PLAAT2
Basic information
Region (hg38): 11:63552770-63563379
Previous symbols: [ "HRASLS2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (15 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAAT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017878.2. 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 | 13 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLAAT2 | protein_coding | protein_coding | ENST00000255695 | 4 | 10614 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000678 | 0.304 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.868 | 76 | 100 | 0.756 | 0.00000609 | 1027 |
| Missense in Polyphen | 23 | 33.192 | 0.69295 | 321 | ||
| Synonymous | 0.369 | 40 | 43.1 | 0.929 | 0.00000274 | 357 |
| Loss of Function | -0.187 | 6 | 5.53 | 1.09 | 2.33e-7 | 75 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000331 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Exhibits PLA1/2 activity, catalyzing the calcium- independent hydrolysis of acyl groups in various phosphatidylcholines (PC) and phosphatidylethanolamine (PE). For most substrates, PLA1 activity is much higher than PLA2 activity. Catalyzes N-acylation of PE using both sn-1 and sn-2 palmitoyl groups of PC as acyl donor. Also catalyzes O-acylation converting lyso-PC into PC. {ECO:0000269|PubMed:19615464, ECO:0000269|PubMed:22605381}.;
- Pathway
- Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE
(Consensus)
Recessive Scores
- pRec
- 0.0472
Intolerance Scores
- loftool
- 0.613
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.0102
- hipred
- N
- hipred_score
- 0.139
- ghis
- 0.486
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0115
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- lipid catabolic process;phosphatidylethanolamine acyl-chain remodeling
- Cellular component
- cytosol;integral component of membrane
- Molecular function
- transferase activity, transferring acyl groups;hydrolase activity