LPCAT4
protein-codinglysophosphatidylcholine acyltransferase 4, the group of 1-acylglycerol-3-phosphate O-acyltransferases
Gene summary
Members of the 1-acylglycerol-3-phosphate O-acyltransferase (EC 2.3.1.51) family, such as AGPAT7, catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA), a precursor in the biosynthesis of all glycerolipids. Both LPA and PA are involved in signal transduction (Ye et al., 2005 [PubMed 16243729]).[supplied by OMIM, May 2008]
- AYTL3
- AGPAT7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.6 kbGenCC 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 LPCAT4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153613.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 68 | 1 | 69 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 73 | 2 | 0 | 75 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_705841.2 | 14 | MANE Select | |
| Ensembl | ENSP00000317300.6 | 14 | MANE Select | |
| Ensembl | ENSP00000454422.1 | 3 | Standard | |
| Ensembl | ENSP00000597868.1 | 14 | Standard |
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)
- Acyl chain remodelling of PG
- Metabolism of lipids
- Metabolism
Biological Process
- phospholipid metabolic process
- phosphatidic acid biosynthetic process
- phosphatidylglycerol acyl-chain remodeling
- phosphatidylserine acyl-chain remodeling
- phosphatidylcholine acyl-chain remodeling
Molecular Function
- 1-acylglycerol-3-phosphate O-acyltransferase activity
- 2-acylglycerol-3-phosphate O-acyltransferase activity
- 1-alkenylglycerophosphoethanolamine O-acyltransferase activity
- 1-acylglycerophosphocholine O-acyltransferase activity
- 1-alkylglycerophosphocholine O-acetyltransferase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000314891
- Coding exons
- 14
- Length
- 8374
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125748
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.55 | 224 | 299 | 0.749 | 0.0000171 | 3300 |
| Missense (PolyPhen) | 60 | 113.72 | 0.52762 | 1209 | ||
| Synonymous | 0.709 | 110 | 120 | 0.918 | 0.00000638 | 1147 |
| Loss of Function | 4.12 | 7 | 32.2 | 0.217 | 0.00000206 | 294 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Displays acyl-CoA-dependent lysophospholipid acyltransferase activity with a subset of lysophospholipids as substrates; converts lysophosphatidylethanolamine to phosphatidylethanolamine, lysophosphatidylcholine to phosphatidycholine, 1-alkenyl-lysophatidylethanolamine to 1- alkenyl-phosphatidylethanolamine, lysophosphatidylglycerol and alkyl-lysophosphatidylcholine to phosphatidylglycerol and alkyl- phosphatidylcholine, respectively. In contrast, has no lysophosphatidylinositol, glycerol-3-phosphate, diacylglycerol or lysophosphatidic acid acyltransferase activity. Prefers long chain acyl-CoAs (C16, C18) as acyl donors. {ECO:0000269|PubMed:18458083}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.121
- RVIS EVS
- -0.4
- RVIS percentile EVS
- 26.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.249
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |