LECT2

gene
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Also known as chm-IIchm2

Summary

LECT2 (leukocyte cell derived chemotaxin 2, HGNC:6550) is a protein-coding gene on chromosome 5q31.1, encoding Leukocyte cell-derived chemotaxin-2 (O14960). Has a neutrophil chemotactic activity.

This gene encodes a secreted, 16 kDa protein that acts as a chemotactic factor to neutrophils and stimulates the growth of chondrocytes and osteoblasts. This protein has high sequence similarity to the chondromodulin repeat regions of the chicken myb-induced myeloid 1 protein. A polymorphism in this gene may be associated with rheumatoid arthritis.

Source: NCBI Gene 3950 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 20 total
  • MANE Select transcript: NM_002302

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6550
Approved symbolLECT2
Nameleukocyte cell derived chemotaxin 2
Location5q31.1
Locus typegene with protein product
StatusApproved
Aliaseschm-II, chm2
Ensembl geneENSG00000145826
Ensembl biotypeprotein_coding
OMIM602882
Entrez3950

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000274507, ENST00000471827, ENST00000512872, ENST00000514447, ENST00000522943

RefSeq mRNA: 1 — MANE Select: NM_002302 NM_002302

CCDS: CCDS4190

Canonical transcript exons

ENST00000274507 — 4 exons

ExonStartEnd
ENSE00000972531135952871135952967
ENSE00001044316135954788135954983
ENSE00001124654135946904135947497
ENSE00003472464135951223135951368

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 98.35.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3041 / max 139.7830, expressed in 7 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
635640.16877
635670.05227
635650.03216
635660.02726
2036980.02406

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233698.35gold quality
liverUBERON:000210795.99gold quality
right lobe of liverUBERON:000111495.26gold quality
spermCL:000001982.63silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.46gold quality
male germ cellCL:000001580.56silver quality
right testisUBERON:000453476.58gold quality
left testisUBERON:000453376.26gold quality
testisUBERON:000047374.77gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099171.33gold quality
adrenal tissueUBERON:001830369.64gold quality
olfactory bulbUBERON:000226464.69gold quality
metanephros cortexUBERON:001053363.32gold quality
right adrenal gland cortexUBERON:003582760.27gold quality
mucosa of stomachUBERON:000119958.79gold quality
lower esophagus mucosaUBERON:003583457.17gold quality
right adrenal glandUBERON:000123356.65gold quality
endothelial cellCL:000011555.24gold quality
cortex of kidneyUBERON:000122555.06gold quality
metanephrosUBERON:000008154.29gold quality
prostate glandUBERON:000236753.71gold quality
apex of heartUBERON:000209853.35gold quality
nucleus accumbensUBERON:000188253.21gold quality
adrenal cortexUBERON:000123552.92gold quality
caudate nucleusUBERON:000187352.82gold quality
left adrenal glandUBERON:000123452.58gold quality
olfactory segment of nasal mucosaUBERON:000538652.45gold quality
adult mammalian kidneyUBERON:000008252.42gold quality
adrenal glandUBERON:000236952.22gold quality
putamenUBERON:000187452.12gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes2.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNB1, FOXN1, MBD2

miRNA regulators (miRDB)

26 targeting LECT2, 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-4668-3P100.0068.742635
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-511-3P99.9968.851467
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-539-5P99.9370.302855
HSA-MIR-469899.8471.414303
HSA-MIR-205299.7969.372031
HSA-MIR-58699.6570.402051
HSA-MIR-57899.4668.361787
HSA-MIR-425199.4069.193363
HSA-MIR-542-3P99.3467.581270
HSA-MIR-450499.1069.141328
HSA-MIR-10B-3P99.0466.98988
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-442498.9170.331145
HSA-MIR-4709-3P98.8868.041594
HSA-MIR-463598.7467.631339
HSA-MIR-96-3P97.4768.03839
HSA-MIR-7161-3P96.7968.79798
HSA-MIR-1225-5P96.7666.85417
HSA-MIR-6857-3P96.7065.43915
HSA-MIR-1236-5P96.6266.38856
HSA-MIR-425696.2267.70669
HSA-MIR-75996.1666.77873
HSA-MIR-11181-5P96.1267.46665

