CLC

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

• Clinical variants (ClinVar): 16 total
• GTEx eGene: eQTL in 4 tissues, sQTL in 2 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.68 (unconstrained)
• MANE Select transcript: NM_001828

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2014
Approved symbol	CLC
Name	Charcot-Leyden crystal galectin
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	LGALS10, MGC149659, Gal-10
Ensembl gene	ENSG00000105205
Ensembl biotype	protein_coding
OMIM	153310
Entrez	1178

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 nonsense_mediated_decay

MANE Select: ENST00000221804

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1

ENST00000221804, ENST00001098442, ENST00001098443, ENST00001098444, ENST00001098445, ENST00001098446, ENST00001127658, ENST00001127659, ENST00001138565

RefSeq mRNA: 1 — MANE Select: NM_001828 NM_001828

CCDS: CCDS33025

Canonical transcript exons

ENST00000221804 — 4 exons

Exon	Start	End
ENSE00000706193	39734283	39734493
ENSE00000877644	39734997	39735073
ENSE00000877645	39731255	39731505
ENSE00001477760	39737938	39738029

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.

Highest expression (Bgee): trabecular bone tissue, bone marrow, bone marrow cell, male germ line stem cell (sensu Vertebrata) in testis, monocyte.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CLC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 4 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

6 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells EBV-transformed lymphocytes	eqtl	1.4e-08	+0.38	19:39728486:G:C
Whole Blood	sqtl	2.3e-07	+0.36	19:39731739:C:G
Whole Blood	eqtl	3.9e-05	+0.17	19:39760534:C:T
Lung	eqtl	3.3e-03	+0.18	19:39728486:G:C
Spleen	eqtl	3.9e-02	+0.29	19:39729557:T:C
Lung	sqtl	4.0e-02	-0.33	19:38943434:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
180898	3.3783	72
180899	2.7384	79

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
trabecular bone tissue	UBERON:0002483	99.74	gold quality
bone marrow	UBERON:0002371	98.48	gold quality
bone marrow cell	CL:0002092	96.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	96.08	gold quality
monocyte	CL:0000576	95.79	gold quality
mononuclear cell	CL:0000842	95.52	gold quality
bone element	UBERON:0001474	95.45	gold quality
blood	UBERON:0000178	94.75	gold quality
leukocyte	CL:0000738	94.56	gold quality
gall bladder	UBERON:0002110	85.51	gold quality
vermiform appendix	UBERON:0001154	81.98	gold quality
caecum	UBERON:0001153	78.06	gold quality
granulocyte	CL:0000094	75.63	gold quality
mucosa of transverse colon	UBERON:0004991	74.50	gold quality
spleen	UBERON:0002106	74.14	gold quality
ileal mucosa	UBERON:0000331	73.52	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.73	gold quality
rectum	UBERON:0001052	70.27	gold quality
smooth muscle tissue	UBERON:0001135	70.21	gold quality
Brodmann (1909) area 10	UBERON:0013541	67.32	gold quality
jejunal mucosa	UBERON:0000399	66.59	gold quality
amniotic fluid	UBERON:0000173	62.28	gold quality
duodenum	UBERON:0002114	62.11	gold quality
germinal epithelium of ovary	UBERON:0001304	61.17	silver quality
right lung	UBERON:0002167	60.06	gold quality
parietal pleura	UBERON:0002400	59.73	gold quality
frontal pole	UBERON:0002795	59.60	gold quality
paraflocculus	UBERON:0005351	59.59	gold quality
middle frontal gyrus	UBERON:0002702	59.48	gold quality
thymus	UBERON:0002370	59.27	silver quality
upper lobe of left lung	UBERON:0008952	58.83	gold quality
pleura	UBERON:0000977	58.62	silver quality
jejunum	UBERON:0002115	58.53	gold quality
adrenal tissue	UBERON:0018303	58.43	gold quality
upper lobe of lung	UBERON:0008948	57.69	gold quality
decidua	UBERON:0002450	56.93	gold quality
right lobe of liver	UBERON:0001114	56.04	gold quality
small intestine	UBERON:0002108	55.12	gold quality
lymph node	UBERON:0000029	54.90	gold quality
lung	UBERON:0002048	54.90	gold quality
visceral pleura	UBERON:0002401	54.82	gold quality
mucosa of sigmoid colon	UBERON:0004993	53.89	silver quality
triceps brachii	UBERON:0001509	53.65	gold quality
tibialis anterior	UBERON:0001385	52.84	silver quality
liver	UBERON:0002107	52.80	gold quality
pylorus	UBERON:0001166	52.69	silver quality
hair follicle	UBERON:0002073	52.43	gold quality
small intestine Peyer’s patch	UBERON:0003454	52.28	gold quality
male germ cell	CL:0000015	52.24	gold quality
quadriceps femoris	UBERON:0001377	52.20	gold quality
sperm	CL:0000019	52.11	gold quality
pancreatic ductal cell	CL:0002079	51.75	silver quality
colonic mucosa	UBERON:0000317	51.27	gold quality
mucosa of urinary bladder	UBERON:0001259	50.96	silver quality
deltoid	UBERON:0001476	50.96	gold quality
cerebellar vermis	UBERON:0004720	50.89	gold quality
vastus lateralis	UBERON:0001379	50.82	gold quality
placenta	UBERON:0001987	50.34	gold quality
epithelial cell of pancreas	CL:0000083	49.77	gold quality
muscle tissue	UBERON:0002385	49.61	gold quality
layer of synovial tissue	UBERON:0007616	49.60	gold quality
renal glomerulus	UBERON:0000074	49.57	gold quality
intestine	UBERON:0000160	49.52	gold quality
metanephric glomerulus	UBERON:0004736	49.47	gold quality
transverse colon	UBERON:0001157	49.37	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
myocardium	UBERON:0002349	48.87	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
skin of hip	UBERON:0001554	48.71	silver quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
kidney epithelium	UBERON:0004819	48.29	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
oviduct epithelium	UBERON:0004804	48.21	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality
right coronary artery	UBERON:0001625	48.08	gold quality
upper arm skin	UBERON:0004263	48.06	gold quality
cervix epithelium	UBERON:0004801	48.04	gold quality
tongue squamous epithelium	UBERON:0006919	47.92	gold quality
nasal cavity epithelium	UBERON:0005384	47.70	gold quality
urinary bladder	UBERON:0001255	47.64	gold quality
large intestine	UBERON:0000059	47.36	gold quality
periodontal ligament	UBERON:0008266	47.14	gold quality
diaphragm	UBERON:0001103	47.05	gold quality
gluteal muscle	UBERON:0002000	47.03	gold quality
hypothalamus	UBERON:0001898	47.00	gold quality
nephron tubule	UBERON:0001231	46.88	gold quality
endometrium epithelium	UBERON:0004811	46.85	gold quality
hindlimb stylopod muscle	UBERON:0004252	46.82	gold quality
endometrium	UBERON:0001295	46.77	gold quality
nasal cavity mucosa	UBERON:0001826	46.11	silver quality
colon	UBERON:0001155	45.95	gold quality
trachea	UBERON:0003126	45.40	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	45.35	gold quality
inferior olivary complex	UBERON:0002127	45.14	gold quality
adult organism	UBERON:0007023	44.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-112	yes	57049.25
E-MTAB-10432	yes	39737.35
E-MTAB-9801	yes	32965.83
E-MTAB-9067	yes	14722.05
E-MTAB-6505	yes	13673.34
E-CURD-6	yes	3354.27
E-CURD-55	yes	3009.74
E-CURD-77	yes	539.50
E-MTAB-8207	yes	300.07
E-MTAB-7249	yes	11.12
E-HCAD-10	yes	7.93
E-ANND-3	yes	3.49
E-MTAB-6678	no	3.51

HPA expression

RNA tissue specificity: Tissue enriched

showing 60 of 132 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Bone marrow	tissue	426.7	medium
Small intestine	tissue	39.1	not detected
Appendix	tissue	28.3	not detected
Duodenum	tissue	23.8	not detected
Smooth muscle	tissue	22.8	not detected
Urinary bladder	tissue	22.5	not detected
Urinary bladder	tissue	16.8	low
Gallbladder	tissue	16.6	low
Gallbladder	tissue	15.5	not detected
Stomach 1	tissue	14.7	not detected
Endometrium 1	tissue	13.2	low
Bone marrow	tissue	12.9	medium
Spleen	tissue	10.6	medium
Adipose tissue	tissue	10.6	low
Colon	tissue	9.6	not detected
Choroid plexus	tissue	8.5
Vagina	tissue	7.9	low
Smooth muscle	tissue	7.8	medium
Rectum	tissue	7.6	not detected
Pituitary gland	tissue	7.6
Appendix	tissue	7.5	low
Thymus	tissue	6.8
Fallopian tube	tissue	6.4	low
Pancreas	tissue	6.2	low
Lung	tissue	5.9	not detected
Hippocampus	tissue	5.7	low
Locus coeruleus	tissue	5.4
Nucleus accumbens	tissue	5.1
Lymph node	tissue	5.0	low
Cervix	tissue	4.8	low
Postcentral gyrus	tissue	4.6
Liver	tissue	4.5	not detected
Kidney	tissue	4.1	medium
Tonsil	tissue	4.1	medium
Placenta	tissue	4.0	low
Spinal cord	tissue	3.9
Lung	tissue	3.8	medium
Spleen	tissue	3.7	low
Thyroid gland	tissue	3.3	low
Adrenal gland	tissue	3.1	low
Stomach 1	tissue	3.0	medium
Ovary	tissue	3.0	low
Prostate	tissue	2.5	not detected
Liver	tissue	2.3	low
Heart muscle	tissue	2.2	medium
Colon	tissue	2.1	low
Adipose tissue	tissue	1.9	not detected
Tongue	tissue	1.8
Seminal vesicle	tissue	1.7	low
Esophagus	tissue	1.7	not detected
Lymph node	tissue	1.6	medium
Fallopian tube	tissue	1.6	not detected
Rectum	tissue	1.6	low
Skin 1	tissue	1.5	low
Medulla oblongata	tissue	1.5
Skin 1	tissue	1.4	not detected
Breast	tissue	1.4	medium
Testis	tissue	1.4	low
Superior colliculi	tissue	1.4
Placenta	tissue	1.3	not detected

Brain sub-regions (HPA Brain Atlas): detected in 209; highest nTPM — Blood vessel (12.6), Anterior thalamic nucleus, ventral (9.6), Precentral gyrus (9.2), Area postrema (8.9), Corticomedial amygdala (8.8).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CLC by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

9 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-541-5P	98.24	67.77	1181
HSA-MIR-4433A-3P	97.75	62.82	1435
HSA-MIR-212-5P	96.83	67.43	950

Functional genomics

gnomAD constraint: pLI 2.35e-06, LOEUF 1.68, missense Z 0.438 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000221804 — one region, missense o/e 0.95.

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

Organism	Symbol	Gene ID
danio_rerio	lgals3b	ENSDARG00000044001
danio_rerio	si:ch211-10a23.2	ENSDARG00000060656
danio_rerio	si:dkey-95h12.2	ENSDARG00000092923
drosophila_melanogaster	galectin	FBGN0031213
drosophila_melanogaster	CG11374	FBGN0031214
drosophila_melanogaster	CG13950	FBGN0031289
caenorhabditis_elegans		WBGENE00002264
caenorhabditis_elegans		WBGENE00002266
caenorhabditis_elegans		WBGENE00002269
caenorhabditis_elegans		WBGENE00002270
caenorhabditis_elegans		WBGENE00002271
caenorhabditis_elegans		WBGENE00004165
caenorhabditis_elegans	C27C7.5	WBGENE00007768
caenorhabditis_elegans	F46A8.3	WBGENE00009746
caenorhabditis_elegans	F46A8.4	WBGENE00009747
caenorhabditis_elegans	F46A8.5	WBGENE00009748
caenorhabditis_elegans	F46A8.8	WBGENE00009751
caenorhabditis_elegans		WBGENE00017080
caenorhabditis_elegans		WBGENE00018255
caenorhabditis_elegans		WBGENE00018649
caenorhabditis_elegans		WBGENE00018650
caenorhabditis_elegans		WBGENE00018651
caenorhabditis_elegans		WBGENE00235368

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)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Rattus norvegicus	P38552	88.3%	Diamond
Mus musculus	Q8K419	88.3%	Diamond
Pongo pygmaeus	P79238	88.2%	Diamond
Haemonchus contortus	O44126	85.2%	Diamond
Sus scrofa	Q29058	79.6%	Diamond
Bos taurus	Q3T0D6	77.1%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
LGALS16	protein-coding	148003
LGALS14	protein-coding	56891
MIR6719	ncRNA	102465974
FBL	protein-coding	2091
LEUTX	protein-coding	342900
DYRK1B	protein-coding	9149

Protein

Protein identifiers

Galectin-10 — Q05315 (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)

ID	Name	Type
IPR001079	Galectin_CRD	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR044156	Galectin-like	Family

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.

