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LRAT lecithin retinol acyltransferase [ Homo sapiens (human) ]

Gene ID: 9227, updated on 5-Mar-2024

Summary

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Official Symbol
LRATprovided by HGNC
Official Full Name
lecithin retinol acyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:6685
See related
Ensembl:ENSG00000121207 MIM:604863; AllianceGenome:HGNC:6685
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
LCA14
Summary
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]
Expression
Biased expression in duodenum (RPKM 4.0), small intestine (RPKM 3.3) and 6 other tissues See more
Orthologs
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Genomic context

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See LRAT in Genome Data Viewer
Location:
4q32.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (154740838..154753120)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (158072645..158084927)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (155661990..155674272)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22080 Neighboring gene uncharacterized LOC124900169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15768 Neighboring gene fibrinogen gamma chain Neighboring gene VISTA enhancer hs1707 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:155640039-155641238 Neighboring gene NANOG hESC enhancer GRCh37_chr4:155641835-155642399 Neighboring gene NADH:ubiquinone oxidoreductase subunit B2 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:155662965-155663478 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:155663479-155663990 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:155663991-155664503 Neighboring gene uncharacterized LOC105377500 Neighboring gene RNA, U2 small nuclear 66, pseudogene Neighboring gene RNA binding motif protein 46

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
  • 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. A novel LRAT mutation affecting splicing in a family with early onset retinitis pigmentosa. Chen Y, et al. Hum Genomics, 2018 Jul 4. PMID 29973277, Free PMC Article
  2. A novel homozygous mutation causing lecithin-cholesterol acyltransferase deficiency in a proband of Romanian origin with a record of extreme gestational hyperlipidemia. Rial-Crestelo D, et al. J Clin Lipidol, 2017 Nov-Dec. PMID 28942093
  3. High incidence of LRAT promoter hypermethylation in colorectal cancer correlates with tumor stage. Cheng YW, et al. Med Oncol, 2014 Nov. PMID 25260806, Free PMC Article
  4. Knockdown of lecithin retinol acyltransferase increases all-trans retinoic acid levels and restores retinoid sensitivity in malignant melanoma cells. Amann PM, et al. Exp Dermatol, 2014 Nov. PMID 25236354
  5. Enzymatic activity of Lecithin:retinol acyltransferase: a thermostable and highly active enzyme with a likely mode of interfacial activation. Horchani H, et al. Biochim Biophys Acta, 2014 Jun. PMID 24613493, Free PMC Article

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The c.541-15T>G mutation in LRAT results in aberrant splicing and is therefore predicted to be causal for the early onset retinitis pigmentosa in this family.
    Title: A novel LRAT mutation affecting splicing in a family with early onset retinitis pigmentosa.
  2. The genetic analysis performed on our proband showed a novel homozygous mutation on codon 119 of lecithin-cholesterol acyltransferase gene that causes the substitution of glycine by aspartate
    Title: A novel homozygous mutation causing lecithin-cholesterol acyltransferase deficiency in a proband of Romanian origin with a record of extreme gestational hyperlipidemia.
  3. instability of LRAT(E14L) did not abrogate the production of the visual chromophore in a cell-based assay. Instead, expression of LRAT(E14L) led to a rapid increase in cellular levels of retinoic acid upon retinoid supplementation.
    Title: Impact of LCA-Associated E14L LRAT Mutation on Protein Stability and Retinoid Homeostasis.
  4. LRAT hypermethylation was associated with decreased mRNA levels in colorectal cancer clinical specimens.
    Title: High incidence of LRAT promoter hypermethylation in colorectal cancer correlates with tumor stage.
  5. lecithin retinol acyltransferase affects all-trans retinoic acid levels and has a role in retinoid sensitivity in malignant melanoma cells.
    Title: Knockdown of lecithin retinol acyltransferase increases all-trans retinoic acid levels and restores retinoid sensitivity in malignant melanoma cells.
  6. These findings reveal structural adaptation that facilitates selective catalysis and mechanism responsible for diverse substrate specificity within the LRAT-like enzyme family
    Title: LRAT-specific domain facilitates vitamin A metabolism by domain swapping in HRASLS3.
  7. high LRAT expression in melanoma might be important in removing retinol as substrate for RA production, thereby inducing signalling pathways leading to dedifferentiation, proliferation and anti-apoptosis
    Title: Lecithin retinol acyltransferase as a potential prognostic marker for malignant melanoma.
  8. Functional hepatic stellate cells coexpressing both LRAT and CRBP-1, that continue to maintain the ability to store vitamin A, contribute in part to the development of portal and parenchymal fibrogenesis in patients with viral hepatitis.
    Title: Hepatic stellate cells that coexpress LRAT and CRBP-1 partially contribute to portal fibrogenesis in patients with human viral hepatitis.
  9. Lecithin-retinol acyltransferase is a thermostable and highly active enzyme with a likely mode of interfacial activation.
    Title: Enzymatic activity of Lecithin:retinol acyltransferase: a thermostable and highly active enzyme with a likely mode of interfacial activation.
  10. A genetic defect was identified in LRAT as a novel cause of retinitis punctata albescens.
    Title: A homozygous frameshift mutation in LRAT causes retinitis punctata albescens.
Submit: New GeneRIF Correction See all GeneRIFs (28)

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

EBI GWAS Catalog

Description
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling.
EBI GWAS Catalog

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ31672, MGC33103

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables O-palmitoyltransferase activity TAS
Traceable Author Statement
more info
  
enables acyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
enables lecithin:11-cis retinol acyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylcholine-retinol O-acyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylcholine-retinol O-acyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylcholine-retinol O-acyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables retinoic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables retinol binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of lipid transport IEA
Inferred from Electronic Annotation
more info
  
involved_in response to bacterium IEA
Inferred from Electronic Annotation
more info
  
involved_in response to retinoic acid IEA
Inferred from Electronic Annotation
more info
  
involved_in response to vitamin A IEA
Inferred from Electronic Annotation
more info
  
involved_in retinoid metabolic process TAS
Traceable Author Statement
more info
  
involved_in retinol metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinol metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retinol metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
involved_in vitamin A metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vitamin A metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in multivesicular body ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in rough endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in rough endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
lecithin retinol acyltransferase
Names
lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)
NP_001288574.1
NP_004735.2
XP_047272361.1
XP_054207217.1

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.

Genomic

  1. NG_009110.1 RefSeqGene

    Range
    4990..14110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301645.2 → NP_001288574.1  lecithin retinol acyltransferase precursor

    See identical proteins and their annotated locations for NP_001288574.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC009567, AY546086, BC031053, DB364008
    Consensus CDS
    CCDS3789.1
    UniProtKB/Swiss-Prot
    A8K983, O95237, Q8N716
    Related
    ENSP00000426761.1, ENST00000507827.5
    Conserved Domains (1) summary
    pfam04970
    Location:59 → 173
    LRAT; Lecithin retinol acyltransferase

  2. NM_004744.5 → NP_004735.2  lecithin retinol acyltransferase precursor

    See identical proteins and their annotated locations for NP_004735.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC009567, AK292598, AY546086, DB364008
    Consensus CDS
    CCDS3789.1
    UniProtKB/Swiss-Prot
    A8K983, O95237, Q8N716
    Related
    ENSP00000337224.3, ENST00000336356.4
    Conserved Domains (1) summary
    pfam04970
    Location:59 → 173
    LRAT; Lecithin retinol acyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    154740838..154753120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416405.1 → XP_047272361.1  lecithin retinol acyltransferase isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    158072645..158084927
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351242.1 → XP_054207217.1  lecithin retinol acyltransferase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95237.2 GenPept UniProtKB/Swiss-Prot:O95237

Gene LinkOut

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