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Aliases for LCN12 Gene

Aliases for LCN12 Gene

  • Lipocalin 12 2 3 5

External Ids for LCN12 Gene

Previous GeneCards Identifiers for LCN12 Gene

  • GC09P135205
  • GC09P137122
  • GC09P138963
  • GC09P139844
  • GC09P109306

Summaries for LCN12 Gene

Entrez Gene Summary for LCN12 Gene

  • Members of the lipocalin family, such as LCN12, have a common structure consisting of an 8-stranded antiparallel beta-barrel that forms a cup-shaped ligand-binding pocket or calyx. Lipocalins generally bind small hydrophobic ligands and transport them to specific cells (Suzuki et al., 2004 [PubMed 15363845]).[supplied by OMIM, Aug 2009]

GeneCards Summary for LCN12 Gene

LCN12 (Lipocalin 12) is a Protein Coding gene. Diseases associated with LCN12 include Keratoconus. Among its related pathways are Transport of vitamins, nucleosides, and related molecules and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include transporter activity and retinoic acid binding. An important paralog of this gene is LCN2.

UniProtKB/Swiss-Prot for LCN12 Gene

  • Binds all-trans retinoic acid and may act as a retinoid carrier protein within the epididymis. May play a role in male fertility (By similarity).

Additional gene information for LCN12 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCN12 Gene

Genomics for LCN12 Gene

GeneHancer (GH) Regulatory Elements for LCN12 Gene

Promoters and enhancers for LCN12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I136942 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 576.8 -1.7 -1734 10.6 CLOCK ZFP64 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC MEF2D GLIS1 LCN12 FBXW5 C8G EHMT1 SDCCAG3 DPH7 ANAPC2 SEC16A LOC651337 NDOR1
GH09I136990 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE 20.3 +46.8 46820 10.9 HDGF PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B PAXX CLIC3 LCN12 ABCA2 PRR31 C9orf139 INPP5E LCNL1 RABL6 CCDC183
GH09I136925 Enhancer 1.2 Ensembl ENCODE dbSUPER 26.7 -21.9 -21944 3.5 HDAC1 HDGF CTCF PKNOX1 ESRRA RAD21 FOSL1 ZFHX2 ZNF316 POLR2A PIR56768 PIR33871 LCN12 TRAF2 CCDC183 PRR31 MAMDC4 PHPT1 AJM1 RABL6
GH09I136787 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 11.3 -154.5 -154482 14.2 MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC TMEM141 CCDC183 DPH7 LCN8 ANAPC2 ABCA2 SNHG7 LCN10 EXD3 LCN12
GH09I136884 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 11.8 -62.9 -62920 3.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZBTB7B POLR2B E2F8 ZNF207 LOC105376326 MIR4479 TRAF2 EHMT1 SDCCAG3 ANAPC2 PHPT1 SNHG7 LOC651337 MAMDC4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LCN12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LCN12 gene promoter:

Genomic Locations for LCN12 Gene

Genomic Locations for LCN12 Gene
6,304 bases
Plus strand

Genomic View for LCN12 Gene

Genes around LCN12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCN12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCN12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCN12 Gene

Proteins for LCN12 Gene

  • Protein details for LCN12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Epididymal-specific lipocalin-12
    Protein Accession:
    Secondary Accessions:
    • A2AMJ7

    Protein attributes for LCN12 Gene

    192 amino acids
    Molecular mass:
    21500 Da
    Quaternary structure:
    • Monomer.

neXtProt entry for LCN12 Gene

Post-translational modifications for LCN12 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LCN12 Gene

Domains & Families for LCN12 Gene

Gene Families for LCN12 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for LCN12 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the calycin superfamily. Lipocalin family.
  • Belongs to the calycin superfamily. Lipocalin family.
genes like me logo Genes that share domains with LCN12: view

Function for LCN12 Gene

Molecular function for LCN12 Gene

UniProtKB/Swiss-Prot Function:
Binds all-trans retinoic acid and may act as a retinoid carrier protein within the epididymis. May play a role in male fertility (By similarity).

