GPAT3
protein-codingglycerol-3-phosphate acyltransferase 3, the group of Glycerol-3-phosphate acyltransferases|1-acylglycerol-3-phosphate O-acyltransferases
Gene summary
This gene encodes a member of the lysophosphatidic acid acyltransferase protein family. The encoded protein is an enzyme which catalyzes the conversion of glycerol-3-phosphate to lysophosphatidic acid in the synthesis of triacylglycerol. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2012]
- AGPAT9
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~70.0 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 GPAT3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032717.5. 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 | ||||
| missense | 63 | 1 | 64 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 67 | 0 | 1 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_116106.2 | 12 | MANE Select | |
| Ensembl | ENSP00000264409.4 | 12 | MANE Select | |
| RefSeq | NP_001243350.1 | 12 | Standard | |
| RefSeq | NP_001243351.1 | 12 | 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)
- HIF1A and PPARG regulation of glycolysis
- Metabolism of lipids
- Metabolism
Biological Process
- phosphatidic acid biosynthetic process
- CDP-diacylglycerol biosynthetic process
- triglyceride biosynthetic process
- regulation of TOR signaling
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
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395226
- Coding exons
- 12
- Length
- 69962
- Individuals with no LoFs
- 125544
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 203
- Defined
- 125747
- p
- 0.000807
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.442 | 220 | 239 | 0.920 | 0.0000120 | 2820 |
| Missense (PolyPhen) | 72 | 75.444 | 0.95436 | 860 | ||
| Synonymous | -1.32 | 103 | 87.3 | 1.18 | 0.00000443 | 854 |
| Loss of Function | 1.12 | 21 | 27.3 | 0.768 | 0.00000159 | 295 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00055 | 0.00055 | rare |
| Latino/Admixed American | 0.00081 | 0.00081 | rare |
| Ashkenazi Jewish | 0.00069 | 0.00069 | rare |
| East Asian | 0.0012 | 0.0012 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00090 | 0.00090 | rare |
| South Asian | 0.00079 | 0.00078 | rare |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May transfer the acyl-group from acyl-coA to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis. Also transfers the acyl-group from acyl-coA to the sn-2 position of 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid, or LPA), forming 1,2-diacyl-sn-glycerol-3- phosphate (phosphatidic acid, or PA). {ECO:0000269|PubMed:17002884, ECO:0000269|PubMed:17170135, ECO:0000269|PubMed:19318427}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 46.99
Essentials
- Essential (gene trap)
- N