LCN1 lipocalin 1 [Homo sapiens (human)] - Gene

Summary

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

Location:: 9q34.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (135521440..135526540)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (147749482..147754582)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (138413286..138418386)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
At the relatively small concentrations in tears, all ceramides were complexed to tear lipocalin.
Title: Interaction of ceramides and tear lipocalin.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:482120

NoName (e-PCR)
- UniSTS:480856

RH66542 (e-PCR)
- UniSTS:51868

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 more info	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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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)

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
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
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
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