LPCAT3
protein-codinglysophosphatidylcholine acyltransferase 3, the group of Membrane bound O-acyltransferase family
Gene summary
Enables 1-acylglycerophosphocholine O-acyltransferase activity; 1-acylglycerophosphoethanolamine O-acyltransferase activity; and 1-acylglycerophosphoserine O-acyltransferase activity. Involved in phosphatidylcholine acyl-chain remodeling; phosphatidylethanolamine acyl-chain remodeling; and phosphatidylserine acyl-chain remodeling. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jul 2025]
- OACT5
- MBOAT5
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~42.3 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 LPCAT3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005768.6. 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 | 1 | 3 | 1 | 5 | ||
| missense | 44 | 1 | 45 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 57 | 4 | 1 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005759.4 | 12 | MANE Select | |
| Ensembl | ENSP00000261407.4 | 12 | MANE Select | |
| Ensembl | ENSP00000438765.1 | 9 | Standard | |
| Ensembl | ENSP00000440550.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerophospholipid metabolism - Homo sapiens (human)
- Ferroptosis - Homo sapiens (human)
- Metabolism of lipids
- Metabolism
- CDP-diacylglycerol biosynthesis
Biological Process
- phospholipid biosynthetic process
- phosphatidylserine acyl-chain remodeling
- phosphatidylcholine acyl-chain remodeling
- phosphatidylethanolamine acyl-chain remodeling
- regulation of plasma lipoprotein particle levels
Molecular Function
- 1-acylglycerol-3-phosphate O-acyltransferase activity
- 2-acylglycerol-3-phosphate O-acyltransferase activity
- 1-acylglycerophosphocholine O-acyltransferase activity
Cellular Component
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000261407
- Coding exons
- 12
- Length
- 40467
- Individuals with no LoFs
- 125736
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125748
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 153 | 266 | 0.576 | 0.0000134 | 3164 |
| Missense (PolyPhen) | 46 | 105.89 | 0.4344 | 1246 | ||
| Synonymous | -0.117 | 107 | 105 | 1.01 | 0.00000546 | 945 |
| Loss of Function | 4.47 | 3 | 29.0 | 0.104 | 0.00000150 | 325 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acyltransferase which mediates the conversion of lysophosphatidylcholine (1-acyl-sn-glycero-3-phosphocholine or LPC) into phosphatidylcholine (1,2-diacyl-sn-glycero-3- phosphocholine or PC) (LPCAT activity). Catalyzes also the conversion of lysophosphatidylserine (1-acyl-2-hydroxy-sn-glycero- 3-phospho-L-serine or LPS) into phosphatidylserine (1,2-diacyl-sn- glycero-3-phospho-L-serine or PS) (LPSAT activity). Has also weak lysophosphatidylethanolamine acyltransferase activity (LPEAT activity). Favors polyunsaturated fatty acyl-CoAs as acyl donors compared to saturated fatty acyl-CoAs. Seems to be the major enzyme contributing to LPCAT activity in the liver. Lysophospholipid acyltransferases (LPLATs) catalyze the reacylation step of the phospholipid remodeling pathway also known as the Lands cycle. {ECO:0000269|PubMed:18195019, ECO:0000269|PubMed:18772128}.;
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- LoFtool
- 0.404
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |