Human Gene LCAT (ENST00000264005.10_7) from GENCODE V47lift37
  Description: lecithin-cholesterol acyltransferase (from RefSeq NM_000229.2)
Gencode Transcript: ENST00000264005.10_7
Gencode Gene: ENSG00000213398.8_13
Transcript (Including UTRs)
   Position: hg19 chr16:67,973,653-67,978,023 Size: 4,371 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr16:67,973,807-67,978,004 Size: 4,198 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:67,973,653-67,978,023)mRNA (may differ from genome)Protein (440 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LCAT_HUMAN
DESCRIPTION: RecName: Full=Phosphatidylcholine-sterol acyltransferase; EC=2.3.1.43; AltName: Full=Lecithin-cholesterol acyltransferase; AltName: Full=Phospholipid-cholesterol acyltransferase; Flags: Precursor;
FUNCTION: Central enzyme in the extracellular metabolism of plasma lipoproteins. Synthesized mainly in the liver and secreted into plasma where it converts cholesterol and phosphatidylcholines (lecithins) to cholesteryl esters and lysophosphatidylcholines on the surface of high and low density lipoproteins (HDLs and LDLs). The cholesterol ester is then transported back to the liver. Has a preference for plasma 16:0-18:2 or 18:O-18:2 phosphatidylcholines. Also produced in the brain by primary astrocytes, and esterifies free cholesterol on nascent APOE-containing lipoproteins secreted from glia and influences cerebral spinal fluid (CSF) APOE- and APOA1 levels. Together with APOE and the cholesterol transporter ABCA1, plays a key role in the maturation of glial-derived, nascent lipoproteins. Required for remodeling high-density lipoprotein particles into their spherical forms.
CATALYTIC ACTIVITY: Phosphatidylcholine + a sterol = 1- acylglycerophosphocholine + a sterol ester.
ENZYME REGULATION: APOA1 is the most potent activator in plasma. Also activated by APOE, APOC1 and APOA4.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=0.97 mM for LDL; KM=0.4 mM for HDL(2); KM=0.10 mM for HDL(3); Vmax=8.3 mmol/min/mg enzyme with LDL as substrate; Vmax=0.58 mmol/min/mg enzyme with HDL(2) as substrate; Vmax=2.0 mmol/min/mg enzyme with HDL(3) as substrate; Note=Affinity for LDL is 2.3 to 4-fold lower than for HDL. Relative reactivities are 16% for HDL(3), 1.3% for HDL(2) and 6.5% for LDL;
SUBCELLULAR LOCATION: Secreted. Note=Secreted into blood plasma. Produced in astrocytes and secreted into cerebral spinal fluid (CSF).
TISSUE SPECIFICITY: Expressed mainly in brain, liver and testes. Secreted into plasma and cerebral spinal fluid. Expressed in Hep- G2 cell line.
PTM: O- and N-glycosylated. O-glycosylation on Thr-431 and Ser-433 consists of sialylated galactose beta 1-->3N-acetylgalactosamine structures. N-glycosylated sites contain sialylated triantennary and/or biantennary complex structures.
DISEASE: Defects in LCAT are the cause of lecithin-cholesterol acyltransferase deficiency (LCATD) [MIM:245900]; also called Norum disease. LCATD is a disorder of lipoprotein metabolism characterized by inadequate esterification of plasmatic cholesterol. Two clinical forms are recognized: familial LCAT deficiency and fish-eye disease. Familial LCAT deficiency is associated with a complete absence of alpha and beta LCAT activities and results in esterification anomalies involving both HDL (alpha-LCAT activity) and LDL (beta-LCAT activity). It causes a typical triad of diffuse corneal opacities, target cell hemolytic anemia, and proteinuria with renal failure.
DISEASE: Defects in LCAT are a cause of fish-eye disease (FED) [MIM:136120]; also known as dyslipoproteinemic corneal dystrophy or alpha-LCAT deficiency. FED is due to a partial LCAT deficiency that affects only alpha-LCAT activity. It is characterized by low plasma HDL and corneal opacities due to accumulation of cholesterol deposits in the cornea ('fish-eye').
MISCELLANEOUS: Levels of LCAT activity correlates inversely with leptin levels as well as with obesity for a wide range of BMI values.
SIMILARITY: Belongs to the AB hydrolase superfamily. Lipase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LCAT";
WEB RESOURCE: Name=Wikipedia; Note=Lecithin-cholesterol acyltransferase entry; URL="http://en.wikipedia.org/wiki/Lecithin-cholesterol_acyltransferase";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LCAT
Diseases sorted by gene-association score: norum disease* (1700), fish-eye disease* (1614), familial lcat deficiency* (419), eye disease (24), arcus senilis (24), tangier disease (18), hypoalphalipoproteinemia (17), algoneurodystrophy (16), abetalipoproteinemia (15), hyperalphalipoproteinemia (15), hypolipoproteinemia (13), hypobetalipoproteinemia (13), apo a-i deficiency (12), coronary artery disease (11), artery disease (9), north american indian childhood cirrhosis (9), sea-blue histiocyte disease (9), lipoprotein lipase deficiency (9), kwashiorkor (9), familial hyperlipidemia (8), defective apolipoprotein b-100 (8), cystinosis (8), fetal macrosomia (8), ethylmalonic encephalopathy (7), hypercholesterolemia, familial (7), lipoprotein glomerulopathy (7), alagille syndrome 1 (7), superficial keratitis (6), corneal disease (6), monocarboxylate transporter 1 deficiency (6), corneal degeneration (6), amyloidosis aa (5), corneal dystrophy, schnyder type (5), niemann-pick disease (5), chandler syndrome (5), corneal dystrophy, thiel-behnke type (4), tyrosinemia, type ii (4), lipid metabolism disorder (3), obesity (2), diabetes mellitus, noninsulin-dependent (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 82.54 RPKM in Liver
Total median expression: 709.99 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.5019-0.079 Picture PostScript Text
3' UTR -53.70154-0.349 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003386 - LACT/PDAT_acylTrfase