Substrate	Km (mM)	Measurements
LYSOPHOSPHATIDYLCHOLINE	0.022–0.26	5
1-OLEOYL-2-LYSOPHOSPHATIDYLCHOLINE	0.306–0.75	2
1-PALMITOYL LYSOPHOSPHATIDYLCHOLINE	0.0273–0.19	2
1-PALMITOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	0.0606–0.17	2
PHOSPHATIDYLCHOLINE	0.18–0.63	2
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	1	1
1,2-DIDECANOYLPHOSPHATIDYLCHOLINE	1.1	1
1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	2.9	1
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	0.82	1
1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE	0.19	1
1-(4Z,7Z,10Z,13Z,16Z,19Z)-DOCOSAHEXAENOYL-2-LYSO	0.045	1
1-ACYL-2-OLEOYL-PHOSPHATIDYLCHOLINE	1.6	1
1-ARACHIDONOYL-2-LYSOPHOSPHATIDYLCHOLINE	0.0676	1
1-DOCOSAHEXAENOYL LYSOPHOSPHATIDYLCHOLINE	0.045	1
1-HEXANOYL LYSOPHOSPHATIDYLCHOLINE	0.0992	1

UniProt features (20 total): strand 10, helix 3, initiator methionine 1, chain 1, turn 1, domain 1, site 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

showing 30 of 47 structures by resolution:

PDB	Title	Method	Resolution (Å)
6GKS	X-ray structure determined from recombinant Charcot-Leyden crystal	X-RAY DIFFRACTION	1.38
6QRN	Galectin-10 complexed with ribose	X-RAY DIFFRACTION	1.4
5XRG	Galectin-10/Charcot-Leyden crystal protein crystal structure	X-RAY DIFFRACTION	1.55
5XRH	Galectin-10/Charcot-Leyden crystal protein crystal structure	X-RAY DIFFRACTION	1.55
9UWN	Crystal structure of E33A mutant of human galectin-10 produced by cell-free protein …	X-RAY DIFFRACTION	1.57
9UWP	Crystal structure of human galectin-10 produced by cell-free protein synthesis in complex …	X-RAY DIFFRACTION	1.57
5XRN	Galectin-10/Charcot-Leyden crystal protein variant K73A crystal structure	X-RAY DIFFRACTION	1.6
5XRO	Galectin-10/Charcot-Leyden crystal protein variant Q74A crystal structure	X-RAY DIFFRACTION	1.6
9UWK	Crystal structure of human galectin-10 produced by cell-free protein synthesis	X-RAY DIFFRACTION	1.6
6A1U	Charcot-Leyden crystal protein/Galectin-10 variant E33D	X-RAY DIFFRACTION	1.62
8JAE	Crystal structure of E33A mutant human galectin-10 produced by cell-free protein …	X-RAY DIFFRACTION	1.62
6A1S	Charcot-Leyden crystal protein/Galectin-10 variant E33A	X-RAY DIFFRACTION	1.63
6A1Y	Charcot-Leyden crystal protein/Galectin-10 variant Y35A	X-RAY DIFFRACTION	1.63
9UWO	Crystal structure of human galectin-10 produced by cell-free protein synthesis in complex …	X-RAY DIFFRACTION	1.64
5XRI	Galectin-10/Charcot-Leyden crystal protein-C29A crystal structure	X-RAY DIFFRACTION	1.68
5XRK	Galectin-10/Charcot-Leyden crystal protein variant C57A crystal structure	X-RAY DIFFRACTION	1.7
6L6C	X-ray structure of human galectin-10 in complex with D-arabinose	X-RAY DIFFRACTION	1.77
9UWS	Crystal structure of human galectin-10 produced by cell-free protein synthesis in complex …	X-RAY DIFFRACTION	1.78
1G86	CHARCOT-LEYDEN CRYSTAL PROTEIN/N-ETHYLMALEIMIDE COMPLEX	X-RAY DIFFRACTION	1.8
1HDK	Charcot-Leyden Crystal Protein - pCMBS Complex	X-RAY DIFFRACTION	1.8
1LCL	CHARCOT-LEYDEN CRYSTAL PROTEIN	X-RAY DIFFRACTION	1.8
1QKQ	CHARCOT-LEYDEN CRYSTAL PROTEIN - MANNOSE COMPLEX	X-RAY DIFFRACTION	1.8
6L6B	X-ray structure of human galectin-10 in complex with L-fucose	X-RAY DIFFRACTION	1.8
6L6A	X-ray structure of human galectin-10 in complex with D-mannose	X-RAY DIFFRACTION	1.81
5XRJ	Galectin-10/Charcot-Leyden crystal protein variant H53A crystal structure	X-RAY DIFFRACTION	1.9
6GLW	Structure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal …	X-RAY DIFFRACTION	1.9
6GKU	Structure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal …	X-RAY DIFFRACTION	1.91
6L68	X-ray structure of human galectin-10 in complex with D-allose	X-RAY DIFFRACTION	1.92
8YQC	Galectin-10 C29AC57A	X-RAY DIFFRACTION	1.92
6L6D	X-ray structure of human galectin-10 in complex with D-N-acetylgalactosamine	X-RAY DIFFRACTION	1.93

