LPGAT1
protein-codinglysophosphatidylglycerol acyltransferase 1
Gene summary
This gene encodes a member of the lysophospholipid acyltransferase family. The encoded protein catalyzes the reacylation of lysophosphatidylglycerol to phosphatidylglycerol, a membrane phospholipid that is an important precursor for the synthesis of cardiolipin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
- FAM34A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~87.3 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 LPGAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014873.3. 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 | 0 | |||||
| missense | 27 | 27 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 0 | 0 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055688.1 | 7 | MANE Select | |
| Ensembl | ENSP00000355964.4 | 7 | MANE Select | |
| RefSeq | NP_001307737.1 | 7 | Standard | |
| RefSeq | NP_001362770.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerophospholipid metabolism - Homo sapiens (human)
- Vitamin D Receptor Pathway
- Acyl chain remodelling of PG
- Metabolism of lipids
- Metabolism
Biological Process
- phospholipid metabolic process
- phospholipid biosynthetic process
- phosphatidylglycerol acyl-chain remodeling
- positive regulation of fatty acid biosynthetic process
Molecular Function
- molecular_function
- 1-acylglycerol-3-phosphate O-acyltransferase activity
- transferase activity, transferring acyl groups
- 2-acylglycerol-3-phosphate O-acyltransferase activity
Cellular Component
- cytoplasm
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000366997
- Coding exons
- 7
- Length
- 87316
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125746
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.39 | 100 | 194 | 0.516 | 0.00000925 | 2437 |
| Missense (PolyPhen) | 17 | 75.353 | 0.2256 | 927 | ||
| Synonymous | 0.884 | 55 | 64.0 | 0.859 | 0.00000294 | 675 |
| Loss of Function | 3.82 | 2 | 20.8 | 0.0960 | 0.00000110 | 231 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Lysophosphatidylglycerol (LPG) specific acyltransferase that recognizes various acyl-CoAs and LPGs as substrates but demonstrates a clear preference for long chain saturated fatty acyl-CoAs and oleoyl-CoA as acyl donors. Prefers oleoyl-LPG over palmitoyl-LPG as an acyl receptor and oleoyl-CoA over lauroyl-CoA as an acyl donor. {ECO:0000269|PubMed:15485873}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.202
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.4
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |