LPCAT2 lysophosphatidylcholine acyltransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LPCAT2provided by HGNC
Official Full Name: lysophosphatidylcholine acyltransferase 2provided by HGNC
Primary source: HGNC:HGNC:26032
See related: Ensembl:ENSG00000087253 MIM:612040; AllianceGenome:HGNC:26032
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: AYTL1; LPLAT9; AGPAT11; LysoPAFAT
Summary: This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi. [provided by RefSeq, Feb 2009]
Expression: Broad expression in thyroid (RPKM 50.3), bone marrow (RPKM 11.0) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q12.2

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (55509072..55586666)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (61307195..61384805)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (55542984..55620578)

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?

Lysophosphatidylcholine acyltransferase 2 (LPCAT2) co-localises with TLR4 and regulates macrophage inflammatory gene expression in response to LPS.
Title: Lysophosphatidylcholine acyltransferase 2 (LPCAT2) co-localises with TLR4 and regulates macrophage inflammatory gene expression in response to LPS.
three of these five genes (CXCL14, ITGAX, and LPCAT2) harbored polymorphisms associated with aggressive disease development in a human GWAS cohort consisting of 1,172 prostate cancer patients.
Title: A systems genetics approach identifies CXCL14, ITGAX, and LPCAT2 as novel aggressive prostate cancer susceptibility genes.
Data indicate a strong negative correlation between ALOX15, FADS2, and IL5RA expression with 2-arachidonoylglycerophosphocholine levels in dual asthmatic responses.
Title: Gene-metabolite expression in blood can discriminate allergen-induced isolated early from dual asthmatic responses.
LPCAT1 and -2 have, in addition to their known function in specialized cells, a ubiquitous role in LD-associated lipid metabolism
Title: Human lysophosphatidylcholine acyltransferases 1 and 2 are located in lipid droplets where they catalyze the formation of phosphatidylcholine.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
Our enzymatic assays strongly suggest that the cDNA previously identified as LPCAT2/lyso platelet-activating factor-acetyltransferase cDNA has AGPAT activity and thus we prefer to identify this clone as AGPAT11 as well.
Title: Enzymatic activity of the human 1-acylglycerol-3-phosphate-O-acyltransferase isoform 11: upregulated in breast and cervical cancers.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
The enzyme acetyl-CoA:LYSO-PAF acetyltransferase catalyzes not only biosynthesis of PAF upon acute inflammatory stimulation but also incorporation of arachidonoyl-CoA to produce PAF precursor membrane glycerophospholipids for membrane biogenesis.
Title: A single enzyme catalyzes both platelet-activating factor production and membrane biogenesis of inflammatory cells. Cloning and characterization of acetyl-CoA:LYSO-PAF acetyltransferase.

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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 meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function. 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

D16S2539E (e-PCR)
- UniSTS:151630

RH94125 (e-PCR)
- UniSTS:85670

RH119098 (e-PCR)
- UniSTS:138431

D11S3316 (e-PCR)
- UniSTS:152558

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 1-acylglycerol-3-phosphate O-acyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables 1-acylglycerol-3-phosphate O-acyltransferase activity	TAS Traceable Author Statement more info
enables 1-acylglycerophosphocholine O-acyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables 1-acylglycerophosphocholine O-acyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 1-alkenylglycerophosphocholine O-acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables 1-alkylglycerophosphocholine O-acetyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 2-acylglycerol-3-phosphate O-acyltransferase activity	TAS Traceable Author Statement more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables lysophosphatidic acid acyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables plasmalogen synthase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in membrane organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphatidylcholine acyl-chain remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylcholine acyl-chain remodeling	TAS Traceable Author Statement more info
involved_in platelet activating factor biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in Golgi stack	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in lipid droplet	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysophosphatidylcholine acyltransferase 2

Names: 1-AGP acyltransferase 11; 1-AGPAT 11; 1-acylglycerol-3-phosphate O-acyltransferase 11; 1-acylglycerophosphocholine O-acyltransferase; 1-alkenylglycerophosphocholine O-acyltransferase; 1-alkylglycerophosphocholine O-acetyltransferase; LPAAT-alpha; LPC acyltransferase 2; LPCAT-2; acetyl-CoA:lyso-PAF acetyltransferase; acetyl-CoA:lyso-platelet-activating factor acetyltransferase; acyl-CoA:lysophosphatidylcholine acyltransferase 2; acyltransferase-like 1; lyso-PAF acetyltransferase; lyso-platelet-activating factor (PAF) acetyltransferase; lysoPC acyltransferase 2; lysophosphatidic acid acyltransferase alpha; lysophospholipid acyltransferase 9

NP_060309.2

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_005256063.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_011521471.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_047290233.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_054236561.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_054236562.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

XP_054236563.1

EC 2.3.1.23

EC 2.3.1.25

EC 2.3.1.51

EC 2.3.1.67

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.

mRNA and Protein(s)

NM_017839.5 → NP_060309.2 lysophosphatidylcholine acyltransferase 2

See identical proteins and their annotated locations for NP_060309.2

Status: REVIEWED

Source sequence(s)

AI915099, AW366682, BC002472, BC005981, BX641069

Consensus CDS

CCDS10753.1

UniProtKB/Swiss-Prot

A3KBM1, Q6MZJ6, Q7L5N7, Q9NX23

Related

ENSP00000262134.5, ENST00000262134.10

Conserved Domains (2) summary

cd07991
Location:116 → 327

LPLAT_LPCAT1-like; Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LPCAT1-like

cl25352
Location:374 → 494

EFh_PEF; The penta-EF hand (PEF) family

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

55509072..55586666

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005256006.4 → XP_005256063.1 lysophosphatidylcholine acyltransferase 2 isoform X2

Conserved Domains (2) summary

cd07991
Location:116 → 287

LPLAT_LPCAT1-like; Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LPCAT1-like

COG0204
Location:103 → 254

PlsC; 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid transport and metabolism]
XM_047434277.1 → XP_047290233.1 lysophosphatidylcholine acyltransferase 2 isoform X1
XM_011523169.4 → XP_011521471.1 lysophosphatidylcholine acyltransferase 2 isoform X3

UniProtKB/Swiss-Prot

Q7L5N7

Related

ENST00000566915.5

Conserved Domains (3) summary

cd00051
Location:126 → 188

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam13499
Location:126 → 187

EF-hand_7; EF-hand domain pair

cl17185
Location:2 → 57

LPLAT; Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

61307195..61384805

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054380587.1 → XP_054236562.1 lysophosphatidylcholine acyltransferase 2 isoform X2
XM_054380586.1 → XP_054236561.1 lysophosphatidylcholine acyltransferase 2 isoform X1
XM_054380588.1 → XP_054236563.1 lysophosphatidylcholine acyltransferase 2 isoform X3