PTAFR
protein-codingplatelet activating factor receptor, the group of Platelet activating factor receptor
Gene summary
This gene encodes a seven-transmembrane G-protein-coupled receptor for platelet-activating factor (PAF) that localizes to lipid rafts and/or caveolae in the cell membrane. PAF (1-0-alkyl-2-acetyl-sn-glycero-3-phosphorylcholine) is a phospholipid that plays a significant role in oncogenic transformation, tumor growth, angiogenesis, metastasis, and pro-inflammatory processes. Binding of PAF to the PAF-receptor (PAFR) stimulates numerous signal transduction pathways including phospholipase C, D, A2, mitogen-activated protein kinases (MAPKs), and the phosphatidylinositol-calcium second messenger system. Following PAFR activation, cells become rapidly desensitized and this refractory state is dependent on PAFR phosphorylation, internalization, and down-regulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~46.8 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 PTAFR variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000952.5. 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 | 41 | 2 | 1 | 44 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 2 | 1 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000943.1 | 1 | MANE Select | |
| Ensembl | ENSP00000362965.3 | 1 | MANE Select | |
| RefSeq | NP_001158193.1 | 1 | Standard | |
| RefSeq | NP_001158194.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Staphylococcus aureus infection - Homo sapiens (human)
- Calcium signaling pathway - Homo sapiens (human)
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
- Small Ligand GPCRs
- Interleukin-10 signaling
Biological Process
- cytokine production
- regulation of transcription by RNA polymerase II
- chemotaxis
- inflammatory response
- immune response
Molecular Function
- lipopolysaccharide binding
- lipopolysaccharide receptor activity
- G protein-coupled receptor activity
- platelet activating factor receptor activity
- phospholipid binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
- integral component of membrane
- secretory granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373857
- Coding exons
- 1
- Length
- 46771
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125743
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.45 | 159 | 219 | 0.725 | 0.0000137 | 2268 |
| Missense (PolyPhen) | 53 | 86.68 | 0.61145 | 984 | ||
| Synonymous | 0.987 | 76 | 87.8 | 0.866 | 0.00000556 | 690 |
| Loss of Function | 1.84 | 2 | 7.42 | 0.269 | 3.16e-7 | 85 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth- muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol- calcium second messenger system. {ECO:0000269|PubMed:1281995, ECO:0000269|PubMed:1374385, ECO:0000269|PubMed:1656963, ECO:0000269|PubMed:1657923}.;
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- LoFtool
- 0.631
- RVIS EVS
- 0.66
- RVIS percentile EVS
- 84.44
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |