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LRAT Gene(Protein Coding)

Lecithin Retinol Acyltransferase

GCID:
GC04P154626
GIFtS:
54
Genes Participants
UDN Logo

Aliases for LRAT Gene

Aliases for LRAT Gene

  • Lecithin Retinol Acyltransferase 2 3 5
  • Lecithin Retinol Acyltransferase (Phosphatidylcholine--Retinol O-Acyltransferase) 2 3
  • Phosphatidylcholine--Retinol O-Acyltransferase 2 4
  • EC 2.3.1.135 4 56
  • LCA14 3

External Ids for LRAT Gene

Previous GeneCards Identifiers for LRAT Gene

  • GC04P156514
  • GC04P156050
  • GC04P156239
  • GC04P156019
  • GC04P155881
  • GC04P155665
  • GC04P155549
  • GC04P151405

Summaries for LRAT Gene

Entrez Gene Summary for LRAT Gene

  • The protein encoded by this gene localizes to the endoplasmic reticulum, where it catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester. This reaction is an important step in vitamin A metabolism in the visual system. Mutations in this gene have been associated with early-onset severe retinal dystrophy and Leber congenital amaurosis 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]

GeneCards Summary for LRAT Gene

LRAT (Lecithin Retinol Acyltransferase) is a Protein Coding gene. Diseases associated with LRAT include Leber Congenital Amaurosis 14 and Severe Early-Childhood-Onset Retinal Dystrophy. Among its related pathways are the visual cycle I (vertebrates) and Metabolism. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring acyl groups and retinol binding.

UniProtKB/Swiss-Prot for LRAT Gene

  • Transfers the acyl group from the sn-1 position of phosphatidylcholine to all-trans retinol, producing all-trans retinyl esters. Retinyl esters are storage forms of vitamin A. LRAT plays a critical role in vision. It provides the all-trans retinyl ester substrates for the isomerohydrolase which processes the esters into 11-cis-retinol in the retinal pigment epithelium; due to a membrane-associated alcohol dehydrogenase, 11 cis-retinol is oxidized and converted into 11-cis-retinaldehyde which is the chromophore for rhodopsin and the cone photopigments.

Gene Wiki entry for LRAT Gene

Additional gene information for LRAT Gene

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

Genomics for LRAT Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for LRAT Gene

Promoters and enhancers for LRAT Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH04I154743 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 550.1 +117.1 117116 1.5 CTCF SP2 ETS1 E2F1 SP1 CTBP1 GLIS2 POLR2A ZNF184 GLIS1 PIR56291 PIR52192 LRAT PIR37413
GH04I154626 Enhancer 1 Ensembl ENCODE 555.7 +0.2 151 1 RB1 ZNF48 RAD21 ZNF335 GLIS2 ZNF143 ZNF654 MXD4 REST ZNF592 LRAT GC04M154691
GH04I154741 Promoter 0.7 EPDnew 560.8 +113.9 113874 0.1 SIN3A EZH2 LRAT GC04M154737 GC04M154751 GC04M154753 GC04M154758 GC04M154774 PIR47588 PIR31824 PIR56291 PIR52192
GH04I154549 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 11.6 -76.7 -76703 1.9 SMAD1 ATF1 ARNT ARID4B SIN3A ZNF2 ZNF48 YY1 ETS1 GTF3C2 PLRG1 FGG LRAT GC04M154544 RNU6-1285P
GH04I154659 Enhancer 1.3 VISTA ENCODE 12 +33.3 33283 1.4 FOXA2 ARID4B ETS1 YY1 TCF12 RXRA MIER2 REST PPARG KAT8 LRAT GC04M154691
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRAT on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LRAT Gene

Genomic Locations for LRAT Gene
chr4:154,626,945-154,753,119
(GRCh38/hg38)
Size:
126,175 bases
Orientation:
Plus strand
chr4:155,548,097-155,674,270
(GRCh37/hg19)

Genomic View for LRAT Gene

Genes around LRAT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LRAT Gene

Proteins for LRAT Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    O95237-LRAT_HUMAN
    Recommended name:
    Lecithin retinol acyltransferase
    Protein Accession:
    O95237
    Secondary Accessions:
    • A8K983
    • Q8N716

    Protein attributes for LRAT Gene

    Size:
    230 amino acids
    Molecular mass:
    25703 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LRAT Gene

Protein Expression for LRAT Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for LRAT Gene

O95237:
  • HYGIYLG
  • ILVNHLD
  • VASIRVDTVEDFAYGA

Post-translational modifications for LRAT Gene

No Post-translational modifications

Other Protein References for LRAT Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for LRAT Gene

Gene Families for LRAT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for LRAT Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LRAT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95237

UniProtKB/Swiss-Prot:

LRAT_HUMAN :
  • Belongs to the H-rev107 family.
Family:
  • Belongs to the H-rev107 family.
genes like me logo Genes that share domains with LRAT: view

Function for LRAT Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LRAT Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Phosphatidylcholine + retinol--[cellular-retinol-binding-protein] = 2-acylglycerophosphocholine + retinyl-ester--[cellular-retinol-binding-protein].
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by all-trans-retinyl alpha-bromoacetate and N-boc-L-biocytinyl-11-aminoundecane chloro-methyl ketone (BACMK).
UniProtKB/Swiss-Prot Function:
Transfers the acyl group from the sn-1 position of phosphatidylcholine to all-trans retinol, producing all-trans retinyl esters. Retinyl esters are storage forms of vitamin A. LRAT plays a critical role in vision. It provides the all-trans retinyl ester substrates for the isomerohydrolase which processes the esters into 11-cis-retinol in the retinal pigment epithelium; due to a membrane-associated alcohol dehydrogenase, 11 cis-retinol is oxidized and converted into 11-cis-retinaldehyde which is the chromophore for rhodopsin and the cone photopigments.
UniProtKB/Swiss-Prot Induction:
LRAT activity is up-regulated by dietary vitamin A. Under conditions of vitamin A depletion, LRAT expression in the liver is induced by retinoic acid (By similarity).

Enzyme Numbers (IUBMB) for LRAT Gene

Phenotypes From GWAS Catalog for LRAT Gene

Gene Ontology (GO) - Molecular Function for LRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001972 retinoic acid binding IEA --
GO:0008374 O-acyltransferase activity IEA --
GO:0016416 O-palmitoyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups TAS 9920938
genes like me logo Genes that share ontologies with LRAT: view
genes like me logo Genes that share phenotypes with LRAT: view

Human Phenotype Ontology for LRAT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LRAT Gene

MGI Knock Outs for LRAT:

Animal Model Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for LRAT Gene

Localization for LRAT Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRAT Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Rough endoplasmic reticulum. Endosome, multivesicular body. Cytoplasm, perinuclear region. Note=Present in the rough endoplasmic reticulum and multivesicular body in hepatic stellate cells. Present in the rough endoplasmic reticulum and perinuclear region in endothelial cells (By similarity). {ECO:0000250}.

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 LRAT gene
Compartment Confidence
endoplasmic reticulum 4
endosome 4
plasma membrane 2
extracellular 2
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (1)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IEA --
GO:0005771 multivesicular body ISS --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
genes like me logo Genes that share ontologies with LRAT: view

Pathways & Interactions for LRAT Gene

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

UniProtKB/Swiss-Prot O95237-LRAT_HUMAN

  • Pathway: Cofactor metabolism; retinol metabolism.

Gene Ontology (GO) - Biological Process for LRAT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0006776 vitamin A metabolic process IEA --
GO:0007601 visual perception IEA --
GO:0032370 positive regulation of lipid transport IEA --
GO:0042572 retinol metabolic process IEA --
genes like me logo Genes that share ontologies with LRAT: view

No data available for SIGNOR curated interactions for LRAT Gene

Drugs & Compounds for LRAT Gene

Products:

  1. Drug

(10) Drugs for LRAT Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin A Approved, Vet_approved Nutra Target 529
Isopropyl alcohol Approved, Investigational Pharma 0
Propyl alcohol Approved, Experimental Pharma 0
1-Butanol Experimental Pharma 0

(17) Additional Compounds for LRAT Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
11-cis-Retinol
  • 11-cis-Vitamin A alcohol
  • cis-11-Retinol
 22737-96-8
Retinyl ester
  • All-trans-Retinyl ester
retinyl palmitate
  • All-trans-Retinol palmitate
  • All-trans-Retinyl palmitate
  • All-trans-Vitamin A palmitate
  • Aquapalm
  • Aquasol A
 79-81-2
11-cis-Retinyl palmitate
1-Hexanol
  • 1-Hexanol
  • 1-Hexyl alcohol
  • 1-Hydroxyhexane
  • Alcohol C-6
  • Alcohol(C6)
 111-27-3
genes like me logo Genes that share compounds with LRAT: view

Transcripts for LRAT Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LRAT Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(22) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LRAT Gene

Lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase):
Representative Sequences:

Clone Products

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

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b · 6c
SP1: - - - - -
SP2: -
SP3:
SP4:

Relevant External Links for LRAT Gene

GeneLoc Exon Structure for
LRAT
ECgene alternative splicing isoforms for
LRAT

Expression for LRAT Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for LRAT Gene
mRNA expression by GTEx for LRAT GenemRNA expression by BioGPS for LRAT Gene

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

This gene is overexpressed in Brain - Hypothalamus (x5.7) and Brain - Spinal cord (cervical c-1) (x5.2).

