CLC

gene
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Also known as LGALS10MGC149659Gal-10

Summary

CLC (Charcot-Leyden crystal galectin, HGNC:2014) is a protein-coding gene on chromosome 19q13.2, encoding Galectin-10 (Q05315). Regulates immune responses through the recognition of cell-surface glycans.

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.

Source: NCBI Gene 1178 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 16 total
  • MANE Select transcript: NM_001828

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2014
Approved symbolCLC
NameCharcot-Leyden crystal galectin
Location19q13.2
Locus typegene with protein product
StatusApproved
AliasesLGALS10, MGC149659, Gal-10
Ensembl geneENSG00000105205
Ensembl biotypeprotein_coding
OMIM153310
Entrez1178

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000221804

RefSeq mRNA: 1 — MANE Select: NM_001828 NM_001828

CCDS: CCDS33025

Canonical transcript exons

ENST00000221804 — 4 exons

ExonStartEnd
ENSE000007061933973428339734493
ENSE000008776443973499739735073
ENSE000008776453973125539731505
ENSE000014777603973793839738029

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 99.74.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 6.1167 / max 2053.0092, expressed in 106 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1808983.378372
1808992.738479

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
trabecular bone tissueUBERON:000248399.74gold quality
bone marrowUBERON:000237198.48gold quality
bone marrow cellCL:000209296.47gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047396.08gold quality
monocyteCL:000057695.79gold quality
mononuclear cellCL:000084295.52gold quality
bone elementUBERON:000147495.45gold quality
bloodUBERON:000017894.75gold quality
leukocyteCL:000073894.56gold quality
gall bladderUBERON:000211085.51gold quality
vermiform appendixUBERON:000115481.98gold quality
caecumUBERON:000115378.06gold quality
granulocyteCL:000009475.63gold quality
mucosa of transverse colonUBERON:000499174.50gold quality
spleenUBERON:000210674.14gold quality
ileal mucosaUBERON:000033173.52silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099172.73gold quality
rectumUBERON:000105270.27gold quality
smooth muscle tissueUBERON:000113570.21gold quality
Brodmann (1909) area 10UBERON:001354167.32gold quality
jejunal mucosaUBERON:000039966.59gold quality
amniotic fluidUBERON:000017362.28gold quality
duodenumUBERON:000211462.11gold quality
germinal epithelium of ovaryUBERON:000130461.17silver quality
right lungUBERON:000216760.06gold quality
parietal pleuraUBERON:000240059.73gold quality
frontal poleUBERON:000279559.60gold quality
paraflocculusUBERON:000535159.59gold quality
middle frontal gyrusUBERON:000270259.48gold quality
thymusUBERON:000237059.27silver quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 12.

ExperimentMarker?Max mean expression
E-CURD-112yes57049.25
E-MTAB-10432yes39737.35
E-MTAB-9801yes32965.83
E-MTAB-9067yes14722.05
E-MTAB-6505yes13673.34
E-CURD-6yes3354.27
E-CURD-55yes3009.74
E-CURD-77yes539.50
E-MTAB-8207yes300.07
E-MTAB-7249yes11.12
E-HCAD-10yes7.93
E-ANND-3yes3.49
E-MTAB-6678no3.51

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1H2, PAX1, POLR2B, PRDM16, RUNX2, SMARCA1, STAT1, TBP, YY1

miRNA regulators (miRDB)

9 targeting CLC, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3616-5P99.5567.02989
HSA-MIR-57399.5567.44955
HSA-MIR-5580-5P99.3866.961139
HSA-MIR-196A-3P99.1967.341204
HSA-MIR-6814-5P99.0366.681273
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-541-5P98.2467.771181
HSA-MIR-4433A-3P97.7562.821435
HSA-MIR-212-5P96.8367.43950

Literature-anchored findings (GeneRIF, showing 23)

