LPGAT1
Basic information
Region (hg38): 1:211743457-211830763
Previous symbols: [ "FAM34A" ]
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 LPGAT1 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 8 | 0 | 1 |
Variants in LPGAT1
This is a list of pathogenic ClinVar variants found in the LPGAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-211749915-T-C | not specified | Uncertain significance (Jun 05, 2023) | ||
| 1-211749929-G-C | not specified | Uncertain significance (Jun 30, 2023) | ||
| 1-211749948-C-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-211750035-G-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-211751029-T-C | not specified | Uncertain significance (Sep 25, 2023) | ||
| 1-211751050-T-C | not specified | Uncertain significance (Jul 14, 2023) | ||
| 1-211751077-G-A | Benign (Jun 22, 2018) | |||
| 1-211783367-C-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 1-211783375-G-A | not specified | Uncertain significance (Jul 15, 2021) | ||
| 1-211793134-C-G | not specified | Uncertain significance (Jun 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LPGAT1 | protein_coding | protein_coding | ENST00000366997 | 7 | 87316 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.980 | 0.0196 | 125742 | 0 | 4 | 125746 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.39 | 100 | 194 | 0.516 | 0.00000925 | 2437 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Vitamin D Receptor Pathway;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.202
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.224
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.551
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lpgat1
- Phenotype
Gene ontology
- Biological process
- phospholipid metabolic process;phospholipid biosynthetic process;phosphatidylglycerol acyl-chain remodeling;positive regulation of fatty acid biosynthetic process
- Cellular component
- cytoplasm;endoplasmic reticulum membrane;membrane;integral component of membrane
- Molecular function
- molecular_function;1-acylglycerol-3-phosphate O-acyltransferase activity;transferase activity, transferring acyl groups;2-acylglycerol-3-phosphate O-acyltransferase activity