LCN1

gene
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Also known as VEGPTPPMFAMGC71975TLC

Summary

LCN1 (lipocalin 1, HGNC:6525) is a protein-coding gene on chromosome 9q34.3, encoding Lipocalin-1 (P31025). Could play a role in taste reception.

This gene encodes a member of the lipocalin family of small secretory proteins. Lipocalins are extracellular transport proteins that bind to a variety of hydrophobic ligands. The encoded protein is the primary lipid binding protein in tears and is overproduced in response to multiple stimuli including infection and stress. The encoded protein may be a marker for chromosome aneuploidy as well as an autoantigen in Sjogren’s syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and two pseudogenes of this gene are also located on the long arm of chromosome 9.

Source: NCBI Gene 3933 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_002297

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6525
Approved symbolLCN1
Namelipocalin 1
Location9q34.3
Locus typegene with protein product
StatusApproved
AliasesVEGP, TP, PMFA, MGC71975, TLC
Ensembl geneENSG00000160349
Ensembl biotypeprotein_coding
OMIM151675
Entrez3933

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000263598, ENST00000371781

RefSeq mRNA: 4 — MANE Select: NM_002297 NM_001252617, NM_001252618, NM_001252619, NM_002297

CCDS: CCDS6991

Canonical transcript exons

ENST00000371781 — 7 exons

ExonStartEnd
ENSE00000828353135525132135525158
ENSE00000828356135523232135523302
ENSE00001347956135526344135526540
ENSE00001456083135521440135521587
ENSE00002339178135524830135524931
ENSE00002369877135522047135522177
ENSE00002380392135523880135523990

Expression profiles

Bgee: expression breadth broad, 90 present calls, max score 96.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 34.3130 / max 54044.1745, expressed in 39 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
9944634.313039

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lacrimal glandUBERON:000181796.88gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.54silver quality
buccal mucosa cellCL:000233679.49silver quality
tongueUBERON:000172377.41gold quality
body of tongueUBERON:001187677.08gold quality
endometrium epitheliumUBERON:000481175.15gold quality
paraflocculusUBERON:000535172.87gold quality
triceps brachiiUBERON:000150972.79gold quality
frontal poleUBERON:000279572.51gold quality
gluteal muscleUBERON:000200072.42gold quality
middle frontal gyrusUBERON:000270271.89silver quality
superior surface of tongueUBERON:000737169.69gold quality
olfactory segment of nasal mucosaUBERON:000538667.65gold quality
Brodmann (1909) area 10UBERON:001354165.28gold quality
parotid glandUBERON:000183165.24gold quality
trabecular bone tissueUBERON:000248362.37gold quality
cerebellar vermisUBERON:000472062.37gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450262.17gold quality
heart right ventricleUBERON:000208061.92gold quality
nasal cavity mucosaUBERON:000182661.37gold quality
tendon of biceps brachiiUBERON:000818860.89gold quality
deltoidUBERON:000147660.46gold quality
quadriceps femorisUBERON:000137760.15gold quality
biceps brachiiUBERON:000150759.00gold quality
nasal cavity epitheliumUBERON:000538459.00gold quality
vastus lateralisUBERON:000137958.94gold quality
deciduaUBERON:000245058.24gold quality
diaphragmUBERON:000110358.03gold quality
myocardiumUBERON:000234957.95gold quality
vena cavaUBERON:000408756.45gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting LCN1, 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-449299.8768.253611
HSA-MIR-451699.6167.783390
HSA-MIR-613299.6065.831554
HSA-MIR-76299.5866.611994
HSA-MIR-449899.4767.422360
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-7160-5P99.1167.172207
HSA-MIR-465199.0667.572002
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-125798.9768.021133
HSA-MIR-60898.9367.832013
HSA-MIR-6829-5P98.8665.121480
HSA-MIR-465698.7966.221306
HSA-MIR-3928-5P98.5067.48980
HSA-MIR-6806-3P98.5067.31980
HSA-MIR-93-3P98.1566.651309
HSA-MIR-146B-3P97.8365.29782
HSA-MIR-467597.6964.82774
HSA-MIR-474197.6964.14883
HSA-MIR-939-5P97.1065.801579
HSA-MIR-1343-5P96.4866.061506
HSA-MIR-447195.1166.84755

Literature-anchored findings (GeneRIF, showing 26)

  • The N-terminal part of recombinant human tear lipocalin/von Ebner’s gland protein confers cysteine proteinase inhibition depending on the presence of the entire cystatin-like sequence motifs. (PMID:11727836)
  • Lcn-1 is specifically produced by corticotrophs (PMID:11850445)
  • LIMR mediating internalization of lipocalin-1 (Lcn-1) in NT2 cells, leading to its degradation. (PMID:12591932)
  • structure, function, and mechanism of action [review] (PMID:12613960)
  • Tear lipocalin is probable protein carrier for vitamin E tears and is candidate to specifically deliver vitamin E as antioxidant to corneal epithelium. (PMID:12613961)
  • Tear surface tension depends partly on presence of tear lipocalin/lipid complex. Tear proteins and lipid-free tear lipocalin lower surface tension. (PMID:12613963)
  • pH-driven ligand release involves ionization changes in several titratable residues associated with CD and EF loop apposition and occlusion of the calyx (PMID:15461462)
  • structural analysis sheds new light on the ligand binding activity of this functionally obscure but abundant human lipocalin (PMID:15489503)
  • Lipocalin is a novel autoantigen target in Sjogren’s syndrome. (PMID:16249071)
  • Hydrodynamic and solution properties of lipocalin from human tears show that the protein size and topology are the major determinants of rotational correlation time and a reason for deviation from the Stokes-Einstein relationship. (PMID:17869594)
  • Selective displacement of ANS molecules from the ANS-apoTL complex by stearic acid discriminates the internal and external binding sites. (PMID:17945179)
  • Tear lipocalin is the principal endonuclease in human tear fluid. (PMID:18334931)
  • Results suggest that the excited protein states in tear lipocalin are not unique but consist of many substates. (PMID:19586017)
  • Tear lipocalin with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2(1) with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 A resolution. (PMID:19770509)
  • Study has identified the first protein, lipocalin-1, in the secretome of human blastocysts that is associated with chromosome aneuploidy. (PMID:21324447)
  • The conserved disulfide bond of human tear lipocalin modulates conformation and lipid binding in a ligand selective manner.( (PMID:21466861)
  • Tear lipocalin (TLC) is a major protein in tears and has a large ligand-binding cavity that allows the lipocalin to bind an extensive and diverse set of lipophilic molecules. (PMID:21791187)
  • Serum concentrations of LCN1 and LCN2 were both elevated in patients with COPD. (PMID:24920892)
  • Tear lysozyme, lactoferrin and lipocalin concentrations were determined via electrophoresis and the results for patients with or without eyelid tumors were compared. (PMID:25914748)
  • Human neutrophil lipocalin (HNL) concentrations in serum or whole blood activated by formyl-methionine-leucine-phenylalanine (fMLP) were shown to distinguish acute infections of bacterial or viral cause with high accuracy. (PMID:26135974)
  • the crosstalk of dendritic cells with lipocalins alone has the potential to direct the type of immune response to these particular antigens. (PMID:26218644)
  • the possible relationship between ocular symptomatology, tear volume and tear break-up time (TBUT) and lipocalin, lactoferrin and lysozyme concentrations in the tear film were explored in a group of symptomatic dry-eyed postmenopausal (PM) women. (PMID:26366224)
  • At the relatively small concentrations in tears, all ceramides were complexed to tear lipocalin. (PMID:29331331)
  • The expression of LCN1 increased gradually from stage 1 to stage 4 in breast cancer patients. (PMID:31424267)
  • Lipocalin-1 is the acceptor protein for phospholipid transfer protein in tears. (PMID:33631671)
  • Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer. (PMID:35995384)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
rattus_norvegicusENSRNOG00000074004
rattus_norvegicusENSRNOG00000085594