Pfam Domains:
PF02450 - Lecithin:cholesterol acyltransferase

SCOP Domains:
46934 - UBA-like
53474 - alpha/beta-Hydrolases

ModBase Predicted Comparative 3D Structure on P04180
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
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     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004607 phosphatidylcholine-sterol O-acyltransferase activity
GO:0005515 protein binding
GO:0008374 O-acyltransferase activity
GO:0016740 transferase activity
GO:0016746 transferase activity, transferring acyl groups
GO:0034186 apolipoprotein A-I binding

Biological Process:
GO:0006629 lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0030301 cholesterol transport
GO:0034372 very-low-density lipoprotein particle remodeling
GO:0034375 high-density lipoprotein particle remodeling
GO:0034435 cholesterol esterification
GO:0042158 lipoprotein biosynthetic process
GO:0042632 cholesterol homeostasis
GO:0043691 reverse cholesterol transport
GO:0046470 phosphatidylcholine metabolic process
GO:0090107 regulation of high-density lipoprotein particle assembly

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0034364 high-density lipoprotein particle
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF208288 - JP 2014500723-A/15791: Polycomb-Associated Non-Coding RNAs.
M12625 - Human lecithin-cholesterol acyltransferase mRNA, complete cds, with 5' and 3' flanking DNA sequences.
BC014781 - Homo sapiens lecithin-cholesterol acyltransferase, mRNA (cDNA clone MGC:17087 IMAGE:4155094), complete cds.
M26268 - Human lecithin:cholesterol acyltransferase (LCAT) mRNA, 3' end.
X06537 - Human mRNA for lecithin:cholesterol acyltransferase (LCAT); EC 2.3.1.43.
E01185 - DNA encoding lectin-cholesterol acyltransferase.
HM005564 - Homo sapiens clone HTL-S-24 testicular secretory protein Li 24 mRNA, complete cds.
BT009748 - Homo sapiens lecithin-cholesterol acyltransferase mRNA, complete cds.
KM576718 - Homo sapiens clone SLC12A4-LCAT_S26middle-L2 mRNA sequence.
AK310027 - Homo sapiens cDNA, FLJ17069.
MA443865 - JP 2018138019-A/15791: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P04180 (Reactome details) participates in the following event(s):

R-HSA-264678 LCAT + discoidal HDL <=> LCAT:discoidal HDL complex
R-HSA-266315 LCAT + spherical HDL <=> LCAT:spherical HDL complex
R-HSA-264689 LCAT:discoidal HDL complex <=> LCAT + discoidal HDL
R-HSA-266310 LCAT:spherical HDL complex <=> LCAT + spherical HDL
R-HSA-264695 cholesterol + phosphatidylcholine (lecithin) => cholesterol ester + 2-lysophosphatidylcholine (lysolecithin)
R-HSA-8964058 HDL remodeling
R-HSA-8963899 Plasma lipoprotein remodeling
R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000264005.1, ENST00000264005.2, ENST00000264005.3, ENST00000264005.4, ENST00000264005.5, ENST00000264005.6, ENST00000264005.7, ENST00000264005.8, ENST00000264005.9, LCAT_HUMAN, NM_000229, P04180, Q53XQ3, uc317hoe.1, uc317hoe.2
UCSC ID: ENST00000264005.10_7
RefSeq Accession: NM_000229.2
Protein: P04180 (aka LCAT_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.