  • downregulated significantly in acute myeloid leukemia patients whose white blood cell count was higher than 100 x 10(9)/L cells (PMID:12031912)
  • Changes in the expressions of galectin-10 are potentially important for myeloid cell differentiation into specific lineages. (PMID:12714580)
  • The five genes, and three of the encoded proteins, were shown differentially expressed between a group of keratoconus patients and a reference group using different techniques (PMID:16015083)
  • Downregulated in whole blood of infants hospitalised with respiratory syncytial virus (RSV), subtype B, bronchiolitis. (PMID:17166282)
  • expressed in human T lymphocytes, galectin-10 is essential for the functional properties of CD25(+) Treg cells. (PMID:17502455)
  • Genetic variation in Charcot-Leyden crystal protein was found to be associated with allergic rhinitis (PMID:19650845)
  • Data show that galectin-10 expression was related to the histological grade and with the number of eosinophils in the lesion. (PMID:19758173)
  • DK-PGD-induced CLC/Gal-10 mRNA level can serve as a potential marker for monitoring pharmacodynamic effects of blood exposure to CRTH2 modulating agents (PMID:20858065)
  • CLC and IFNAR1 were identified to be overall differentially expressed between early- and late-onset CRC, and are important in the development of early-onset CRC. (PMID:21716316)
  • The results support the potential for galectin-10 to be used as a surrogate biomarker of eosinophilic airway inflammation. (PMID:22880030)
  • findings show that galectin-10 functions as a T cell-suppressive molecule in eosinophils (PMID:28515279)
  • Because Trp72 is the highly conserved in the ligand binding sites of galectins, we used EGFP-tagged W72A to show that Gal-10 could not be transported into the nucleus, indicating that Trp72 is crucial for Gal-10 transport into that organelle. (PMID:30239701)
  • Increased CLC/Gal-10 and MBP-1 levels in the sputum were strongly correlated with sputum eosinophils in patients with asthma. CLC/Gal-10 and MBP-1 may be useful biomarkers for differentiation of eosinophilic airway inflammation in asthma. (PMID:31157540)
  • CLC mRNA levels based on the qRT-PCR may serve as a reliable and alternative method for the identification of eosinophilic chronic rhinosinusitis with nasal polyps (PMID:31269798)
  • Galectin-10, the protein that forms Charcot-Leyden crystals, is not stored in granules but resides in the peripheral cytoplasm of human eosinophils. (PMID:32108369)
  • [Expression and pathological role of galectin-10 in different types of nasal polyps]. (PMID:32911886)
  • Identification of galectin10 as a biomarker for periodontitis based on proteomic analysis of gingival crevicular fluid. (PMID:33300083)
  • Chronic rhinosinusitis with nasal polyposis (CRSwNP): the correlation between expression of Galectin-10 and Clinical-Cytological Grading (CCG). (PMID:34647485)
  • Crystalline State Determines the Potency of Galectin-10 Protein Assembly to Induce Inflammation. (PMID:35274950)
  • Galectin-10 as a Potential Biomarker for Eosinophilic Diseases. (PMID:36291593)
  • Glutathione disrupts galectin-10 Charcot-Leyden crystal formation to possibly ameliorate eosinophil-based diseases such as asthma. (PMID:36988350)
  • Behcet syndrome: The disturbed balance between anti- (CLEC12A, CLC) and proinflammatory (IFI27) gene expressions. (PMID:37102643)
  • Eosinophil-derived galectin-10 upregulates matrix metalloproteinase expression in bullous pemphigoid blisters. (PMID:37640566)

