LPCAT2
Basic information
Region (hg38): 16:55509072-55586666
Previous symbols: [ "AYTL1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (81 variants)
- not_provided (4 variants)
- Multicentric_osteolysis_nodulosis_arthropathy_spectrum (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPCAT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017839.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 45 | 53 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 6 | 3 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LPCAT2 | protein_coding | protein_coding | ENST00000262134 | 14 | 77673 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.12e-10 | 0.754 | 125683 | 0 | 62 | 125745 | 0.000247 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.01 | 189 | 285 | 0.664 | 0.0000143 | 3490 |
| Missense in Polyphen | 51 | 84.448 | 0.60392 | 1051 | ||
| Synonymous | -0.829 | 115 | 104 | 1.10 | 0.00000524 | 1086 |
| Loss of Function | 1.58 | 20 | 29.2 | 0.684 | 0.00000163 | 346 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00138 | 0.00137 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.0000926 | 0.0000924 |
| European (Non-Finnish) | 0.000171 | 0.000167 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.000263 | 0.000261 |
| Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Possesses both acyltransferase and acetyltransferase activities. Activity is calcium-dependent. Involved in platelet- activating factor (PAF) biosynthesis by catalyzing the conversion of the PAF precursor, 1-O-alkyl-sn-glycero-3-phosphocholine (lyso- PAF) into 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF). Also converts lyso-PAF to 1-O-alkyl-2-acyl-sn-glycero-3- phosphocholine (PC), a major component of cell membranes and a PAF precursor. Under resting conditions, acyltransferase activity is preferred. Upon acute inflammatory stimulus, acetyltransferase activity is enhanced and PAF synthesis increases. Also catalyzes the conversion of 1-acyl-sn-glycero-3-phosphocholine to 1,2- diacyl-sn-glycero-3-phosphocholine. {ECO:0000269|PubMed:20363836, ECO:0000269|PubMed:21498505}.;
- Pathway
- Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Acyl chain remodelling of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.0959
Intolerance Scores
- loftool
- 0.475
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 77.06
Haploinsufficiency Scores
- pHI
- 0.0714
- hipred
- N
- hipred_score
- 0.307
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.290
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lpcat2
- Phenotype
Gene ontology
- Biological process
- platelet activating factor biosynthetic process;phosphatidylcholine acyl-chain remodeling;membrane organization
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi stack;lipid droplet;integral component of membrane
- Molecular function
- 1-acylglycerol-3-phosphate O-acyltransferase activity;calcium ion binding;2-acylglycerol-3-phosphate O-acyltransferase activity;1-acylglycerophosphocholine O-acyltransferase activity;1-alkylglycerophosphocholine O-acetyltransferase activity