Literature-anchored findings (GeneRIF, showing 40)

  • LECT2, which encodes a protein with chemotactic properties for human neutrophils, is a direct target gene of Wnt/beta-catenin signaling in the liver. (PMID:15239100)
  • LECT2 participates in liver regeneration and injury following hepatectomy. (PMID:15561248)
  • Serum LECT2 levels may be a prognostic indicator of recovery from liver failure. (PMID:15561249)
  • LECT2-associated renal amyloidosis represents a unique and perhaps not uncommon disease, especially in Mexican Americans. (PMID:20951486)
  • Re-expression of LECT2 significantly reduced the migration and invasion of human hepatocellular carcinoma cells in vitro and significantly reduced their growth in vivo. (PMID:21394108)
  • preliminary X-ray analysis of human leukocyte cell-derived chemotaxin 2 (LECT2). (PMID:23519812)
  • These findings reveal a novel, specific inhibitory function of LECT2 in hepatocellular carcinoma by the direct binding and inactivation of MET. (PMID:24114941)
  • The study indicates that serum LECT2 levels are increased by obesity and fatty liver, and suggests that LECT2 is a novel obesity-related protein. (PMID:24390366)
  • ALect2 is a common cause of hepatic amyloidosis in the population of the United States, and subtyping hepatic amyloid deposits by an accurate analytic method such as MS is required for optimal clinical management of hepatic amyloidosis patients (PMID:24415538)
  • Amyloidosis derived from leukocyte chemotactic factor 2 (ALECT2) is a recently described disease. Here, we report the characteristics and outcome of 72 patients with renal ALECT2, which included 19 who had another kidney disease on biopsy. (PMID:24451324)
  • These results demonstrate the involvement of LECT2 in glucose metabolism and suggest that LECT2 may be a therapeutic target for obesity-associated insulin resistance. (PMID:24478397)
  • There were no mutations detected in the LECT2 gene, although all renal leukocyte chemotactic factor 2 amyloidosis patients tested were homozygous for the G nucleotide in a non-synonymous SNP at position 172. (PMID:24522497)
  • The data from this study show that weak LECT2 staining should be regarded as indeterminate or a negative result and does not per se allow diagnosis of specific amyloid type. The diagnosis of LECT2 renal amyloidosis may require LMD/MS confirmation. (PMID:24792621)
  • LECT2 is regulated by beta-catenin in HCC in both mice and men, but serum LECT2 reflects beta-catenin activity only in mice. Serum LECT2 could be a potential biomarker of HCC in patients. (PMID:24892551)
  • First Nations people from British Columbia who presented with chronic kidney disease, were found to be due to LECT2 amyloidosis. (PMID:25064673)
  • LECT2 immunostain is useful in confirming subtype of amyloid within the liver in ALECT2.. (PMID:25602789)
  • Localized LECT2 amyloidosis of the adrenal gland with coexisting MGUS: a diagnostic challenge. (PMID:26048244)
  • ALECT2, which was initially thought to affect mainly Hispanics in the United States, appears to represent an important and likely underrecognized etiology of chronic kidney disease among Egyptians and probably in other ethnic groups around the world (PMID:26867784)
  • LECT2 amyloidosis is prevalent among Hispanic decedents in New Mexico. (PMID:26912093)
  • LECT2 was found to be catalytically inactive as a metalloendopeptidase against various types of peptide sequences, including pentaglycine. (PMID:27334921)