Cross-species orthologs

23 orthologs

OrganismSymbolGene ID
danio_reriolgals3bENSDARG00000044001
danio_reriosi:ch211-10a23.2ENSDARG00000060656
danio_reriosi:dkey-95h12.2ENSDARG00000092923
drosophila_melanogastergalectinFBGN0031213
drosophila_melanogasterCG11374FBGN0031214
drosophila_melanogasterCG13950FBGN0031289
caenorhabditis_elegansWBGENE00002264
caenorhabditis_elegansWBGENE00002266
caenorhabditis_elegansWBGENE00002269
caenorhabditis_elegansWBGENE00002270
caenorhabditis_elegansWBGENE00002271
caenorhabditis_elegansWBGENE00004165
caenorhabditis_elegansC27C7.5WBGENE00007768
caenorhabditis_elegansF46A8.3WBGENE00009746
caenorhabditis_elegansF46A8.4WBGENE00009747
caenorhabditis_elegansF46A8.5WBGENE00009748
caenorhabditis_elegansF46A8.8WBGENE00009751
caenorhabditis_elegansWBGENE00017080
caenorhabditis_elegansWBGENE00018255
caenorhabditis_elegansWBGENE00018649
caenorhabditis_elegansWBGENE00018650
caenorhabditis_elegansWBGENE00018651
caenorhabditis_elegansWBGENE00235368

Paralogs (16): LGALS14 (ENSG00000006659), LGALS2 (ENSG00000100079), LGALS1 (ENSG00000100097), LGALS13 (ENSG00000105198), LGALS8 (ENSG00000116977), LGALSL (ENSG00000119862), LGALS3 (ENSG00000131981), LGALS12 (ENSG00000133317), LGALS9 (ENSG00000168961), LGALS9B (ENSG00000170298), LGALS4 (ENSG00000171747), LGALS9C (ENSG00000171916), LGALS7B (ENSG00000178934), LGALS7 (ENSG00000205076), LGALS16 (ENSG00000249861), GRIFIN (ENSG00000275572)

Protein

Protein identifiers

Galectin-10Q05315 (reviewed: Q05315)

Alternative names: Charcot-Leyden crystal protein, Eosinophil lysophospholipase, Lysolecithin acylhydrolase

All UniProt accessions (1): Q05315

UniProt curated annotations — full annotation on UniProt →

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).

Subunit / interactions. Interacts with CEL.

Subcellular location. Cytoplasm. Cytosol. Cytoplasmic granule.

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).

Miscellaneous. Forms hexagonal bipyramidal crystals, known as Charcot-Leyden crystals, in tissues and secretions from sites of eosinophil-associated inflammation and some myeloid leukemias.

RefSeq proteins (1): NP_001819* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001079Galectin_CRDDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR044156Galectin-likeFamily

Pfam: PF00337

Enzyme classification (BRENDA):

  • EC 3.1.1.5 — lysophospholipase (BRENDA: 46 organisms, 226 substrates, 153 inhibitors, 43 Km, 4 kcat entries)

Substrate kinetics (BRENDA)

35 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
LYSOPHOSPHATIDYLCHOLINE0.022–0.265
1-OLEOYL-2-LYSOPHOSPHATIDYLCHOLINE0.306–0.752
1-PALMITOYL LYSOPHOSPHATIDYLCHOLINE0.0273–0.192
1-PALMITOYL-SN-GLYCERO-3-PHOSPHOCHOLINE0.0606–0.172
PHOSPHATIDYLCHOLINE0.18–0.632
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE11
1,2-DIDECANOYLPHOSPHATIDYLCHOLINE1.11
1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE2.91
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHOCHOLINE0.821
1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE0.191
1-(4Z,7Z,10Z,13Z,16Z,19Z)-DOCOSAHEXAENOYL-2-LYSO0.0451
1-ACYL-2-OLEOYL-PHOSPHATIDYLCHOLINE1.61
1-ARACHIDONOYL-2-LYSOPHOSPHATIDYLCHOLINE0.06761
1-DOCOSAHEXAENOYL LYSOPHOSPHATIDYLCHOLINE0.0451
1-HEXANOYL LYSOPHOSPHATIDYLCHOLINE0.09921

UniProt features (19 total): strand 10, helix 2, initiator methionine 1, chain 1, turn 1, domain 1, site 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

47 structures, top 30 by resolution.

