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 structu... See more...

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
  • LGALS10 2 3 4
  • Gal-10 2 3 4
  • Lectin, Galactoside-Binding, Soluble, 10 2 3
  • Galectin-10 3 4
  • LGALS10A 3 4
  • Galectin 10 2
  • LPPL_HUMAN 3
  • MGC149659 2
  • GAL10 3
  • CLC 5

External Ids for CLC Gene

Previous GeneCards Identifiers for CLC Gene

  • GC19M040862
  • GC19M040613
  • GC19M044897
  • GC19M044913
  • GC19M040221
  • GC19M036668
  • GC19M039733
  • GC19M040238
  • GC19M040296
  • GC19M039949
  • GC19M041448
  • GC19M039739
  • GC19M039801
  • GC19M039994

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 Allergic Rhinitis and Galactosemia I. 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 Summary 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

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

Genomics for CLC Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLC 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
GH19J039737 Promoter/Enhancer 0.9 EPDnew FANTOM5 Ensembl 616 -0.3 -271 3 IKZF1 SPI1 KLF1 CREB1 CLC LGALS17A piR-61101-344 LEUTX
GH19J039676 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 10.9 +59.4 59444 3.6 SP1 GATAD2A PRDM10 REST ZNF692 POLR2A BACH1 ZHX2 FOXA1 LARP7 LGALS17A ENSG00000269460 LGALS14 ENSG00000268088 HNRNPL LEUTX FBL CLC EID2B ZNF780A
GH19J039703 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 11.7 +32.5 32486 3.5 ZNF300 ZNF776 IKZF2 TRIM22 GABPA ZNF311 PKNOX1 EED ZBTB44 RELB LGALS14 ZNF780B HNRNPL LGALS17A NUMBL CLC AKT2 PAK4 EID2B piR-40110-341
GH19J039677 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 10.9 +61.9 61873 0.2 BACH1 JUND IKZF2 EED ARID3A DPF2 RUNX3 GATAD2B NFE2 BCLAF1 LEUTX FBL CLC EID2B PLEKHG2 MED29 ZFP36 PAF1 ENSG00000269460 LGALS17A
GH19J039558 Enhancer 1 FANTOM5 ENCODE 10.8 +179.5 179485 1.8 CREB1 FOXA1 PRDM1 TCF12 IRF2 IKZF2 SP1 ZNF600 PKNOX1 CEBPA HSALNG0126023 PLEKHG2 EID2B CLC DLL3 LEUTX MED29 LGALS4 RPS16 PAF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLC on the GeneHancer Hub at the UCSC Golden Path

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

Top Transcription factor binding sites by QIAGEN in the CLC gene promoter:
  • FOXI1
  • FOXL1
  • HFH-1
  • HFH-3
  • p53
  • STAT3

Genomic Locations for CLC Gene

Genomic Locations for CLC Gene
chr19:39,731,255-39,738,029
(GRCh38/hg38)
Size:
6,775 bases
Orientation:
Minus strand
chr19:40,221,890-40,228,668
(GRCh37/hg19)
Size:
6,779 bases
Orientation:
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:
    Q05315-LEG10_HUMAN
    Recommended name:
    Galectin-10
    Protein Accession:
    Q05315
    Secondary Accessions:
    • C5HZ13
    • C5HZ14
    • Q0VDE3

    Protein attributes for CLC Gene

    Size:
    142 amino acids
    Molecular mass:
    16453 Da
    Quaternary structure:
    • Interacts with CEL.
    Miscellaneous:
    • 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CLC Gene

InterPro:
Blocks:
  • Galectin, galactose-binding lectin
ProtoNet:

Suggested Antigen Peptide Sequences for CLC Gene

GenScript: Design optimal peptide antigens:
  • Galectin-10A (C5HZ13_HUMAN)
  • Galectin-10A (C5HZ14_HUMAN)
  • Lysolecithin acylhydrolase (LPPL_HUMAN)
genes like me logo Genes that share domains with CLC: view

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

Function for CLC Gene

Molecular function for CLC Gene

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).
GENATLAS Biochemistry:
Charcot-Leyden crystal protein,eosinophil lysophospholipase,also expressed in basophil,galectin family of galactoride-beta binding protein

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLC

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

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 CLC gene
Compartment Confidence
cytosol 5
extracellular 4
nucleus 3
mitochondrion 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CLC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA,IDA 17502455
GO:0062023 collagen-containing extracellular matrix HDA 28344315
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

PathCards logo

SuperPathways for CLC Gene

No Data Available

Interacting Proteins for CLC Gene

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 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 Pharma Agonist, Full agonist 27
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
  • Arachidinic acid
  • Arachinsaeure
  • C20:0
  • CH3-[CH2]18-COOH
  • Eicosanoic acid
506-30-9
Glycerylphosphorylethanolamine
  • 2-Aminoethyl ester 1-glycerophosphoric acid
  • a-Glycerophosphorylethanolamine
  • alpha-Glycerophosphorylethanolamine
  • Glycerol 3-phosphoethanolamine
  • Glycerol 3-phosphorylethanolamine
1190-00-7
Heptadecanoic acid
  • 17:0
  • C17:0
  • CH3-[CH2]15-COOH
  • Heptadecoic acid
  • Heptadecylic acid
506-12-7
Heptadecanoyl CoA
  • Heptadecanoyl-coenzyme A
  • Heptadecanoate
  • Heptadecanoic acid
  • Heptadecanoic acid CoA
  • Heptadecanoyl coenzyme A
3546-17-6
LysoPC(0:0/18:0)
  • (2R)-3-Hydroxy-2-(stearoyloxy)propyl 2-(trimethylazaniumyl)ethyl phosphate
  • 2-Octadecanoyl-sn-glycero-3-phosphocholine
  • 2-Stearoyllysophosphatidylcholine
  • LPC (18:0)
  • PC(0:0/18:0)
4421-58-3
genes like me logo Genes that share compounds with CLC: view

Transcripts for CLC Gene

mRNA/cDNA for CLC Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLC

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

No ASD Table

Relevant External Links for CLC Gene

GeneLoc Exon Structure for
CLC

Expression for CLC Gene

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



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

SOURCE GeneReport for Unigene cluster for CLC Gene:

Hs.889

mRNA Expression by UniProt/SwissProt for CLC Gene:

Q05315-LEG10_HUMAN
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(4.3)
  • Blood(3.1)
  • Bone marrow(2.8)
  • Intestine(2.3)
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
Chimpanzee
(Pan troglodytes)
Mammalia LOC100610880 30
  • 80.38 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 41 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia -- 31
  • 41 (a)
ManyToMany
Species where no ortholog for CLC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

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

Paralogs for CLC Gene

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

  • LEG10_HUMAN

Pseudogenes.org Pseudogenes for CLC Gene

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

Variants for CLC Gene

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

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs117361485 Benign: Abnormality of neuronal migration 39,731,420(-) A/C MISSENSE_VARIANT
rs17608 - p.Ala28Val

Additional dbSNP identifiers (rs#s) for CLC Gene

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
CLC

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

(5) MalaCards diseases for CLC Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
allergic rhinitis
  • alrh
galactosemia i
  • galk deficiency
hypereosinophilic syndrome
  • hypereosinophilic syndrome, idiopathic
galactosemia iii
  • galac3
asthma
  • asthma, susceptibility to
- 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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 23
  3. CLC- a novel susceptibility gene for allergic rhinitis? (PMID: 19650845) Bryborn M … Cardell LO (Allergy 2010) 3 23 41
  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 23
  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 23

Products for CLC Gene

Sources for CLC Gene