GeneBe

LPCAT2

protein-coding

lysophosphatidylcholine acyltransferase 2, the group of EF-hand domain containing|1-acylglycerol-3-phosphate O-acyltransferases

Gene 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]

Previous symbols:
  • AYTL1

MANE transcript

NM_017839.5

Inheritance

—

ClinVar variants

U:57B:10

Top phenotype

Multicentric osteolysis nodulosis arthropathy spectrum

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr16:55,509,072-55,586,666

External References & Databases

Ensembl (ENSG00000087253)NCBI Gene (54947)OMIM (612040)HGNC:26032GenCCUniProt (Q7L5N7)AlphaFoldClinVar (LPCAT2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~77.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LPCAT2 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 88
not providedTotal: 4
Multicentric osteolysis nodulosis arthropathy spectrumTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017839.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
53
clinvar
6
clinvar
3
clinvar
 62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total00577367
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_017839.5RefSeqNP_060309.214MANE Select
ENST00000262134.10EnsemblENSP00000262134.514MANE Select
ENST00000564084.1EnsemblENSP00000457496.17Standard
ENST00000929286.1EnsemblENSP00000599345.113Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ether lipid metabolism - Homo sapiens (human)
  • Glycerophospholipid metabolism - Homo sapiens (human)
  • Metabolism of lipids
  • Metabolism
  • Acyl chain remodelling of PC

Biological Process

  • platelet activating factor biosynthetic process
  • phosphatidylcholine acyl-chain remodeling
  • membrane organization

Molecular Function

  • 1-acylglycerol-3-phosphate O-acyltransferase activity
  • calcium ion binding
  • 2-acylglycerol-3-phosphate O-acyltransferase activity
  • 1-acylglycerophosphocholine O-acyltransferase activity
  • 1-alkylglycerophosphocholine O-acetyltransferase activity

Cellular Component

  • Golgi membrane
  • endoplasmic reticulum
  • endoplasmic reticulum membrane
  • Golgi stack
  • lipid droplet

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000262134
Coding exons
14
Length
77673
Individuals with no LoFs
125683
Homozygous LoFs
0
Heterozygous LoFs
62
Defined
125745
p
0.000247
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.011892850.6640.00001433490
Missense (PolyPhen)5184.4480.603921051
Synonymous-0.8291151041.100.000005241086
Loss of Function1.582029.20.6840.00000163346

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00110.0011notable
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000170.00017rare
South Asian0.000260.00026rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Possesses both acyltransferase and acetyltransferase activities. Activity is calcium-dependent. Involved in platelet- activating factor (PAF) biosynthesis by catalyzing the conversion of the PAF precursor, 1-O-alkyl-sn-glycero-3-phosphocholine (lyso- PAF) into 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF). Also converts lyso-PAF to 1-O-alkyl-2-acyl-sn-glycero-3- phosphocholine (PC), a major component of cell membranes and a PAF precursor. Under resting conditions, acyltransferase activity is preferred. Upon acute inflammatory stimulus, acetyltransferase activity is enhanced and PAF synthesis increases. Also catalyzes the conversion of 1-acyl-sn-glycero-3-phosphocholine to 1,2- diacyl-sn-glycero-3-phosphocholine. {ECO:0000269|PubMed:20363836, ECO:0000269|PubMed:21498505}.;

Recessive Scores

pRec
0.0959

Intolerance Scores

LoFtool
0.475
RVIS EVS
0.42
RVIS percentile EVS
77.06

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.290

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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