PTAFR

platelet activating factor receptor, the group of Platelet activating factor receptor

Basic information

Region (hg38): 1:28147166-28193936

Links

ENSG00000169403 ∙ NCBI:5724 ∙ OMIM:173393 ∙ HGNC:9582 ∙ Uniprot:P25105 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTAFR gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	1

Variants in PTAFR

This is a list of pathogenic ClinVar variants found in the PTAFR region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-28150010-T-C		not specified	Uncertain significance (Nov 17, 2023)
1-28150034-C-A		not specified	Uncertain significance (Jun 29, 2023)
1-28150057-G-A		not specified	Uncertain significance (Oct 26, 2024)
1-28150088-G-T		not specified	Uncertain significance (Jan 02, 2025)
1-28150120-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-28150202-C-T			Benign (Feb 26, 2018)
1-28150219-T-A		not specified	Uncertain significance (Dec 21, 2023)
1-28150223-A-G		not specified	Uncertain significance (Nov 08, 2022)
1-28150232-C-A		not specified	Uncertain significance (Feb 22, 2023)
1-28150274-C-T		not specified	Likely benign (Oct 21, 2024)
1-28150315-G-A		not specified	Uncertain significance (Dec 05, 2022)
1-28150327-C-A		not specified	Uncertain significance (Dec 21, 2022)
1-28150328-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-28150337-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-28150357-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-28150372-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-28150412-A-G		not specified	Uncertain significance (Nov 19, 2024)
1-28150448-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-28150460-G-A		not specified	Uncertain significance (Mar 04, 2024)
1-28150508-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-28150535-C-G		not specified	Uncertain significance (Dec 21, 2022)
1-28150535-C-T		not specified	Likely benign (Nov 09, 2024)
1-28150609-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-28150660-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-28150661-G-A		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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