  • findings indicated that serum LECT2 level is negatively associated with the presence of diabetic retinopathy and suggest that low circulating LECT2 level is a risk factor for diabetic retinopathy (PMID:27816666)
  • the tissue levels of THBS2 and LECT-2 may correlate with the stage of atherosclerosis. (PMID:28039493)
  • VFA was the strongest predictor of plasma LECT2 that is a potential biomarker linking visceral obesity to dyslipidemia (PMID:28278265)
  • Circulating LECT2 concentrations were increased in individuals with NAFLD and those with MetS, but not in those with atherosclerosis. The relationship between LECT2 and both NAFLD and MetS might be mediated by its association with abdominal obesity and lipid metabolism. (PMID:28376109)
  • Overexpression of LECT2 or treatment with a recombinant LECT2 protein impaired the colony-forming ability and motility of non-small cell lung cancer cells harboring high levels of activated EGFR and MET. (PMID:30453282)
  • Data indicate the explicit amyloidogenic core of human leukocyte chemotactic factor 2 (LECT2) and pinpoints regions with distinct amyloidogenic properties. (PMID:31170474)
  • This study reports novel findings on the important role of LECT2/Tie1 signaling in pathogenesis of liver fibrosis and the underlying mechanisms. The serum LECT2 level may represent a potential diagnostic marker for liver fibrosis, and more importantly, LECT2 may serve as a potential therapeutic target for liver fibrosis. (PMID:31474362)
  • Down-regulation of LECT2 promotes osteogenic differentiation of MSCs via activating Wnt/beta-catenin pathway. (PMID:32763823)
  • Plasma half-life and tissue distribution of leukocyte cell-derived chemotaxin 2 in mice. (PMID:32764719)
  • Leukocyte cell-derived chemotaxin 2 promotes the development of nonalcoholic fatty liver disease through STAT-1 pathway in mice. (PMID:33555112)
  • Loss of bound zinc facilitates amyloid fibril formation of leukocyte-cell-derived chemotaxin 2 (LECT2). (PMID:33617884)
  • Plasma Leukocyte Cell-Derived Chemotaxin 2 (LECT2) as a Risk Factor of Coronary Artery Disease: A Cross-Sectional Study. (PMID:34318706)
  • Serum leukocyte cell-derived chemotaxin 2 level is associated with atopic dermatitis patients. (PMID:34763463)
  • Endoplasmic reticulum stress increases LECT2 expression via ATF4. (PMID:34808500)
  • Adipose tissue LECT2 expression is associated with obesity and insulin resistance in Korean women. (PMID:35722819)
  • Serum Leukocyte Cell-Derived Chemotaxin 2 (LECT2) Level Is Associated with Osteoporosis. (PMID:35976970)
  • Leukocyte cell-derived chemotaxin 2 regulates epithelial-mesenchymal transition and cancer stemness in hepatocellular carcinoma. (PMID:36055405)
  • Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core. (PMID:37657439)
  • Leukocyte cell-derived chemotaxin 2 correlates with pediatric non-alcoholic fatty liver disease. (PMID:37877453)
  • Role of LECT2 in exacerbating atopic dermatitis: insight from in vivo and in vitro models via NF-kappaB signaling pathway. (PMID:39206203)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriolect2.1ENSDARG00000033227
danio_reriolect2.3ENSDARG00000086483
danio_reriolect2.2ENSDARG00000090889
mus_musculusLect2ENSMUSG00000021539
rattus_norvegicusLect2ENSRNOG00000012189
caenorhabditis_elegansWBGENE00019407

Protein

Protein identifiers

Leukocyte cell-derived chemotaxin-2O14960 (reviewed: O14960)

All UniProt accessions (4): D6RD58, D6RGX8, E5RHW6, O14960

UniProt curated annotations — full annotation on UniProt →

Function. Has a neutrophil chemotactic activity. Also a positive regulator of chondrocyte proliferation. Does not show metalloendopeptidase activity.

Subunit / interactions. Interacts with MET.

Subcellular location. Cytoplasm. Secreted.

Tissue specificity. Highly expressed in adult and fetal liver and weakly in testis. Not expressed in bone marrow.

Induction. By phytohemagglutinin (PHA).

Similarity. Belongs to the LECT2/MIM-1 family.

RefSeq proteins (1): NP_002293* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008663LECT2Family
IPR011055Dup_hybrid_motifHomologous_superfamily
IPR016047M23ase_b-sheet_domDomain
IPR017381LECT2_chordataFamily

Pfam: PF01551

UniProt features (22 total): strand 10, binding site 3, disulfide bond 3, helix 2, signal peptide 1, chain 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
7N2IELECTRON CRYSTALLOGRAPHY1.4
5B0HX-RAY DIFFRACTION1.94
9WL6ELECTRON MICROSCOPY1.95
9WL5ELECTRON MICROSCOPY1.96
9NONELECTRON MICROSCOPY2.4
8G2VELECTRON MICROSCOPY2.71
9WL7ELECTRON MICROSCOPY2.93
9WL9ELECTRON MICROSCOPY3.05
9WL8ELECTRON MICROSCOPY3.09

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O14960-F192.820.85

Functional residue map

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

Ligand- & substrate-binding residues (3): 53; 57; 138

Disulfide bonds (3): 25–60, 36–41, 99–142

Mutagenesis-validated functional residues (1):

PositionPhenotype
104no metalloendopeptidase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_SKELETAL_SYSTEM_DEVELOPMENT, LEE_LIVER_CANCER_CIPROFIBRATE_DN, MORF_RAD51L3, GOBP_TAXIS, MORF_CTSB, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, GATA6_01, MORF_IL4, MORF_PRKCA, GNF2_HPX, MODULE_88, PU1_Q6, LEE_LIVER_CANCER_ACOX1_DN, LEE_LIVER_CANCER_E2F1_DN, HNF1_01

GO Biological Process (2): skeletal system development (GO:0001501), chemotaxis (GO:0006935)

GO Molecular Function (3): identical protein binding (GO:0042802), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
system development1
response to chemical1
taxis1
protein binding1
cation binding1
binding1
intracellular anatomical structure1

Protein interactions and networks

STRING

720 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LECT2CNMDO75829910
LECT2TIE1P35590752
LECT2CEBPAP49715530
LECT2SELENOPP49908507
LECT2AHSGP02765503
LECT2ANGPTL6Q8NI99496
LECT2FGL1Q08830469
LECT2SAA1P02735450
LECT2FGF21Q9NSA1434
LECT2SAA1P02735428
LECT2A0A096LPE2A0A096LPE2410
LECT2SAA4P35542409
LECT2TXNDC15Q96J42377
LECT2GLULP15104370
LECT2ENHOQ6UWT2370

IntAct

9 interactions, top by confidence:

ABTypeScore
LECT2LECT2psi-mi:“MI:0407”(direct interaction)0.440
LECT2NPM1psi-mi:“MI:0915”(physical association)0.400
LECT2RSL1D1psi-mi:“MI:0915”(physical association)0.400
LECT2psi-mi:“MI:0915”(physical association)0.400
LECT2ITIH2psi-mi:“MI:0914”(association)0.350
LECT2APODpsi-mi:“MI:0914”(association)0.350

BioGRID (23): RSL1D1 (Proximity Label-MS), NPM1 (Proximity Label-MS), THUMPD3 (Affinity Capture-MS), GID4 (Affinity Capture-MS), RMND5A (Affinity Capture-MS), WDR26 (Affinity Capture-MS), AKAP11 (Affinity Capture-MS), DICER1 (Affinity Capture-MS), ITIH2 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS), UBAC1 (Affinity Capture-MS), MKLN1 (Affinity Capture-MS), MAEA (Affinity Capture-MS), RNF123 (Affinity Capture-MS), CSPG4 (Affinity Capture-MS)

ESM2 similar proteins: A0A0W0FPC8, A1CC33, B8N7Z6, C0JAR9, C0JAS1, C0JAS2, C0JAS3, C0JAS4, C0JAU4, C0JAU8, C0JAU9, C0JAX5, D4AUH1, O14960, O62644, O88803, P08940, P45582, P48981, P49676, Q00662, Q10NX8, Q10RB4, Q2FYD8, Q2U1H5, Q2UI81, Q4R1C4, Q4ZD58, Q67VU7, Q6DW73, Q6ZJJ0, Q75HQ3, Q7G3T8, Q875I9, Q8GX69, Q8NK76, Q8W0A1, Q8WPJ2, Q9C6W4, Q9FN08

Diamond homologs: O14960, O62644, O88803, P08940

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance15
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

374 predictions. Top by Δscore:

VariantEffectΔscore
5:135951366:CTT:Cacceptor_gain0.9900
5:135951374:A:Cacceptor_gain0.9900
5:135952968:C:CCacceptor_gain0.9900
5:135954781:GACTT:Gdonor_loss0.9900
5:135954782:ACTTA:Adonor_loss0.9900
5:135954783:CTTAC:Cdonor_loss0.9900
5:135954784:TTAC:Tdonor_loss0.9900
5:135954785:TACCG:Tdonor_loss0.9900
5:135954786:A:ACdonor_gain0.9900
5:135954786:ACCGG:Adonor_loss0.9900
5:135954787:C:CCdonor_gain0.9900
5:135951209:TC:Tdonor_gain0.9800
5:135951210:CC:Cdonor_gain0.9800
5:135951217:TCTTA:Tdonor_loss0.9800
5:135951218:CTTA:Cdonor_loss0.9800
5:135951219:TTAC:Tdonor_loss0.9800
5:135951220:TACCT:Tdonor_loss0.9800
5:135951221:A:AGdonor_loss0.9800
5:135951222:C:Tdonor_loss0.9800
5:135951222:CCT:Cdonor_gain0.9800
5:135951374:A:ACacceptor_gain0.9800
5:135952965:GTGC:Gacceptor_gain0.9800
5:135952966:TGCT:Tacceptor_gain0.9800
5:135952966:TGCTA:Tacceptor_loss0.9800
5:135952967:GCTA:Gacceptor_gain0.9800
5:135952967:GCTAA:Gacceptor_loss0.9800
5:135951367:TT:Tacceptor_gain0.9700
5:135951369:C:CCacceptor_gain0.9700
5:135952963:CAGTG:Cacceptor_gain0.9700
5:135952964:AGTGC:Aacceptor_gain0.9700

AlphaMissense

977 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:135951302:G:CF70L0.986
5:135951302:G:TF70L0.986
5:135951304:A:GF70L0.986
5:135951332:G:CC60W0.977
5:135951240:A:TV91D0.976
5:135951333:C:GC60S0.973
5:135951334:A:TC60S0.973
5:135951303:A:GF70S0.972
5:135951334:A:GC60R0.971
5:135951333:C:TC60Y0.970
5:135952951:C:AW21C0.968
5:135952951:C:GW21C0.968
5:135951303:A:CF70C0.966
5:135947362:C:GC142S0.965
5:135947363:A:TC142S0.965
5:135947425:C:TG121E0.963
5:135951309:G:TA68E0.963
5:135952940:C:GC25S0.961
5:135952941:A:TC25S0.961
5:135951315:A:TV66E0.960
5:135947371:A:TI139N0.959
5:135947488:A:TV100D0.959
5:135947426:C:GG121R0.958
5:135947426:C:TG121R0.958
5:135947428:A:TL120H0.956
5:135951243:C:TG90D0.955
5:135947377:A:TV137E0.954
5:135951343:C:GD57H0.952
5:135947381:G:CH136D0.951
5:135951342:T:AD57V0.951

dbSNP variants (sampled 300 via entrez): RS1000208019 (5:135953801 T>G), RS1000845122 (5:135951721 GAAA>G,GAAAA), RS1001107852 (5:135948319 A>G), RS1001319621 (5:135951094 A>G), RS1001478138 (5:135956846 C>G,T), RS1001884041 (5:135955287 C>T), RS1002380151 (5:135949458 C>G), RS1002481269 (5:135955605 C>T), RS1002757129 (5:135949774 G>A), RS1002803129 (5:135946679 A>G), RS1002860235 (5:135954693 A>G), RS1003060117 (5:135952082 A>G), RS1003190451 (5:135955899 T>C), RS1003396525 (5:135952383 C>G), RS1003783104 (5:135950299 C>T)

Disease associations

OMIM: gene MIM:602882 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006585_2537Blood protein levels4.000000e-33

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2107506LECT20.000

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

ChemicalActions (top 5)PubMed papers
pirinixic acidaffects binding, decreases expression, increases activity1
Acetaminophendecreases expression1
Diethylhexyl Phthalateincreases expression1
Rotenoneincreases expression1
Tetrachlorodibenzodioxinaffects expression1
Valproic Aciddecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1decreases 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.