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

Summary

Official Symbol: LCATprovided by HGNC
Official Full Name: lecithin-cholesterol acyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:6522
See related: Ensembl:ENSG00000213398 MIM:606967; AllianceGenome:HGNC:6522
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]
Expression: Broad expression in liver (RPKM 51.1), skin (RPKM 11.1) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (67939750..67944120, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (73735523..73739893, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (67973653..67978023, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rapidly progressive renal failure to reveal LCAT deficiency in an Algerian family.
Title: Rapidly progressive renal failure to reveal LCAT deficiency in an Algerian family.
Plasma FA composition in familial LCAT deficiency indicates SOAT2-derived cholesteryl ester formation in humans.
Title: Plasma FA composition in familial LCAT deficiency indicates SOAT2-derived cholesteryl ester formation in humans.
Altered HDL proteome predicts incident CVD in chronic kidney disease patients.
Title: Altered HDL proteome predicts incident CVD in chronic kidney disease patients.
LCAT deficiency: a systematic review with the clinical and genetic description of Mexican kindred.
Title: LCAT deficiency: a systematic review with the clinical and genetic description of Mexican kindred.
Genetic, biochemical, and clinical features of LCAT deficiency: update for 2020.
Title: Genetic, biochemical, and clinical features of LCAT deficiency: update for 2020.
Esterification of 4beta-hydroxycholesterol and other oxysterols in human plasma occurs independently of LCAT.
Title: Esterification of 4β-hydroxycholesterol and other oxysterols in human plasma occurs independently of LCAT.
Common plasma protein marker LCAT in aggressive human breast cancer and canine mammary tumor.
Title: Common plasma protein marker LCAT in aggressive human breast cancer and canine mammary tumor.
Single nucleotide polymorphisms in LCAT may contribute to dyslipidaemia in HIV-infected individuals on HAART in a Ghanaian population.
Title: Single nucleotide polymorphisms in LCAT may contribute to dyslipidaemia in HIV-infected individuals on HAART in a Ghanaian population.
ApoE and apoC-III-defined HDL subtypes: a descriptive study of their lecithin cholesterol acyl transferase and cholesteryl ester transfer protein content and activity.
Title: ApoE and apoC-III-defined HDL subtypes: a descriptive study of their lecithin cholesterol acyl transferase and cholesteryl ester transfer protein content and activity.
LCAT, ApoD, and ApoA1 Expression and Review of Cholesterol Deposition in the Cornea.
Title: LCAT, ApoD, and ApoA1 Expression and Review of Cholesterol Deposition in the Cornea.

Submit: New GeneRIF Correction See all GeneRIFs (104)

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

Associated conditions

Description	Tests
Fish-eye disease MedGen: C0342895 OMIM: 136120 GeneReviews: Not available	Compare labs
Norum disease MedGen: CN296455 OMIM: 245900 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants influencing circulating lipid levels and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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

Homology

Homologs of the LCAT gene: The LCAT gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 513 organisms have orthologs with human gene LCAT
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 1-alkyl-2-acetylglycerophosphocholine esterase activity	IDA Inferred from Direct Assay more info	PubMed
enables apolipoprotein A-I binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatidylcholine-sterol O-acyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables phosphatidylcholine-sterol O-acyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine-sterol O-acyltransferase activity	NAS Non-traceable Author Statement more info	PubMed
enables phosphatidylcholine-sterol O-acyltransferase activity	TAS Traceable Author Statement more info
enables phospholipase A2 activity	IEA Inferred from Electronic Annotation more info
enables platelet-activating factor acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sterol esterase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cholesterol homeostasis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cholesterol metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol metabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
involved_in high-density lipoprotein particle remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in high-density lipoprotein particle remodeling	TAS Traceable Author Statement more info
involved_in lipid metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in lipoprotein biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylcholine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylcholine biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphatidylcholine metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of high-density lipoprotein particle assembly	IEA Inferred from Electronic Annotation more info
involved_in response to copper ion	IEA Inferred from Electronic Annotation more info
involved_in response to glucocorticoid	IEA Inferred from Electronic Annotation more info
involved_in reverse cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
involved_in very-low-density lipoprotein particle remodeling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
part_of 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: 1-alkyl-2-acetylglycerophosphocholine esterase; PAF acetylhydrolase; phosphatidylcholine--sterol O-acyltransferase; phospholipid-cholesterol acyltransferase; platelet-activating factor acetylhydrolase; testicular secretory protein Li 24

NP_000220.1

EC 2.3.1.43

EC 3.1.1.47

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.