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Aliases for CLC Gene

Aliases for CLC Gene

  • Charcot-Leyden Crystal Galectin 2 3 5
  • Charcot-Leyden Crystal Protein 2 3 4
  • Eosinophil Lysophospholipase 2 3 4
  • Lysolecithin Acylhydrolase 2 3 4
  • Lectin, Galactoside-Binding, Soluble, 10 2 3
  • LGALS10A 3 4
  • LGALS10 3 4
  • Gal-10 3 4
  • Galectin 10 2
  • Galectin-10 3
  • GAL10 3

External Ids for CLC Gene

Previous GeneCards Identifiers for CLC Gene

  • GC19M040862
  • GC19M040613
  • GC19M044897
  • GC19M044913
  • GC19M040221
  • GC19M036668
  • GC19M039733

Summaries for CLC Gene

Entrez Gene Summary for CLC Gene

  • Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene is a lysophospholipase expressed in eosinophils and basophils. It hydrolyzes lysophosphatidylcholine to glycerophosphocholine and a free fatty acid. This protein may possess carbohydrate or IgE-binding activities. It is both structurally and functionally related to the galectin family of beta-galactoside binding proteins. It may be associated with inflammation and some myeloid leukemias. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLC Gene

CLC (Charcot-Leyden Crystal Galectin) is a Protein Coding gene. Diseases associated with CLC include Autoinflammation, Lipodystrophy, And Dermatosis Syndrome. Gene Ontology (GO) annotations related to this gene include carbohydrate binding and cysteine-type endopeptidase activity involved in apoptotic process. An important paralog of this gene is LGALS13.

UniProtKB/Swiss-Prot for CLC Gene

  • Regulates immune responses through the recognition of cell-surface glycans. Essential for the anergy and suppressive function of CD25-positive regulatory T-cells (Treg).

Gene Wiki entry for CLC Gene

Additional gene information for CLC Gene

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

Genomics for CLC Gene

GeneHancer (GH) Regulatory Elements for CLC Gene

Promoters and enhancers for CLC 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
GH19I039737 Promoter 0.6 EPDnew 550.8 +0.0 11 0.1 KLF1 CLC ENSG00000278813
GH19I039738 Enhancer 0.4 FANTOM5 566.1 -1.0 -1024 0.1 IKZF1 SPI1 CLC LEUTX
GH19I039703 Promoter/Enhancer 1.5 EPDnew ENCODE dbSUPER 11.7 +32.5 32486 3.5 HDGF PKNOX1 SMAD1 NFIB ZNF350 ATF7 IKZF2 RUNX3 EGR2 SMARCA5 LGALS14 ZNF780B HNRNPL LGALS17A NUMBL CLC AKT2 PAK4 EID2B ENSG00000278813
GH19I039677 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.9 +59.5 59457 3.6 HDGF PKNOX1 FOXA2 SMAD1 IRF4 ETS1 YY1 ZNF121 ZNF207 ATF7 LGALS17A ENSG00000268088 HNRNPL LEUTX FBL CLC EID2B ZNF780A LGALS16
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLC on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for CLC Gene

Genomic Locations for CLC Gene
6,780 bases
Minus strand

Genomic View for CLC Gene

Genes around CLC on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLC Gene

Proteins for CLC Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • C5HZ13
    • C5HZ14
    • Q0VDE3

    Protein attributes for CLC Gene

    142 amino acids
    Molecular mass:
    16453 Da
    Quaternary structure:
    • Interacts with CEL.
    • Forms hexagonal bipyramidal crystals, known as Charcot-Leyden crystals, in tissues and secretions from sites of eosinophil-associated inflammation and some myeloid leukemias.

