PLAAT3
phospholipase A and acyltransferase 3, the group of Phospholipase A and acyltransferase family|Phospholipases
Basic information
Region (hg38): 11:63573195-63616883
Previous symbols: [ "HRASLS3", "PLA2G16" ]
Links
Phenotypes
GenCC
Source:
- lipodystrophy, familial partial, type 9 (Limited), mode of inheritance: AR
- lipodystrophy, familial partial, type 9 (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Lipodystrophy, familial partial, type 9 | AR | Cardiovascular; Endocrine | The condition has been described as involving dyslipidemia, fatty liver, and insulin-resistant diabetes mellitus, and awareness may enable early identification and management | Cardiovascular; Craniofacial; Endocrine; Musculoskeletal; Neurologic | 37919452 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- Lipodystrophy,_familial_partial,_type_9 (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAAT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001128203.2. 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 | 0 | |||||
| missense | 34 | 34 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 4 | 0 | 34 | 0 | 0 |
Highest pathogenic variant AF is 0.0000065695253
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLAAT3 | protein_coding | protein_coding | ENST00000323646 | 4 | 43689 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000181 | 0.145 | 125728 | 0 | 19 | 125747 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.178 | 97 | 102 | 0.950 | 0.00000600 | 1056 |
| Missense in Polyphen | 30 | 28.192 | 1.0641 | 336 | ||
| Synonymous | -0.479 | 45 | 41.1 | 1.10 | 0.00000267 | 315 |
| Loss of Function | -0.490 | 8 | 6.64 | 1.21 | 2.80e-7 | 87 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Lipid-modifying enzyme that acts as major regulator of adipocyte lipolysis by catalyzing the release of fatty acids from phospholipids in adipose tissue (PubMed:19615464, PubMed:19047760, PubMed:20837014, PubMed:22605381, PubMed:22923616). Shows phospholipase A1 and A2 activity, catalyzing the calcium- independent hydrolysis of acyl groups in various phosphatidylcholines (PC) and phosphatidylethanolamine (PE) (PubMed:19615464, PubMed:19047760, PubMed:20837014, PubMed:22605381, PubMed:22923616). For most substrates, phospholipase A1 activity is much higher than phospholipase A2 activity (PubMed:19047760). Phospholipase activity causes decreased intracellular levels of ether-type lipids, affecting peroxisome metabolism (By similarity). May also have acyltransferase activity: catalyzes both N-acylation of phosphatidylethanolamine to form N-acyl-phosphatidylethanolamine and O-acylation of lyso-phosphatidylcholines to form phosphatidylcholines (PubMed:22605381, PubMed:25383759). The relevance of acyltransferase activity in vivo is however unclear and would require additional evidences (PubMed:22605381, PubMed:25383759). Also has weak lysophospholipase activity (By similarity). {ECO:0000250|UniProtKB:Q8R3U1, ECO:0000269|PubMed:17374643, ECO:0000269|PubMed:19047760, ECO:0000269|PubMed:19615464, ECO:0000269|PubMed:20837014, ECO:0000269|PubMed:22605381, ECO:0000269|PubMed:22923616, ECO:0000269|PubMed:25383759}.;
- Pathway
- Regulation of lipolysis in adipocytes - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Ras Signaling;Acyl chain remodelling of PI;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE
(Consensus)
Recessive Scores
- pRec
- 0.0873
Intolerance Scores
- loftool
- 0.675
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.478
- hipred
- N
- hipred_score
- 0.131
- ghis
- 0.469
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.881
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pla2g16
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); liver/biliary system phenotype;
Gene ontology
- Biological process
- triglyceride metabolic process;phospholipid metabolic process;peroxisome organization;phospholipid biosynthetic process;response to bacterium;lipid catabolic process;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;negative regulation of cell cycle;ether lipid metabolic process;regulation of adipose tissue development
- Cellular component
- cellular_component;peroxisome;peroxisomal membrane;endoplasmic reticulum;cytosol;integral component of membrane;perinuclear region of cytoplasm
- Molecular function
- phospholipase A2 activity;protein binding;phospholipase A1 activity;transferase activity, transferring acyl groups;phosphatidylserine 1-acylhydrolase activity;1-acyl-2-lysophosphatidylserine acylhydrolase activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)