AGPAT1
Basic information
Region (hg38): 6:32168212-32178096
Links
Phenotypes
GenCC
Source:
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 AGPAT1 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 | 0 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in AGPAT1
This is a list of pathogenic ClinVar variants found in the AGPAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-32169284-C-T | not specified | Likely benign (May 21, 2024) | ||
| 6-32169319-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 6-32169340-C-T | not specified | Uncertain significance (May 16, 2023) | ||
| 6-32171310-C-T | not specified | Uncertain significance (Jul 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AGPAT1 | protein_coding | protein_coding | ENST00000395499 | 6 | 9885 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0278 | 125745 | 0 | 3 | 125748 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.61 | 80 | 178 | 0.450 | 0.0000116 | 1810 |
| Missense in Polyphen | 10 | 43.6 | 0.22936 | 445 | ||
| Synonymous | 1.64 | 56 | 74.0 | 0.757 | 0.00000468 | 616 |
| Loss of Function | 3.41 | 1 | 15.5 | 0.0647 | 0.00000102 | 133 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000180 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
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. {ECO:0000269|PubMed:21873652}.;
- Pathway
- Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Familial lipoprotein lipase deficiency;Plasmalogen Synthesis;Glycerolipid Metabolism;Glycerol Kinase Deficiency;Phospholipid Biosynthesis;D-glyceric acidura;Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA
(Consensus)
Intolerance Scores
- loftool
- 0.214
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.382
- hipred
- Y
- hipred_score
- 0.631
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Agpat1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- positive regulation of cytokine production;positive regulation of cytokine-mediated signaling pathway;phospholipid metabolic process;phosphatidic acid biosynthetic process;CDP-diacylglycerol biosynthetic process;positive regulation of cellular metabolic process
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane
- Molecular function
- 1-acylglycerol-3-phosphate O-acyltransferase activity;protein binding