    Three dimensional structures from OCA and Proteopedia for CLC Gene

neXtProt entry for CLC Gene

Post-translational modifications for CLC Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLC Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLC Gene

Domains & Families for CLC Gene

Gene Families for CLC Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CLC Gene

Suggested Antigen Peptide Sequences for CLC Gene

Graphical View of Domain Structure for InterPro Entry

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

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

Function for CLC Gene

Molecular function for CLC Gene

GENATLAS Biochemistry:
Charcot-Leyden crystal protein,eosinophil lysophospholipase,also expressed in basophil,galectin family of galactoride-beta binding protein
UniProtKB/Swiss-Prot Function:
Regulates immune responses through the recognition of cell-surface glycans. Essential for the anergy and suppressive function of CD25-positive regulatory T-cells (Treg).

Phenotypes From GWAS Catalog for CLC Gene

Gene Ontology (GO) - Molecular Function for CLC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004622 NOT contributes_to lysophospholipase activity IDA 11834744
GO:0005515 protein binding IPI 11834744
GO:0030246 carbohydrate binding IEA --
GO:0042802 identical protein binding IPI 25416956
GO:0097153 cysteine-type endopeptidase activity involved in apoptotic process IDA 17502455
genes like me logo Genes that share ontologies with CLC: view
genes like me logo Genes that share phenotypes with CLC: view

Clone Products

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

Localization for CLC Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLC Gene

Cytoplasm, cytosol. Cytoplasmic granule. Note=Localized in granules from where it may be secreted or transported to other locations in the cell.

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 CLC gene
Compartment Confidence
cytosol 5
extracellular 3
nucleus 3
plasma membrane 1
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CLC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA,IEA 17502455
genes like me logo Genes that share ontologies with CLC: view

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

Pathways & Interactions for CLC Gene

No Data Available

Interacting Proteins for CLC Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 9)
Selected Interacting proteins: Q05315-LEG10_HUMAN ENSP00000221804 for CLC Gene via IID STRING UniProtKB

Gene Ontology (GO) - Biological Process for CLC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002667 regulation of T cell anergy IMP 17502455
GO:0002724 regulation of T cell cytokine production IMP 17502455
GO:0007275 multicellular organism development TAS 8400237
GO:0046006 regulation of activated T cell proliferation IMP 17502455
GO:0070231 T cell apoptotic process IEA,IDA 17502455
genes like me logo Genes that share ontologies with CLC: view

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

Drugs & Compounds for CLC Gene

(10) Drugs for CLC Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Palmitic Acid Approved, Experimental Pharma Full agonist, Agonist 23
Stearic acid Approved, Experimental Pharma 0
Water Approved Pharma 0
N-Ethylmaleimide Experimental Pharma Target 0
Para-Mercury-Benzenesulfonic Acid Experimental Pharma Target 0

(43) Additional Compounds for CLC Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Arachidic acid
  • Arachate
  • Arachic acid
  • Arachidate
  • Arachidic acid
  • Eicosanoate
  • 2-Aminoethyl ester 1-Glycerophosphoric acid
  • a-Glycerophosphorylethanolamine
  • alpha-Glycerophosphorylethanolamine
  • Glycerol 3-phosphoethanolamine
  • Glycerol 3-phosphorylethanolamine
Heptadecanoic acid
  • Heptadecanoate
  • Heptadecanoic acid
  • Margarate
  • Margaric acid
  • Margarinate
Heptadecanoyl CoA
  • Heptadecanoate
  • Heptadecanoic acid
  • Heptadecanoic acid coa
  • Heptadecanoyl coenzyme A
  • Heptadecanoyl-coA
  • 1-Hydroxy-2-Octadecanoyl-sn-glycero-3-phosphocholine
  • 1-Hydroxy-2-stearoyl-sn-glycero-3-phosphocholine
  • Lysophosphatidylcholine
  • Stearoyl lysophosphatidylcholine
genes like me logo Genes that share compounds with CLC: view

Transcripts for CLC Gene

mRNA/cDNA for CLC Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(56) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLC Gene

Charcot-Leyden crystal protein:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for CLC Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLC Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (x47.6).