PDBMethodResolution (Å)
6GKSX-RAY DIFFRACTION1.38
6QRNX-RAY DIFFRACTION1.4
5XRGX-RAY DIFFRACTION1.55
5XRHX-RAY DIFFRACTION1.55
9UWNX-RAY DIFFRACTION1.57
9UWPX-RAY DIFFRACTION1.57
5XRNX-RAY DIFFRACTION1.6
5XROX-RAY DIFFRACTION1.6
9UWKX-RAY DIFFRACTION1.6
6A1UX-RAY DIFFRACTION1.62
8JAEX-RAY DIFFRACTION1.62
6A1SX-RAY DIFFRACTION1.63
6A1YX-RAY DIFFRACTION1.63
9UWOX-RAY DIFFRACTION1.64
5XRIX-RAY DIFFRACTION1.68
5XRKX-RAY DIFFRACTION1.7
6L6CX-RAY DIFFRACTION1.77
9UWSX-RAY DIFFRACTION1.78
1G86X-RAY DIFFRACTION1.8
1HDKX-RAY DIFFRACTION1.8
1LCLX-RAY DIFFRACTION1.8
1QKQX-RAY DIFFRACTION1.8
6L6BX-RAY DIFFRACTION1.8
6L6AX-RAY DIFFRACTION1.81
5XRJX-RAY DIFFRACTION1.9
6GLWX-RAY DIFFRACTION1.9
6GKUX-RAY DIFFRACTION1.91
6L68X-RAY DIFFRACTION1.92
8YQCX-RAY DIFFRACTION1.92
6L6DX-RAY DIFFRACTION1.93

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q05315-F196.950.96

Antibody-complex structures (SAbDab): 36GKU, 6GLW, 6GLX

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 136 (not glycosylated)

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 163 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, FXR_IR1_Q6, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, MYOGENIN_Q6, GOBP_TOLERANCE_INDUCTION, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GCANCTGNY_MYOD_Q6, TGACCTY_ERR1_Q2, HNF1_Q6, GOBP_REGULATION_OF_TOLERANCE_INDUCTION, GGGTGGRR_PAX4_03, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, AACWWCAANK_UNKNOWN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (4): regulation of T cell anergy (GO:0002667), regulation of T cell cytokine production (GO:0002724), regulation of activated T cell proliferation (GO:0046006), T cell apoptotic process (GO:0070231)

GO Molecular Function (3): carbohydrate binding (GO:0030246), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), extracellular matrix (GO:0031012), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular anatomical structure2
regulation of T cell tolerance induction1
T cell anergy1
regulation of lymphocyte anergy1
T cell cytokine production1
regulation of T cell mediated immunity1
regulation of cytokine production involved in immune response1
regulation of T cell proliferation1
activated T cell proliferation1
lymphocyte apoptotic process1
protein binding1
cytoplasm1
external encapsulating structure1
intracellular anatomical structure1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLCGALEQ14376932
CLCLGALS2P05162699
CLCLGALS12Q96DT0608
CLCCHD7Q9P2D1601
CLCRNASE2P10153581
CLCLGALS3P17931576
CLCEPXP11678571
CLCGALK1P51570571
CLCRNASE3P12724570
CLCISYNA1Q9NPH2540
CLCADH1AP07327517
CLCHDAC3O15379510
CLCPAICSP22234507
CLCHDAC8Q9BY41492
CLCPRG2P13727480

IntAct

4 interactions, top by confidence:

ABTypeScore
CLCCLCpsi-mi:“MI:0915”(physical association)0.670
CLCCLCpsi-mi:“MI:0915”(physical association)0.000

BioGRID (2): CLC (Two-hybrid), CLC (Two-hybrid)

ESM2 similar proteins: A0A3Q1N1R0, A4D1Z8, A8MUM7, D3ZGS3, O00214, O08573, O14727, O23547, O44126, O54891, O88644, O88879, P07583, P08520, P11762, P23668, P26788, P36573, P38552, P47967, P56180, P56217, P56470, P79238, P97400, P97840, Q01968, Q05315, Q09581, Q09605, Q29058, Q3MHZ8, Q62665, Q6DGJ1, Q6NVF0, Q801X7, Q8C726, Q8K419, Q8LEV3, Q8TCE9

