GPAT4
protein-codingglycerol-3-phosphate acyltransferase 4, the group of Glycerol-3-phosphate acyltransferases|1-acylglycerol-3-phosphate O-acyltransferases
Gene summary
Lysophosphatidic acid acyltransferases (EC 2.3.1.51) catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are involved in signal transduction and lipid biosynthesis.[supplied by OMIM, Apr 2004]
- AGPAT6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.8 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 GPAT4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_178819.4. 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 | 1 | 2 | |||
| missense | 31 | 1 | 32 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 37 | 1 | 1 | 39 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_848934.1 | 12 | MANE Select | |
| Ensembl | ENSP00000380184.3 | 12 | MANE Select | |
| RefSeq | NP_001350126.1 | 12 | Standard | |
| RefSeq | NP_001350127.1 | 8 | Standard |
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)
- Metabolism of lipids
- Metabolism
- CDP-diacylglycerol biosynthesis
Biological Process
- glandular epithelial cell maturation
- fatty acid metabolic process
- acyl-CoA metabolic process
- phosphatidic acid biosynthetic process
- phosphatidylcholine biosynthetic process
Molecular Function
- 1-acylglycerol-3-phosphate O-acyltransferase activity
- glycerol-3-phosphate O-acyltransferase activity
- sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase 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
- ENST00000396987
- Coding exons
- 12
- Length
- 47815
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.70 | 140 | 263 | 0.531 | 0.0000144 | 2996 |
| Missense (PolyPhen) | 35 | 77.196 | 0.45339 | 838 | ||
| Synonymous | 0.0446 | 100 | 101 | 0.994 | 0.00000583 | 872 |
| Loss of Function | 3.47 | 7 | 26.2 | 0.268 | 0.00000135 | 293 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| 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) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Esterifies acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis. Active against both saturated and unsaturated long- chain fatty acyl-CoAs. {ECO:0000269|PubMed:18238778}.;
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- RVIS EVS
- -0.41
- RVIS percentile EVS
- 26.23
Essentials
- Essential (gene trap)
- N