Protein differential expression in normal tissues from HIPED for CLC Gene

This gene is overexpressed in Neutrophil (44.4).

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

NURSA nuclear receptor signaling pathways regulating expression of CLC Gene:


SOURCE GeneReport for Unigene cluster for CLC Gene:


mRNA Expression by UniProt/SwissProt for CLC Gene:

Tissue specificity: Expressed abundantly in the bone marrow. Expressed exclusively by eosinophils and basophils. Not detected in monocytes and neutrophils. Expressed in CD25-positive regulatory T-cells (Treg) (at protein level). Found in intestinal tissue from patients with Celiac disease, expression is directly related to the histological grade of mucosal damage and to the number of eosinophils found in the duodenal lesion (at protein level). Found in sputum of patients with eosinophilic inflammatory diseases such as asthma (at protein level).

Evidence on tissue expression from TISSUES for CLC Gene

  • Liver(4.1)
  • Blood(2.9)
  • Bone marrow(2.2)
genes like me logo Genes that share expression patterns with CLC: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLC Gene

Orthologs for CLC Gene

This gene was present in the common ancestor of mammals.

Orthologs for CLC Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC100610880 33
  • 80.38 (n)
(Bos Taurus)
Mammalia -- 34
  • 41 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 41 (a)
Species where no ortholog for CLC 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)
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 CLC Gene

Gene Tree for CLC (if available)
Gene Tree for CLC (if available)

Paralogs for CLC Gene

Paralogs for CLC Gene

(9) SIMAP similar genes for CLC Gene using alignment to 1 proteins: Pseudogenes for CLC Gene

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

Variants for CLC Gene

Sequence variations from dbSNP and Humsavar for CLC Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs117361485 benign, Abnormality of neuronal migration 39,731,420(-) A/C coding_sequence_variant, missense_variant
rs1000900444 -- 39,736,792(-) A/T intron_variant
rs1001076151 -- 39,737,083(-) C/T intron_variant
rs1001641615 -- 39,737,890(-) T/C/G intron_variant
rs1001874840 -- 39,734,039(-) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
dgv3529n100 CNV loss 25217958
esv2758760 CNV gain 17122850
nsv1123254 CNV deletion 24896259
nsv579511 CNV loss 21841781
nsv9723 CNV loss 18304495

Variation tolerance for CLC Gene

Residual Variation Intolerance Score: 81.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.70; 46.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLC Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for CLC Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLC Gene - From: Novoseek

- elite association - COSMIC cancer census association via MalaCards
Search CLC in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLC

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CLC: view

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

Publications for CLC Gene

  1. Charcot-Leyden crystal protein (galectin-10) is not a dual function galectin with lysophospholipase activity but binds a lysophospholipase inhibitor in a novel structural fashion. (PMID: 11834744) Ackerman SJ … Acharya KR (The Journal of biological chemistry 2002) 2 3 4 22 58
  2. Localization of the human eosinophil Charcot-Leyden crystal protein (lysophospholipase) gene (CLC) to chromosome 19 and the human ribonuclease 2 (eosinophil-derived neurotoxin) and ribonuclease 3 (eosinophil cationic protein) genes (RNS2 and RNS3) to chromosome 14. (PMID: 1577491) Mastrianni DM … Ackerman SJ (Genomics 1992) 2 3 4 22 58
  3. CLC- a novel susceptibility gene for allergic rhinitis? (PMID: 19650845) Bryborn M … Cardell LO (Allergy 2010) 3 22 44 58
  4. Galectin-10, eosinophils, and celiac disease. (PMID: 19758173) De Re V … Canzonieri V (Annals of the New York Academy of Sciences 2009) 3 4 22 58
  5. Human CD4+CD25+ regulatory T cells: proteome analysis identifies galectin-10 as a novel marker essential for their anergy and suppressive function. (PMID: 17502455) Kubach J … Jonuleit H (Blood 2007) 3 4 22 58

Products for CLC Gene

Sources for CLC Gene

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