LCLAT1
protein-codinglysocardiolipin acyltransferase 1, the group of 1-acylglycerol-3-phosphate O-acyltransferases
Gene summary
Enables 1-acylglycerol-3-phosphate O-acyltransferase activity. Predicted to be involved in phosphatidylinositol acyl-chain remodeling. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]
- LYCAT
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~197.0 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 LCLAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001002257.3. 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 | 2 | ||||
| missense | 46 | 2 | 48 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 50 | 2 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001002257.1 | 5 | MANE Select | |
| Ensembl | ENSP00000368823.3 | 5 | MANE Select | |
| RefSeq | NP_001291374.1 | 5 | Standard | |
| RefSeq | NP_001291375.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lclat1 | Danio rerio | Structure: endothelial cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerolipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
Biological Process
- phospholipid metabolic process
- phosphatidic acid biosynthetic process
- multicellular organism development
- CDP-diacylglycerol biosynthetic process
- cardiolipin acyl-chain remodeling
Molecular Function
- 1-acylglycerol-3-phosphate O-acyltransferase activity
- protein binding
- O-acyltransferase activity
- transferase activity, transferring acyl groups
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- cytosol
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309052
- Coding exons
- 6
- Length
- 197000
- Individuals with no LoFs
- 125721
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 27
- Defined
- 125748
- p
- 0.000107
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.923 | 189 | 228 | 0.828 | 0.0000118 | 2753 |
| Missense (PolyPhen) | 30 | 59.562 | 0.50367 | 716 | ||
| Synonymous | -1.04 | 89 | 77.3 | 1.15 | 0.00000396 | 749 |
| Loss of Function | 2.15 | 9 | 19.2 | 0.470 | 9.59e-7 | 218 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acyl-CoA:lysocardiolipin acyltransferase. Possesses both lysophosphatidylinositol acyltransferase (LPIAT) and lysophosphatidylglycerol acyltransferase (LPGAT) activities. Recognizes both monolysocardiolipin and dilysocardiolipin as substrates with a preference for linoleoyl-CoA and oleoyl-CoA as acyl donors. Acts as a remodeling enzyme for cardiolipin, a major membrane polyglycerophospholipid. Converts lysophosphatidic acid (LPA) into phosphatidic acid (PA) with a relatively low activity. Required for establishment of the hematopoietic and endothelial lineages. {ECO:0000269|PubMed:16620771, ECO:0000269|PubMed:19075029}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.317
- RVIS EVS
- -0.11
- RVIS percentile EVS
- 45.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.530
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |