PLAAT4
protein-codingphospholipase A and acyltransferase 4, the group of Phospholipase A and acyltransferase family
Gene summary
Retinoids exert biologic effects such as potent growth inhibitory and cell differentiation activities and are used in the treatment of hyperproliferative dermatological diseases. These effects are mediated by specific nuclear receptor proteins that are members of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. RARRES1, RARRES2, and RARRES3 are genes whose expression is upregulated by the synthetic retinoid tazarotene. RARRES3 is thought act as a tumor suppressor or growth regulator. [provided by RefSeq, Jul 2008]
- RARRES3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLAAT4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004585.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 30 | 3 | 33 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 33 | 4 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004576.2 | 4 | MANE Select | |
| Ensembl | ENSP00000255688.3 | 4 | MANE Select | |
| Ensembl | ENSP00000346431.2 | 4 | Standard | |
| Ensembl | ENSP00000402943.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Glycerophospholipid biosynthesis
- Phospholipid metabolism
- Acyl chain remodelling of PE
Biological Process
- phospholipid metabolic process
- negative regulation of cell population proliferation
- lipid catabolic process
- phosphatidylethanolamine acyl-chain remodeling
Molecular Function
- phospholipase A2 activity
- protein binding
- transferase activity, transferring acyl groups
Cellular Component
- cytosol
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000255688
- Coding exons
- 4
- Length
- 9654
- Individuals with no LoFs
- 125593
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 20
- Defined
- 125613
- p
- 0.0000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.362 | 88 | 98.1 | 0.897 | 0.00000614 | 1062 |
| Missense (PolyPhen) | 19 | 27.888 | 0.6813 | 328 | ||
| Synonymous | -0.149 | 39 | 37.8 | 1.03 | 0.00000231 | 321 |
| Loss of Function | -1.03 | 9 | 6.23 | 1.45 | 2.64e-7 | 79 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000054 | rare |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
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. N- and O-acylation activity is hardly detectable. {ECO:0000269|PubMed:19615464}.;
Intolerance Scores
- LoFtool
- 0.723
- RVIS EVS
- -0.41
- RVIS percentile EVS
- 26.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.559
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |