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] See more...

Aliases for LCN12 Gene

Aliases for LCN12 Gene

  • Lipocalin 12 2 3 5
  • Epididymal-Specific Lipocalin-12 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • Lipocalcin 12 3

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 Corneal Ectasia and Irregular Astigmatism. 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 Summary 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 , Rfam classification and piRNA Summary for LCN12 Gene

Genomics for LCN12 Gene

GeneHancer (GH) Regulatory Elements for LCN12 Gene

Promoters and enhancers for LCN12 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCN12 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCN12

Top Transcription factor binding sites by QIAGEN in the LCN12 gene promoter:
  • AML1a
  • AP-2gamma
  • ATF6
  • HEN1
  • p53
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT3
  • USF-1
  • USF1

Genomic Locations for LCN12 Gene

Genomic Locations for LCN12 Gene
chr9:136,949,195-136,955,498
(GRCh38/hg38)
Size:
6,304 bases
Orientation:
Plus strand
chr9:139,844,003-139,849,949
(GRCh37/hg19)
Size:
5,947 bases
Orientation:
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:
    Q6JVE5-LCN12_HUMAN
    Recommended name:
    Epididymal-specific lipocalin-12
    Protein Accession:
    Q6JVE5
    Secondary Accessions:
    • A2AMJ7

    Protein attributes for LCN12 Gene

    Size:
    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

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

Protein Domains for LCN12 Gene

Blocks:
  • Lipocalin signature
  • Prostaglandin D synthase signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LCN12 Gene

GenScript: Design optimal peptide antigens:
  • Epididymal-specific lipocalin-12 (LCN12_HUMAN)
  • Lipocalin 12 (Q5SQ16_HUMAN)
  • Lipocalcin 12, isoform CRA_d (Q8IW14_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6JVE5

UniProtKB/Swiss-Prot:

LCN12_HUMAN :
  • Belongs to the calycin superfamily. Lipocalin family.
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 --
GO:0036094 small molecule binding IEA --
genes like me logo Genes that share ontologies with LCN12: view
genes like me logo Genes that share phenotypes with LCN12: view

Animal Model Products

CRISPR Products

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

Secreted.

Subcellular locations from

COMPARTMENTS
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 0
cytosol 0

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
MYC
;

Gene Ontology (GO) - Biological Process for LCN12 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

mRNA/cDNA for LCN12 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

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

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6
SP1:
SP2: -
SP3: - -

Relevant External Links for LCN12 Gene

GeneLoc Exon Structure for
LCN12

Expression for LCN12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCN12

SOURCE GeneReport for Unigene cluster for LCN12 Gene:

Hs.440519
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
chimpanzee
(Pan troglodytes)
Mammalia LCN12 31 30
  • 97.57 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LCN12 31 30
  • 70.64 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LCN12 31 30
  • 69.16 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lcn12 17 31 30
  • 68.27 (n)
rat
(Rattus norvegicus)
Mammalia Lcn12 30
  • 66.89 (n)
oppossum
(Monodelphis domestica)
Mammalia LCN12 31
  • 25 (a)
OneToOne
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

ENSEMBL:
Gene Tree for LCN12 (if available)
TreeFam:
Gene Tree for LCN12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCN12: view image

Paralogs for LCN12 Gene

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

  • LCN12_HUMAN
  • Q5SQ16_HUMAN
  • Q8IW14_HUMAN
  • R4GN38_HUMAN
genes like me logo Genes that share paralogs with LCN12: view

Variants for LCN12 Gene

Additional dbSNP identifiers (rs#s) for LCN12 Gene

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)
LCN12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCN12

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCN12 Gene

Disorders for LCN12 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
corneal ectasia
irregular astigmatism
keratoconus
  • conical cornea
brittle cornea syndrome 2
  • fragilitas oculi with joint hyperextensibility
- 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 23 54
  2. Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. (PMID: 27976729) Lee N … Choi KY (Scientific reports 2016) 3 54
  3. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. (PMID: 23291589) Lu Y … Wong TY (Nature genetics 2013) 3 54
  4. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 4 54
  5. 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 54

Products for LCN12 Gene

  • Signalway ELISA kits for LCN12
  • Signalway Proteins for LCN12

Sources for LCN12 Gene