AGPAT3
1-acylglycerol-3-phosphate O-acyltransferase 3, the group of 1-acylglycerol-3-phosphate O-acyltransferases
Basic information
Region (hg38): 21:43865223-43987592
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGPAT3 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 3 | 1 |
Variants in AGPAT3
This is a list of pathogenic ClinVar variants found in the AGPAT3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-43959714-C-T | Benign (Dec 01, 2022) | |||
| 21-43959715-G-A | not specified | Uncertain significance (Jul 26, 2023) | ||
| 21-43959814-C-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 21-43959835-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 21-43968104-G-A | not specified | Uncertain significance (Jun 13, 2023) | ||
| 21-43968122-G-A | Likely benign (Apr 01, 2023) | |||
| 21-43969132-C-A | Likely benign (Apr 01, 2023) | |||
| 21-43969173-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 21-43969224-G-A | not specified | Uncertain significance (Feb 21, 2024) | ||
| 21-43969250-C-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 21-43969251-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 21-43969268-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 21-43970676-G-A | Likely benign (Aug 01, 2023) | |||
| 21-43971390-G-A | not specified | Uncertain significance (May 27, 2022) | ||
| 21-43971429-A-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 21-43971470-C-A | Intellectual disability | Pathogenic (-) | ||
| 21-43978083-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 21-43981058-C-G | not specified | Uncertain significance (Sep 29, 2022) | ||
| 21-43982362-C-T | not specified | Likely benign (Feb 26, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AGPAT3 | protein_coding | protein_coding | ENST00000398063 | 8 | 121351 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000672 | 125734 | 0 | 7 | 125741 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.54 | 131 | 242 | 0.541 | 0.0000165 | 2434 |
| Missense in Polyphen | 12 | 62.055 | 0.19338 | 573 | ||
| Synonymous | 0.816 | 97 | 108 | 0.900 | 0.00000790 | 758 |
| Loss of Function | 4.25 | 0 | 21.1 | 0.00 | 0.00000109 | 213 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone. Acts on LPA containing saturated or unsaturated fatty acids C16:0-C20:4 at the sn-1 position using C18:1, C20:4 or C18:2-CoA as the acyl donor. Also acts on lysophosphatidylcholine, lysophosphatidylinositol and lysophosphatidylserine using C18:1 or C20:4-CoA (PubMed:21173190). Has a preference for arachidonoyl-CoA as a donor. Has also a modest lysophosphatidylinositol acyltransferase (LPIAT) activity, converts lysophosphatidylinositol (LPI) into phosphatidylinositol (By similarity). {ECO:0000250|UniProtKB:Q9D517, ECO:0000269|PubMed:21173190}.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Triacylglyceride Synthesis;Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;triacylglycerol biosynthesis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.36
Haploinsufficiency Scores
- pHI
- 0.112
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.538
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Agpat3
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- phospholipid metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;CDP-diacylglycerol biosynthetic process
- Cellular component
- Golgi membrane;nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
- Molecular function
- 1-acylglycerol-3-phosphate O-acyltransferase activity;transferase activity, transferring acyl groups