLEC3A Gene
44,247 bases
Plus strand
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=Extended N-terminus.; 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

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for CLEC3A Gene

Suggested Antigen Peptide Sequences for CLEC3A Gene

GenScript: Design optimal peptide antigens:
  • Cartilage-derived C-type lectin (CLC3A_HUMAN)
  • C-type lectin domain family 3, member A (Q3SX92_HUMAN)
genes like me logo Genes that share domains with CLEC3A: view

No data available for Graphical View of Domain Structure and 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

CRISPR Products

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 4
plasma membrane 1
cytoskeleton 1
cytosol 0

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 21873635
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

PathCards logo

SuperPathways for CLEC3A Gene

No Data Available

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 21873635
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

10 NCBI additional mRNA sequence :
4 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 CLEC3A Gene

No ASD Table

Relevant External Links for CLEC3A Gene

GeneLoc Exon Structure for

Expression for CLEC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLEC3A

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 31 30
  • 99.32 (n)
(Canis familiaris)
Mammalia CLEC3A 31 30
  • 91.16 (n)
(Bos Taurus)
Mammalia CLEC3A 31 30
  • 89.51 (n)
(Rattus norvegicus)
Mammalia Clec3a 30
  • 87.41 (n)
(Mus musculus)
Mammalia Clec3a 17 31 30
  • 86.05 (n)
(Monodelphis domestica)
Mammalia CLEC3A 31
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia CLEC3A 31
  • 79 (a)
(Gallus gallus)
Aves CLEC3A 31 30
  • 74.27 (n)
(Anolis carolinensis)
Reptilia CLEC3A 31
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clec3a 30
  • 69.43 (n)
(Danio rerio)
Actinopterygii LOC100330122 30
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLEC3A Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs2072663 - p.Gln197Lys

Additional dbSNP identifiers (rs#s) for CLEC3A Gene

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 23 54
  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 23 54
  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 41 54
  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 54
  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 54

Products for CLEC3A Gene

Sources for CLEC3A Gene