Diamond homologs: A8MUM7, O00182, O08573, O54891, P38486, P38552, P47929, P79238, P97400, P97840, Q05315, Q29058, Q3B8N2, Q3MHZ8, Q3T0D6, Q6DKI2, Q8K419, Q8TCE9, Q9UHV8, A8N3G7, C0HJQ1, C0HJR3, O44126, O54974, P08520, P08699, P09382, P11116, P16110, P17931, P36573, P47845, P47953, P47967, P56470, P81184, P97590, Q09581, Q1ECW6, Q206Z5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

16 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance11
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

937 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:39734319:A:CF89L0.951
19:39734319:A:TF89L0.951
19:39734321:A:GF89L0.951
19:39731473:A:CF112L0.939
19:39731473:A:TF112L0.939
19:39731475:A:GF112L0.939
19:39734412:A:CF58L0.913
19:39734412:A:TF58L0.913
19:39734414:A:GF58L0.913
19:39734337:A:CF83L0.911
19:39734337:A:TF83L0.911
19:39734339:A:GF83L0.911
19:39734430:G:CF52L0.895
19:39734430:G:TF52L0.895
19:39734432:A:GF52L0.895
19:39734466:G:CF40L0.892
19:39734466:G:TF40L0.892
19:39734468:A:GF40L0.892
19:39734287:T:GY100S0.878
19:39734999:G:CF30L0.866
19:39734999:G:TF30L0.866
19:39735001:A:GF30L0.866
19:39734370:C:AW72C0.860
19:39734370:C:GW72C0.860
19:39734386:C:GR67P0.858
19:39734467:A:GF40S0.849
19:39734372:A:GW72R0.848
19:39734372:A:TW72R0.848
19:39734308:A:GI93T0.847
19:39734288:A:GY100H0.838

dbSNP variants (sampled 300 via entrez): RS1000900444 (19:39736792 A>T), RS1001076151 (19:39737083 C>G,T), RS1001641615 (19:39737890 T>C,G), RS1001874840 (19:39734039 A>G), RS1002019444 (19:39731969 G>A,C), RS1002910765 (19:39739148 T>C), RS1002956488 (19:39738092 TCA>T), RS1003020204 (19:39733850 T>A,C), RS1003370739 (19:39735080 G>A,C), RS1003549246 (19:39735356 T>C), RS1003886458 (19:39733557 A>C,G), RS1003938946 (19:39733760 T>A), RS1004446928 (19:39738408 C>T), RS1004584434 (19:39732235 C>T), RS1005068796 (19:39738946 A>C)

Disease associations

OMIM: gene MIM:153310 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

11 associations (top):

StudyTraitp-value
GCST001851_5Schizophrenia2.000000e-06
GCST004600_109Eosinophil percentage of white cells4.000000e-53
GCST004606_38Eosinophil count6.000000e-58
GCST004617_36Eosinophil percentage of granulocytes2.000000e-47
GCST004623_96Neutrophil percentage of granulocytes2.000000e-33
GCST005975_3Eosinophil count1.000000e-12
GCST90002379_153Basophil count4.000000e-13
GCST90002380_18Basophil percentage of white cells4.000000e-18
GCST90002380_19Basophil percentage of white cells3.000000e-11
GCST90002381_343Eosinophil count9.000000e-134
GCST90002382_465Eosinophil percentage of white cells3.000000e-129

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0007991eosinophil percentage of leukocytes
EFO:0004842eosinophil count
EFO:0007996eosinophil percentage of granulocytes
EFO:0007994neutrophil percentage of granulocytes
EFO:0005090basophil count
EFO:0007992basophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
Arsenic Trioxideincreases expression2
bisphenol Fdecreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
coumarinaffects phosphorylation1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
Acetaminophendecreases expression1
Air Pollutantsaffects expression, increases abundance1
Aspirinaffects response to substance1
Benzo(a)pyreneaffects methylation1
Cisplatindecreases expression1
Irondecreases expression1
Ozoneaffects expression, increases abundance1
Tretinoinincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.