Phenotypes From GWAS Catalog for LCN12 Gene

Gene Ontology (GO) - Molecular Function for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001972 retinoic acid binding ISS --
genes like me logo Genes that share ontologies with LCN12: view

Phenotypes for LCN12 Gene

GenomeRNAi human phenotypes for LCN12:
genes like me logo Genes that share phenotypes with LCN12: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCN12 Gene

Localization for LCN12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCN12 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCN12 gene
Compartment Confidence
extracellular 5
mitochondrion 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with LCN12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LCN12 Gene

Pathways & Interactions for LCN12 Gene

genes like me logo Genes that share pathways with LCN12: view

Interacting Proteins for LCN12 Gene

Selected Interacting proteins: Q6JVE5-LCN12_HUMAN for LCN12 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0015909 long-chain fatty acid transport TAS --
genes like me logo Genes that share ontologies with LCN12: view

No data available for SIGNOR curated interactions for LCN12 Gene

Drugs & Compounds for LCN12 Gene

No Compound Related Data Available

Transcripts for LCN12 Gene

Unigene Clusters for LCN12 Gene

Lipocalin 12:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCN12 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6
SP2: -
SP3: - -

Relevant External Links for LCN12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LCN12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCN12 Gene

mRNA differential expression in normal tissues according to GTEx for LCN12 Gene

This gene is overexpressed in Thyroid (x13.7) and Liver (x4.8).

NURSA nuclear receptor signaling pathways regulating expression of LCN12 Gene:


SOURCE GeneReport for Unigene cluster for LCN12 Gene:

genes like me logo Genes that share expression patterns with LCN12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCN12 Gene

Orthologs for LCN12 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LCN12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LCN12 33 34
  • 97.57 (n)
(Canis familiaris)
Mammalia LCN12 33 34
  • 70.64 (n)
(Bos Taurus)
Mammalia LCN12 33 34
  • 69.16 (n)
(Mus musculus)
Mammalia Lcn12 33 16 34
  • 68.27 (n)
(Rattus norvegicus)
Mammalia Lcn12 33
  • 66.89 (n)
(Monodelphis domestica)
Mammalia LCN12 34
  • 25 (a)
Species where no ortholog for LCN12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LCN12 Gene

Gene Tree for LCN12 (if available)
Gene Tree for LCN12 (if available)

Paralogs for LCN12 Gene

Paralogs for LCN12 Gene

(2) SIMAP similar genes for LCN12 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with LCN12: view

Variants for LCN12 Gene

Sequence variations from dbSNP and Humsavar for LCN12 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000661052 -- 136,950,229(+) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000671889 -- 136,955,975(+) G/A downstream_transcript_variant
rs1000824416 -- 136,950,101(+) G/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001110918 -- 136,950,211(+) A/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001413138 -- 136,950,755(+) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LCN12 Gene

Variant ID Type Subtype PubMed ID
esv2422220 CNV deletion 17116639
esv2661667 CNV deletion 23128226
nsv469918 CNV loss 18288195
nsv524322 CNV loss 19592680
nsv615988 CNV loss 21841781
nsv818738 CNV gain 17921354
nsv951206 CNV deletion 24416366

Variation tolerance for LCN12 Gene

Residual Variation Intolerance Score: 82.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.47; 28.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCN12 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCN12 Gene

Disorders for LCN12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LCN12 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
  • conical cornea
- elite association - COSMIC cancer census association via MalaCards
Search LCN12 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LCN12

genes like me logo Genes that share disorders with LCN12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCN12 Gene

Publications for LCN12 Gene

  1. Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2. (PMID: 15363845) Suzuki K … Orgebin-Crist MC (Gene 2004) 2 3 4 22 58
  2. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. (PMID: 23291589) Lu Y … Wong TY (Nature genetics 2013) 3 58
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 4 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for LCN12 Gene

Sources for LCN12 Gene

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