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q05315-F1	96.95	0.96

Antibody-complex structures (SAbDab)

3 antibodies co-crystallized with this protein: 6GKU, 6GLW, 6GLX

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH enhanced

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)

Position	Role
136	not glycosylated

Post-translational modifications (1)

Type	Positions
N-acetylserine	2

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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 (2): cytosol (GO:0005829), extracellular matrix (GO:0031012)

GO top-level categories

14 GO namespaces:

Category	Terms
binding	2
regulation of T cell tolerance induction	1
T cell anergy	1
regulation of lymphocyte anergy	1
T cell cytokine production	1
regulation of T cell mediated immunity	1
regulation of cytokine production involved in immune response	1
regulation of T cell proliferation	1
activated T cell proliferation	1
lymphocyte apoptotic process	1
protein binding	1
cytoplasm	1
cellular anatomical structure	1
external encapsulating structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 7 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

7 experimentally-supported GO terms:

GO term	NS	Evidence
T cell apoptotic process	BP	direct assay
regulation of T cell anergy	BP	mutant phenotype
regulation of T cell cytokine production	BP	mutant phenotype
regulation of activated T cell proliferation	BP	mutant phenotype
cytosol	CC	direct assay
extracellular matrix	CC	high-throughput assay
identical protein binding	MF	physical interaction

Protein interactions and networks

STRING

showing 15 of 526 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLC	GALE	Q14376	926
CLC	LGALS2	P05162	919
CLC	LGALS3	P17931	880
CLC	GALK1	P51570	828
CLC	LGALS12	Q96DT0	668
CLC	LGALS4	P56470	659
CLC	RNASE2	P10153	606
CLC	EPX	P11678	580
CLC	RNASE3	P12724	574
CLC	CHD7	Q9P2D1	569
CLC	LGALS1	P09382	499
CLC	ISYNA1	Q9NPH2	497
CLC	ADH1A	P07327	490
CLC	PAICS	P22234	464
CLC	PRG2	P13727	442

Disease & clinical

Genetic variants

Variant evidence for CLC: 16 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	0
Benign	2

AlphaMissense

129 missense substitutions predicted likely pathogenic (of 937 scored), across 52 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
W72	7	0.778	0.860
F112	6	0.799	0.939
F89	5	0.889	0.951
F83	5	0.861	0.911
F40	5	0.837	0.892
F52	5	0.814	0.895
F58	5	0.795	0.913
Y100	5	0.792	0.878
G24	4	0.793	0.834
F54	4	0.779	0.783
D39	4	0.672	0.731
M64	4	0.647	0.665
F135	4	0.639	0.657
F30	3	0.866	0.866
I22	3	0.814	0.838
I93	3	0.812	0.847
S66	3	0.810	0.810
N65	3	0.777	0.793
L91	3	0.748	0.788
N105	3	0.731	0.807

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Rectum Adenocarcinoma)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Rectum Adenocarcinoma (validation)	favorable	0.000109
Pancreatic Adenocarcinoma (validation)	unfavorable	0.000205
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA)	unfavorable	0.000603

Disease associations

OMIM: gene MIM:153310 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Arsenic Trioxide	increases expression	2
bisphenol F	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
coumarin	affects phosphorylation	1
pentanal	increases expression	1
di-n-butylphosphoric acid	affects expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Aspirin	affects response to substance	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	decreases expression	1
Iron	decreases expression	1
Ozone	affects expression, increases abundance	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.