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), OBP2A (ENSG00000122136), LCN2 (ENSG00000148346), LCN9 (ENSG00000148386), OBP2B (ENSG00000171102), LCN15 (ENSG00000177984), LCN12 (ENSG00000184925), LCN10 (ENSG00000187922), LCN8 (ENSG00000204001), LCNL1 (ENSG00000214402), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Lipocalin-1P31025 (reviewed: P31025)

Alternative names: Tear lipocalin, Tear prealbumin, von Ebner gland protein

All UniProt accessions (1): P31025

UniProt curated annotations — full annotation on UniProt →

Function. Could play a role in taste reception. Could be necessary for the concentration and delivery of sapid molecules in the gustatory system. Can bind various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampicin and even to microbial siderophores. Exhibits an extremely wide ligand pocket.

Subunit / interactions. Predominantly monomer. May form homodimer. Interacts with LMBR1L; this interaction mediates the endocytosis of LCN1.

Subcellular location. Secreted.

Tissue specificity. Mainly expressed in lachrymal and salivary glands. Also expressed in the prostate.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

RefSeq proteins (4): NP_001239546, NP_001239547, NP_001239548, NP_002288* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000566Lipocln_cytosolic_FA-bd_domDomain
IPR002345LipocalinFamily
IPR002450von_Ebner_glandFamily
IPR012674CalycinHomologous_superfamily

Pfam: PF00061

UniProt features (20 total): strand 14, helix 2, signal peptide 1, chain 1, disulfide bond 1, turn 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
1XKIX-RAY DIFFRACTION1.8
4QAFX-RAY DIFFRACTION1.8
3EYCX-RAY DIFFRACTION2.6
5T43SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P31025-F188.760.72

Functional residue map

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

Disulfide bonds (1): 79–171

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-804914Transport of fatty acids
R-HSA-382551Transport of small molecules
R-HSA-425397Transport of vitamins, nucleosides, and related molecules
R-HSA-425407SLC-mediated transmembrane transport

MSigDB gene sets: 46 (showing top): GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, GOBP_SENSORY_PERCEPTION_OF_TASTE, GOBP_SENSORY_PERCEPTION, GOMF_SIGNALING_RECEPTOR_BINDING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_REGULATOR_ACTIVITY, GOMF_ENZYME_INHIBITOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, GOMF_CYSTEINE_TYPE_ENDOPEPTIDASE_INHIBITOR_ACTIVITY, GOMF_CHLORIDE_ION_BINDING, GOMF_ENDOPEPTIDASE_REGULATOR_ACTIVITY, REACTOME_TRANSPORT_OF_SMALL_MOLECULES, CTIP_DN.V1_DN, REACTOME_TRANSPORT_OF_FATTY_ACIDS

GO Biological Process (2): proteolysis (GO:0006508), sensory perception of taste (GO:0050909)

GO Molecular Function (6): cysteine-type endopeptidase inhibitor activity (GO:0004869), signaling receptor binding (GO:0005102), zinc ion binding (GO:0008270), chloride ion binding (GO:0031404), protein binding (GO:0005515), small molecule binding (GO:0036094)

GO Cellular Component (2): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Transport of vitamins, nucleosides, and related molecules1
SLC-mediated transmembrane transport1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
protein metabolic process1
sensory perception of chemical stimulus1
cysteine-type endopeptidase activity1
endopeptidase inhibitor activity1
protein binding1
transition metal ion binding1
anion binding1
cellular anatomical structure1

Protein interactions and networks

STRING

738 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LCN1LMBR1LQ6UX01946
LCN1LTFP02788922
LCN1CST4P01036891
LCN1LCN2P30150858
LCN1LACRTQ9GZZ8851
LCN1APODP05090851
LCN1PAEPP09466839
LCN1C8GP07360794
LCN1WNT8BQ93098794
LCN1LYZL1Q6UWQ5787
LCN1KIF22Q14807780
LCN1PTGDSP41222764
LCN1LYZP00695715
LCN1RBP4P02753692
LCN1ORM1P02763668

IntAct

78 interactions, top by confidence:

ABTypeScore
Cdca5RAD21psi-mi:“MI:0915”(physical association)0.670
NKAPNOS1APpsi-mi:“MI:0914”(association)0.660
KLHL22METTL15psi-mi:“MI:0914”(association)0.640
NPHP4BAG2psi-mi:“MI:0914”(association)0.610
LCN1PDYNpsi-mi:“MI:0915”(physical association)0.590
RECKLCN1psi-mi:“MI:0915”(physical association)0.560
LCN1UBQLN2psi-mi:“MI:0915”(physical association)0.560
FAM25CLCN1psi-mi:“MI:0915”(physical association)0.560
ALOX5LCN1psi-mi:“MI:0915”(physical association)0.560
LCN1RECKpsi-mi:“MI:0915”(physical association)0.560
DARS2GAPDHSpsi-mi:“MI:0914”(association)0.560
DDX31IGLL5psi-mi:“MI:0914”(association)0.530
HBMSCGB2A1psi-mi:“MI:0914”(association)0.530
DNAJB8SCGB2A1psi-mi:“MI:0914”(association)0.530
PECRLCN1psi-mi:“MI:0914”(association)0.530
ARMC6SLC27A2psi-mi:“MI:0914”(association)0.530
KISS1RERLIN1psi-mi:“MI:0915”(physical association)0.400
SPATA4LCN1psi-mi:“MI:0915”(physical association)0.400
ALKBH2LCN1psi-mi:“MI:0915”(physical association)0.400
STK4ANXA2P2psi-mi:“MI:0914”(association)0.350
UBE3ATXNL1psi-mi:“MI:0914”(association)0.350
UBE3AIGLC7psi-mi:“MI:0914”(association)0.350
SNX27IGLL5psi-mi:“MI:0914”(association)0.350
TDRKHGGCTpsi-mi:“MI:0914”(association)0.350

BioGRID (117): LCN1 (Affinity Capture-MS), PDYN (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), PDYN (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS)

ESM2 similar proteins: B3EY83, B5X0G2, H2B3G5, O02853, O09114, O18873, O97921, P02758, P02761, P04119, P07380, P09466, P11588, P11672, P13613, P19647, P20289, P22057, P30152, P31025, P33685, P33686, P33687, P33688, P41222, P41244, P53715, P62502, P62503, P80188, Q28388, Q29095, Q29487, Q29562, Q5VSP4, Q6JVE6, Q6JVL5, Q6UWW0, Q810Z1, Q8K1H9

Diamond homologs: O18873, P20289, P20462, P31025, P41244, P53715, Q29144, Q5VSP4, Q62471, Q62472, Q8K1H9, Q8SQ30, Q9NPH6, Q9NY56, P02755, P02756, Q8WX39, P07380

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1199 predictions. Top by Δscore:

VariantEffectΔscore
9:135521584:GGAT:Gdonor_gain1.0000
9:135521585:G:GTdonor_gain1.0000
9:135521585:GAT:Gdonor_gain1.0000
9:135521588:G:GGdonor_gain1.0000
9:135521603:G:GTdonor_gain1.0000
9:135521603:G:Tdonor_gain1.0000
9:135522158:G:GTdonor_gain1.0000
9:135522174:TGCT:Tdonor_gain1.0000
9:135522175:GCT:Gdonor_gain1.0000
9:135522175:GCTG:Gdonor_gain1.0000
9:135522176:CTG:Cdonor_loss1.0000
9:135522177:TGT:Tdonor_loss1.0000
9:135522178:G:Cdonor_loss1.0000
9:135522178:G:GGdonor_gain1.0000
9:135522179:TGAG:Tdonor_loss1.0000
9:135523298:GGCCG:Gdonor_gain1.0000
9:135523299:GCCG:Gdonor_gain1.0000
9:135523299:GCCGG:Gdonor_gain1.0000
9:135523300:CCGGT:Cdonor_loss1.0000
9:135523301:CGGTG:Cdonor_loss1.0000
9:135523302:GGTGA:Gdonor_loss1.0000
9:135523303:G:GGdonor_gain1.0000
9:135523303:G:Tdonor_loss1.0000
9:135523304:T:Adonor_loss1.0000
9:135523878:A:AGacceptor_gain1.0000
9:135523878:AGAC:Aacceptor_gain1.0000
9:135523879:G:GAacceptor_gain1.0000
9:135523879:GAC:Gacceptor_gain1.0000
9:135523879:GACG:Gacceptor_gain1.0000
9:135523962:G:GTdonor_gain1.0000

AlphaMissense

1142 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:135522071:G:CA39P0.913
9:135522059:T:AW35R0.909
9:135522059:T:CW35R0.909
9:135524868:T:CF148L0.897
9:135524870:T:AF148L0.897
9:135524870:T:GF148L0.897
9:135523293:T:GY95D0.883
9:135522061:G:CW35C0.882
9:135522061:G:TW35C0.882
9:135523294:A:CY95S0.871
9:135523990:G:CG135R0.869
9:135523985:T:AL133H0.855
9:135522156:T:CL67P0.829
9:135523245:T:AC79S0.829
9:135523246:G:CC79S0.829
9:135524830:G:AG135D0.824
9:135523985:T:CL133P0.822
9:135523293:T:CY95H0.818
9:135522161:G:CA69P0.813
9:135524830:G:TG135V0.803
9:135521522:A:CS9R0.799
9:135521524:C:AS9R0.799
9:135521524:C:GS9R0.799
9:135522070:G:CK38N0.798
9:135522070:G:TK38N0.798
9:135522132:T:CL59P0.790
9:135524869:T:GF148C0.790
9:135523245:T:CC79R0.788
9:135525139:C:GC171W0.782
9:135524869:T:CF148S0.772

dbSNP variants (sampled 300 via entrez): RS1000097919 (9:133317280 C>T), RS1000349069 (9:135526261 C>T), RS1000403103 (9:135525813 C>G,T), RS1001531238 (9:135525567 G>C), RS1002532162 (9:135524705 G>A,T), RS1002722501 (9:133317531 G>A), RS1003106095 (9:135519975 A>G), RS1003523105 (9:133316883 G>A), RS1003852504 (9:135521432 A>G), RS1004247127 (9:135519887 A>G,T), RS1004439353 (9:135524020 A>C), RS1004505833 (9:135526931 G>C,T), RS1004614769 (9:135521048 G>C,T), RS1004845289 (9:133318402 C>T), RS1005388323 (9:135523384 C>A,G,T)

Disease associations

OMIM: gene MIM:151675 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST005091_4Subcutaneous adipose tissue1.000000e-06
GCST005092_1Subcutaneous adipose tissue (sex interaction)1.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008343sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsdecreases expression, increases abundance, increases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
bisphenol Aaffects cotreatment, decreases methylation1
deoxynivalenolincreases expression1
potassium persulfateincreases expression1
terbufosincreases methylation1
1-anilino-8-naphthalenesulfonateaffects binding1
11-(dansylamino)undecanoic acidaffects binding1
tebuconazoledecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
Arsenic Trioxidedecreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Cadmiumincreases expression1
Clozapinedecreases expression1
Fonofosincreases methylation1
Parathionincreases methylation1
Tretinoinaffects binding1
Triclosanincreases expression1
Valproic Acidincreases methylation1

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.