LCAT lecithin-cholesterol acyltransferase [Homo sapiens (human)] - Gene

Summary

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Official Symbol: LCATprovided by HGNC
Official Full Name: lecithin-cholesterol acyltransferaseprovided by HGNC
Primary source: HGNC:6522
See related: Ensembl:ENSG00000213398; HPRD:06098; MIM:606967; Vega:OTTHUMG00000137551
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
Summary: This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency. [provided by RefSeq, Jul 2008]

Genomic context

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Location :: 16q22.1

Sequence :: Chromosome: 16; NC_000016.9 (67973787..67978015, complement)

See LCAT in Epigenomics, MapViewer

Chromosome 16 - NC_000016.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

Pulse wave velocity is increased in LCAT mutation carriers with low HDL-c and is associated with carotid wall thickening.
Title: Patients with low HDL-cholesterol caused by mutations in LCAT have increased arterial stiffness.
carriers of LCAT mutations present with significant reductions in LCAT activity, HDL cholesterol, apoA-I, platelet-activating factor-acetylhydrolase activity and antioxidative potential of HDL, but this is not associated with parameters of increased lipid peroxidation
Title: Lipid oxidation in carriers of lecithin:cholesterol acyltransferase gene mutations.
while LCAT activity is decreased in patients with T2DM, LCAT levels is increased. Patients with NIDDM exhibit opposing effects on LCAT activity and LCAT production which is more severe in women
Title: Diabetes induces gender gap on LCAT levels and activity.
Studies suggest that absence of lecithin cholesterol acyltransferase (LCAT) may protect against insulin resistance, diabetes and obesity.
Title: The role of lecithin:cholesterol acyltransferase in the modulation of cardiometabolic risks - a clinical update and emerging insights from animal models.
mutations in ABCA1, APOA1, and LCAT are sufficient to explain more tha 40 percent of familial hypoalphalipoproteinemia
Title: Increased risk of coronary artery disease in Caucasians with extremely low HDL cholesterol due to mutations in ABCA1, APOA1, and LCAT.
This review focuses on mutations in the LCAT gene as cause of familial hypoalphalipoproteinemia, and on their impact on plasma HDL-C, HDL profile and coronary heart disease.
Title: Genetic lecithin:cholesterol acyltransferase deficiency and cardiovascular disease.
Studies indicate the direct effects of HDL and its major modulators, ATP-binding cassette transporter A1 (ABCA1), apolipoprotein A-I (ApoA-I), and lecithin cholesterol acyltransferase (LCAT) on the development of type 2 diabetes mellitus (T2D).
Title: The role of HDL and its modulators in the development of diabetes.
functional mutations in LCAT were found in 29% of patients with low HDL-c, thus constituting a common cause of low HDL-c in referred patients in The Netherlands (LCAT)
Title: High prevalence of mutations in LCAT in patients with low HDL cholesterol levels in The Netherlands: identification and characterization of eight novel mutations.
Low plasma HDL cholesterol levels robustly associated with increased risk of MI but genetically decreased HDL cholesterol did not.
Title: LCAT, HDL cholesterol and ischemic cardiovascular disease: a Mendelian randomization study of HDL cholesterol in 54,500 individuals.
Continuous and intermittent walking alters HDL(2)-C and LCATa
Title: Continuous and intermittent walking alters HDL(2)-C and LCATa.

Submit: New GeneRIF Correction See all (63)

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

NHGRI GWAS Catalog

Biological, clinical and population relevance of 95 loci for blood lipids.

Common variants at 30 loci contribute to polygenic dyslipidemia.

Genetic variants influencing circulating lipid levels and risk of coronary artery disease.

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.

Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
P04180	P01023	A2M	HPRD	PubMed
P04180	P02647	APOA1	HPRD	PubMed
BioGRID:110123	BioGRID:106524	A2M	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex
BioGRID:110123	BioGRID:106832	APOA1	BioGRID	PubMed	Biochemical Activity; Co-purification; Reconstituted Complex
BioGRID:110123	BioGRID:106833	APOA2	BioGRID	PubMed	Co-purification