Protein differential expression in normal tissues from HIPED for LRAT Gene

This gene is overexpressed in Monocytes (41.9) and Fetal testis (27.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRAT Gene



Protein tissue co-expression partners for LRAT Gene

NURSA nuclear receptor signaling pathways regulating expression of LRAT Gene:

LRAT

SOURCE GeneReport for Unigene cluster for LRAT Gene:

Hs.658427

mRNA Expression by UniProt/SwissProt for LRAT Gene:

O95237-LRAT_HUMAN
Tissue specificity: Hepatic stellate cells and endothelial cells (at protein level). Found at high levels in testis and liver, followed by retinal pigment epithelium, small intestine, prostate, pancreas and colon. Low expression observed in brain. In fetal tissues, expressed in retinal pigment epithelium and liver, and barely in the brain.

Evidence on tissue expression from TISSUES for LRAT Gene

  • Liver(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LRAT Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • olfactory bulb
  • outer ear
  • skull
Abdomen:
  • liver
Pelvis:
  • penis
  • testicle
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with LRAT: view

Orthologs for LRAT Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRAT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia LRAT 33 34
  • 99.57 (n)
dog
(Canis familiaris)
 Mammalia LRAT 33 34
  • 88.84 (n)
cow
(Bos Taurus)
 Mammalia LRAT 33 34
  • 88.7 (n)
oppossum
(Monodelphis domestica)
 Mammalia LRAT 34
  • 82 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia LRAT 34
  • 82 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Lrat 33 16 34
  • 81.14 (n)
rat
(Rattus norvegicus)
 Mammalia Lrat 33
  • 80.56 (n)
chicken
(Gallus gallus)
 Aves LRAT 33 34
  • 71.3 (n)
lizard
(Anolis carolinensis)
 Reptilia LRAT 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lrat 33
  • 66.67 (n)
MGC75880 33
zebrafish
(Danio rerio)
 Actinopterygii lratb 33
  • 60.32 (n)
LRAT 34
  • 47 (a)
 OneToOne
Species where no ortholog for LRAT 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRAT Gene

ENSEMBL:
Gene Tree for LRAT (if available)
TreeFam:
Gene Tree for LRAT (if available)

Paralogs for LRAT Gene

No data available for Paralogs for LRAT Gene

Variants for LRAT Gene

Sequence variations from dbSNP and Humsavar for LRAT Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs104893848 pathogenic, not-provided, RETINAL DYSTROPHY, EARLY-ONSET SEVERE, LRAT-RELATED, not provided, Leber congenital amaurosis 14 (LCA14) [MIM:613341] 154,744,851(+) T/A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs115053323 uncertain-significance, Retinal dystrophy, Retinitis Pigmentosa, Recessive, Leber congenital amaurosis 154,752,400(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs12507608 likely-benign, Leber congenital amaurosis, Retinitis Pigmentosa, Recessive, Retinal dystrophy 154,750,474(+) T/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs139819099 uncertain-significance, Retinitis Pigmentosa, Recessive, Retinal dystrophy, Leber congenital amaurosis 154,744,729(+) G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs144961748 uncertain-significance, Leber congenital amaurosis, Retinitis Pigmentosa, Recessive, Retinal dystrophy 154,752,848(+) G/C 3_prime_UTR_variant, genic_downstream_transcript_variant

Variation tolerance for LRAT Gene

Residual Variation Intolerance Score: 60.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.36; 26.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRAT Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LRAT Gene

Disorders for LRAT Gene

MalaCards: The human disease database

(7) MalaCards diseases for LRAT Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LRAT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LRAT_HUMAN
  • Leber congenital amaurosis 14 (LCA14) [MIM:613341]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269 PubMed:11381255, ECO:0000269 PubMed:17011878, ECO:0000269 PubMed:18055821}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LRAT

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LRAT: view

No data available for Genatlas for LRAT Gene

Publications for LRAT Gene

  1. Molecular and biochemical characterization of lecithin retinol acyltransferase. (PMID: 9920938) Ruiz A … Bok D (The Journal of biological chemistry 1999) 2 3 4 22 58
  2. Lecithin: retinol acyltransferase protein is distributed in both hepatic stellate cells and endothelial cells of normal rodent and human liver. (PMID: 18544127) Nagatsuma K … Matsuura T (Liver international : official journal of the International Association for the Study of the Liver 2009) 3 4 22 58
  3. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. (PMID: 18823527) Abraham R … Kirov G (BMC medical genomics 2008) 3 22 44 58
  4. Identification of novel mutations in patients with Leber congenital amaurosis and juvenile RP by genome-wide homozygosity mapping with SNP microarrays. (PMID: 18055821) den Hollander AI … Koenekoop RK (Investigative ophthalmology & visual science 2007) 3 4 22 58
  5. Screening genes of the retinoid metabolism: novel LRAT mutation in leber congenital amaurosis. (PMID: 17011878) Sénéchal A … Hamel CP (American journal of ophthalmology 2006) 3 4 22 58

Products for LRAT Gene

Sources for LRAT Gene

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