PTAFR
platelet activating factor receptor, the group of Platelet activating factor receptor
Basic information
Region (hg38): 1:28147166-28193936
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTAFR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000952.5. 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 | 0 | |||||
| missense | 37 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTAFR | protein_coding | protein_coding | ENST00000373857 | 1 | 46771 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.242 | 0.730 | 125735 | 0 | 8 | 125743 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.45 | 159 | 219 | 0.725 | 0.0000137 | 2268 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Cytokine Signaling in Immune system;Innate Immune System;Immune System;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Interferon gamma signaling;G alpha (q) signalling events;GPCR downstream signalling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- loftool
- 0.631
- rvis_EVS
- 0.66
- rvis_percentile_EVS
- 84.44
Haploinsufficiency Scores
- pHI
- 0.121
- hipred
- Y
- hipred_score
- 0.672
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptafr
- Phenotype
- immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- cytokine production;regulation of transcription by RNA polymerase II;chemotaxis;inflammatory response;immune response;G protein-coupled receptor signaling pathway;parturition;response to symbiotic bacterium;positive regulation of phospholipase C activity;cytokine-mediated signaling pathway;lipopolysaccharide-mediated signaling pathway;positive regulation of tumor necrosis factor production;inositol trisphosphate biosynthetic process;G protein-coupled purinergic nucleotide receptor signaling pathway;neutrophil degranulation;positive regulation of neutrophil degranulation;transcytosis;positive regulation of interleukin-6 biosynthetic process;positive regulation of translation;negative regulation of blood pressure;positive regulation of vasoconstriction;phosphatidylinositol-mediated signaling;positive regulation of smooth muscle cell proliferation;interferon-gamma-mediated signaling pathway;positive regulation of inositol phosphate biosynthetic process;cellular response to gravity;cellular response to cAMP;cellular response to fatty acid;response to dexamethasone;positive regulation of blood vessel diameter;positive regulation of voltage-gated chloride channel activity;positive regulation of leukocyte tethering or rolling;positive regulation of sensory perception of pain;positive regulation of transcytosis;positive regulation of maternal process involved in parturition;positive regulation of gastro-intestinal system smooth muscle contraction;cellular response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine
- Cellular component
- plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;secretory granule membrane;tertiary granule membrane
- Molecular function
- lipopolysaccharide binding;lipopolysaccharide receptor activity;G protein-coupled receptor activity;platelet activating factor receptor activity;phospholipid binding;G protein-coupled purinergic nucleotide receptor activity;mitogen-activated protein kinase binding