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    LCN1 lipocalin 1 [ Homo sapiens (human) ]

    Gene ID: 3933, updated on 3-Nov-2024

    Summary

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    Official Symbol
    LCN1provided by HGNC
    Official Full Name
    lipocalin 1provided by HGNC
    Primary source
    HGNC:HGNC:6525
    See related
    Ensembl:ENSG00000160349 MIM:151675; AllianceGenome:HGNC:6525
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TP; TLC; PMFA; VEGP
    Summary
    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. [provided by RefSeq, Nov 2011]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See LCN1 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (135521440..135526540)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (147749482..147754582)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (138413286..138418386)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene piercer of microtubule wall 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20487 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:138392753-138393377 Neighboring gene uncharacterized LOC101928525 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:138396029-138396183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138397212-138398185 Neighboring gene mitochondrial ribosomal protein S2 Neighboring gene NANOG hESC enhancer GRCh37_chr9:138403278-138403841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138406747-138407428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138408918-138409418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138409419-138409919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:138416151-138417034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:138418857-138419510 Neighboring gene odorant binding protein 2A Neighboring gene uncharacterized LOC107987040

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Intracavitary ligand distribution in tear lipocalin by site-directed tryptophan fluorescence. Gasymov OK, et al. Biochemistry, 2009 Aug 4. PMID 19586017, Free PMC Article
    2. Assignment of the human tear lipocalin gene (LCN1) to 9q34 by in situ hybridization. Lassagne H, et al. Genomics, 1993 Oct. PMID 8276406
    3. Cloning of a human lacrimal lipocalin secreted in tears. Lassagne H, et al. Exp Eye Res, 1993 May. PMID 8500570
    4. Interaction of ceramides and tear lipocalin. Glasgow BJ, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2018 Apr. PMID 29331331, Free PMC Article
    5. Expression of the gene for tear lipocalin/von Ebner's gland protein in human prostate. Holzfeind P, et al. FEBS Lett, 1996 Oct 21. PMID 8898072

    See all (84) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer.
      Title: Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer.
    2. Lipocalin-1 is the acceptor protein for phospholipid transfer protein in tears.
      Title: Lipocalin-1 is the acceptor protein for phospholipid transfer protein in tears.
    3. The expression of LCN1 increased gradually from stage 1 to stage 4 in breast cancer patients.
      Title: Identification of LCN1 as a Potential Biomarker for Breast Cancer by Bioinformatic Analysis.
    4. At the relatively small concentrations in tears, all ceramides were complexed to tear lipocalin.
      Title: Interaction of ceramides and tear lipocalin.
    5. 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.
      Title: Human Neutrophil Lipocalin as a Superior Diagnostic Means To Distinguish between Acute Bacterial and Viral Infections.
    6. 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.
      Title: Tear lipocalin, lysozyme and lactoferrin concentrations in postmenopausal women.
    7. Tear lysozyme, lactoferrin and lipocalin concentrations were determined via electrophoresis and the results for patients with or without eyelid tumors were compared.
      Title: Correlations between eyelid tumors and tear lipocalin, lysozyme and lactoferrin concentrations in postmenopausal women.
    8. the crosstalk of dendritic cells with lipocalins alone has the potential to direct the type of immune response to these particular antigens.
      Title: Allergenic Can f 1 and its human homologue Lcn-1 direct dendritic cells to induce divergent immune responses.
    9. Serum concentrations of LCN1 and LCN2 were both elevated in patients with COPD.
      Title: Increased serum levels of lipocalin-1 and -2 in patients with stable chronic obstructive pulmonary disease.
    10. 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.
      Title: Tear lipocalin: structure and function.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC71975

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chloride ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type endopeptidase inhibitor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proteolysis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in sensory perception of taste IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lipocalin-1
    Names
    VEG protein
    Von Ebner gland protein
    protein migrating faster than albumin
    tear prealbumin

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001252617.2 → NP_001239546.1  lipocalin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001239546.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      CK429694, CK431106, M90424
      Consensus CDS
      CCDS6991.1
      UniProtKB/Swiss-Prot
      P31025, Q5T8A1, Q5VSP4
      Related
      ENSP00000263598.2, ENST00000263598.6
      Conserved Domains (1) summary
      pfam00061
      Location:32 → 169
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    2. NM_001252618.2 → NP_001239547.1  lipocalin-1 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, which results in a translational frameshift, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      CD721968, CK431106, M90424
      UniProtKB/Swiss-Prot
      P31025
      Conserved Domains (1) summary
      pfam00061
      Location:32 → 135
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    3. NM_001252619.2 → NP_001239548.1  lipocalin-1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region, which results in a translational frameshift, compared to variant 1. The encoded isoform (3) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      CK430667, CK431106, M90424
      UniProtKB/Swiss-Prot
      P31025
      Conserved Domains (1) summary
      pfam00061
      Location:32 → 132
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    4. NM_002297.4 → NP_002288.1  lipocalin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_002288.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the shortest isoform (1). Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      CK431106, M90424, X62418
      Consensus CDS
      CCDS6991.1
      UniProtKB/Swiss-Prot
      P31025, Q5T8A1, Q5VSP4
      Related
      ENSP00000360846.3, ENST00000371781.4
      Conserved Domains (1) summary
      pfam00061
      Location:32 → 169
      Lipocalin; Lipocalin / cytosolic fatty-acid binding protein family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      135521440..135526540
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518675.3 → XP_011516977.2  lipocalin-1 isoform X1

    2. XM_047423375.1 → XP_047279331.1  lipocalin-1 isoform X2

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646201.1 Reference GRCh38.p14 PATCHES

      Range
      143832..144566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      147749482..147754582
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362961.1 → XP_054218936.1  lipocalin-1 isoform X1

    2. XM_054362962.1 → XP_054218937.1  lipocalin-1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P31025.1 GenPept UniProtKB/Swiss-Prot:P31025

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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