Gene Gene information from NCBI Gene database.
Entrez ID 9227
Gene name Lecithin retinol acyltransferase
Gene symbol LRAT
Synonyms (NCBI Gene)
LCA14
Chromosome 4
Chromosome location 4q32.1
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
SNPs SNP information provided by dbSNP.
12
SNP ID Visualize variation Clinical significance Consequence
rs104893848 T>A,C Pathogenic, not-provided Missense variant, non coding transcript variant, synonymous variant, coding sequence variant
rs398124185 ->T Pathogenic Coding sequence variant, non coding transcript variant, frameshift variant
rs527236079 C>G,T Likely-pathogenic Coding sequence variant, missense variant, non coding transcript variant
rs761717462 AA>-,AAA Pathogenic Coding sequence variant, frameshift variant, non coding transcript variant
rs765063151 ->C Likely-pathogenic Coding sequence variant, frameshift variant, non coding transcript variant
miRNA miRNA information provided by mirtarbase database.
413
miRTarBase ID miRNA Experiments Reference
MIRT017703 hsa-miR-335-5p Microarray 18185580
MIRT616650 hsa-miR-6514-5p HITS-CLIP 22927820
MIRT616649 hsa-miR-1304-3p HITS-CLIP 22927820
MIRT616648 hsa-miR-143-3p HITS-CLIP 22927820
MIRT616647 hsa-miR-4770 HITS-CLIP 22927820
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
44
GO ID Ontology Definition Evidence Reference
GO:0001523 Process Retinoid metabolic process IEA
GO:0001523 Process Retinoid metabolic process TAS
GO:0001972 Function Retinoic acid binding IEA
GO:0005515 Function Protein binding IPI 28514442, 32296183, 33961781
GO:0005737 Component Cytoplasm IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
604863 6685 ENSG00000121207
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O95237
Protein name Lecithin retinol acyltransferase (EC 2.3.1.135) (Phosphatidylcholine--retinol O-acyltransferase)
Protein function Transfers the acyl group from the sn-1 position of phosphatidylcholine to all-trans retinol, producing all-trans retinyl esters (PubMed:9920938). Retinyl esters are storage forms of vitamin A (Probable). LRAT plays a critical role in vision (Pro
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF04970 LRAT 43 174 Lecithin retinol acyltransferase Domain
Tissue specificity 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 feta
Sequence
MKNPMLEVVSLLLEKLLLISNFTLFSSGAAGEDKGRNSFYETSSFHRGDVLEVPRTHLTH
YGIYLGDNRVAHMMPDILLALTDDMGRTQKVVSNKRLILGVIVKVASIRVDTVEDFAYGA
NILVNHLDESLQKKALLNEEVARRAEKLLGFTPYSLLWNNCEHFVTYCRYGTPI
SPQSDK
FCETVKIIIRDQRSVLASAVLGLASIVCTGLVSYTTLPAIFIPFFLWMAG
Sequence length 230
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Retinol metabolism
Metabolic pathways
Vitamin digestion and absorption
  Retinoid cycle disease events
The canonical retinoid cycle in rods (twilight vision)
Retinoid metabolism and transport
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
28
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of the eye Pathogenic rs2111032416 RCV001814350
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal recessive retinitis pigmentosa Likely pathogenic; Pathogenic rs786205644, rs1732840025 RCV001257788
RCV001257787
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Leber congenital amaurosis Pathogenic; Likely pathogenic rs527236079, rs2529971841, rs768255532 RCV005431484
RCV003236542
RCV000826116
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Leber congenital amaurosis 1 Likely pathogenic; Pathogenic rs527236079 RCV000987482
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMAUROSIS CONGENITA OF LEBER, TYPE 1 Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Breast ductal adenocarcinoma Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Alzheimer`s Disease Alzheimer disease GWASDB_DG 21460841
★☆☆☆☆
Found in Text Mining only
Amaurosis congenita of Leber, type 1 Leber congenital amaurosis BEFREE 17438524, 18055816, 19339306, 21555576, 24664772
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bladder Neoplasm Bladder Neoplasm LHGDN 15161698
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Celiac Disease Celiac disease CTD_human_DG 30097691
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Ciliopathies Ciliopathies GENOMICS_ENGLAND_DG
★☆☆☆☆
Found in Text Mining only
Colonic Polyps Colonic polyps Pubtator 25260806 Associate
★☆☆☆☆
Found in Text Mining only
Colorectal Neoplasms Colorectal neoplasm Pubtator 24608339, 25260806 Associate
★☆☆☆☆
Found in Text Mining only
Conductive hearing loss Hearing Loss HPO_DG
★☆☆☆☆
Found in Text Mining only
Congenital Amaurosis of Retinal Origin Dysgenesis Neuroepithelialis Retinae CTD_human_DG 19339306
★☆☆☆☆
Found in Text Mining only