Pathways from BioSystems

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Glycerophospholipid metabolism, organism-specific biosystem (from KEGG)
Glycerophospholipid metabolism, organism-specific biosystem
Glycerophospholipid metabolism
Glycerophospholipid metabolism, conserved biosystem (from KEGG)
Glycerophospholipid metabolism, conserved biosystem
Glycerophospholipid metabolism
HDL-mediated lipid transport, organism-specific biosystem (from REACTOME)
HDL-mediated lipid transport, organism-specific biosystemHDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and e...
Lipid digestion, mobilization, and transport, organism-specific biosystem (from REACTOME)
Lipid digestion, mobilization, and transport, organism-specific biosystemProcesses annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids thr...
Lipoprotein metabolism, organism-specific biosystem (from REACTOME)
Lipoprotein metabolism, organism-specific biosystemBecause of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport ...
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
Statin Pathway, organism-specific biosystem (from WikiPathways)
Statin Pathway, organism-specific biosystemStatins inhibit endogenous cholesterol production by competitive inhibition of HMG-CoA reductase (HMGCR), the enzyme that catalyzes conversion of HMG-CoA to mevalonate, an early rate-limiting step in...

General gene information

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Markers

RH70676 (e-PCR)
- UniSTS:14116

SHGC-61154 (e-PCR)
- UniSTS:20352

Lcat (e-PCR), detects polymorphism
- UniSTS:507015

G11801 (e-PCR)
- UniSTS:77448

GDB:181557 (e-PCR)
- UniSTS:155283

SLC12A4_2007 (e-PCR)
- UniSTS:281001

RH79953 (e-PCR)
- UniSTS:84909

GDB:180918 (e-PCR)
- UniSTS:155123

Genotypes

See LCAT SNP Geneview Report
See LCAT SNP Genotype Report
See LCAT SNP Variation Viewer Report

Homology

Homologs of the LCAT gene: The LCAT gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, and zebrafish.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
apolipoprotein A-I binding	IPI Inferred from Physical Interaction more info	PubMed
phosphatidylcholine-sterol O-acyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
phosphatidylcholine-sterol O-acyltransferase activity	NAS Non-traceable Author Statement more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
cholesterol esterification	IDA Inferred from Direct Assay more info	PubMed
cholesterol homeostasis	IDA Inferred from Direct Assay more info	PubMed
cholesterol metabolic process	IDA Inferred from Direct Assay more info	PubMed
cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
high-density lipoprotein particle remodeling	IDA Inferred from Direct Assay more info	PubMed
lipid metabolic process	TAS Traceable Author Statement more info
lipoprotein biosynthetic process	IEA Inferred from Electronic Annotation more info
lipoprotein metabolic process	TAS Traceable Author Statement more info
phosphatidylcholine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
phospholipid metabolic process	IDA Inferred from Direct Assay more info	PubMed
regulation of high-density lipoprotein particle assembly	IEA Inferred from Electronic Annotation more info
reverse cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
small molecule metabolic process	TAS Traceable Author Statement more info
very-low-density lipoprotein particle remodeling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
extracellular region	TAS Traceable Author Statement more info
extracellular space	IDA Inferred from Direct Assay more info	PubMed
high-density lipoprotein particle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phosphatidylcholine-sterol acyltransferase

Names: phosphatidylcholine-sterol acyltransferase; phospholipid-cholesterol acyltransferase

NP_000220.1

EC 2.3.1.43

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

NG_009778.1 RefSeqGene

Range

5001..9229

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000229.1 → NP_000220.1 phosphatidylcholine-sterol acyltransferase precursor

Status: REVIEWED

Source sequence(s)

M12625

Consensus CDS

CCDS10854.1

UniProtKB/Swiss-Prot

P04180

Related

ENSP00000264005, OTTHUMP00000174856, ENST00000264005, OTTHUMT00000268885

Conserved Domains (2) summary

PLN02517
Location:321 – 351
Blast Score: 106

PLN02517; phosphatidylcholine-sterol O-acyltransferase

pfam02450
Location:81 – 408
Blast Score: 1129

LACT; Lecithin:cholesterol acyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000016.9 Reference GRCh37.p10 Primary Assembly

Range

67973787..67978015, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000148.1 Alternate HuRef

Range

53847357..53851585, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018927.1 Alternate CHM1_1.0

Range

68980216..68984444, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01025467.1 (22444..26672)	None
genomic	AC040162.5 (71765..75993)	None
genomic	AF140503.1	AAD28484.1
genomic	AMYH01007754.1 (92756..96984)	None
genomic	AY422210.1	AAR03499.1
genomic	CH471092.1	EAW83190.1
genomic	M17959.1	AAA59500.1
genomic	S74079.1	AAB20750.1
genomic	X04981.1	CAA28651.1
mRNA	BC014781.1	AAH14781.1
mRNA	BT009748.1	AAP88750.1
mRNA	M12625.1	AAA59498.1
mRNA	M26268.1	AAA59499.1
mRNA	X06537.1	CAB56610.1