TBXA2R

thromboxane A2 receptor, the group of Prostaglandin receptors

Basic information

Region (hg38): 19:3594507-3606875

Links

ENSG00000006638 ∙ NCBI:6915 ∙ OMIM:188070 ∙ HGNC:11608 ∙ Uniprot:P21731 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• bleeding diathesis due to thromboxane synthesis deficiency (Moderate), mode of inheritance: AD
• bleeding diathesis due to thromboxane synthesis deficiency (Limited), mode of inheritance: Unknown
• qualitative platelet defect (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bleeding disorder, platelet-type 13, susceptibility to	AD	Hematologic; Pharmacogenomic	Surveillance and prompt treatment of bleeding diatheses may be beneficial; Avoidance of agents that may provoke or worsen bleeding episodes is warranted	Hematologic	7929844; 19828703; 21070398; 22101342
Heterozygosity may cause abnormal in vitro platelet functional responses, but do not cause in vivo clinically significant dysfunction; Susceptibility is inherited in an autosomal dominant pattern, but clinical features, including mild mucocutaneous bleeding, occur only in the presence of a "second hit" affecting platelet function

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBXA2R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBXA2R 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				23	5	28
missense		1	58	12	4	75
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel			5			5
splice donor/acceptor (+/-2bp)		1				1
splice region			1			1
non coding			1	9	16	26
Total	0	2	67	44	25

Variants in TBXA2R

This is a list of pathogenic ClinVar variants found in the TBXA2R region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3594842-C-G		TBXA2R-related disorder	Likely benign (Jul 31, 2023)
19-3594847-T-C		not specified	Uncertain significance (Nov 07, 2023)
19-3594871-G-A		not specified	Uncertain significance (Jul 30, 2024)
19-3594937-G-A		TBXA2R-related disorder	Likely benign (Aug 23, 2024)
19-3594950-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-3594973-G-A		TBXA2R-related disorder	Uncertain significance (Jul 26, 2024)
19-3594973-G-C		TBXA2R-related disorder	Uncertain significance (Sep 15, 2024)
19-3595008-A-G		not specified	Benign (Jul 09, 2018)
19-3595034-C-T		not specified	Benign (Jul 09, 2018)
19-3595035-G-A			Benign (Jul 09, 2018)
19-3595078-TA-T			Benign (Oct 05, 2019)
19-3595078-TAA-T			Likely benign (Oct 05, 2019)
19-3595078-T-TA			Benign (Oct 05, 2019)
19-3595078-T-TAA			Benign (Oct 06, 2019)
19-3595374-G-A			Benign (Oct 07, 2019)
19-3595406-C-G			Benign (Jul 09, 2018)
19-3595413-T-C			Likely benign (Jul 10, 2018)
19-3595524-G-A			Benign (Jul 09, 2018)
19-3595660-G-A			Likely benign (Sep 01, 2023)
19-3595684-C-A		TBXA2R-related disorder	Likely benign (Sep 10, 2019)
19-3595692-T-C			Uncertain significance (May 20, 2023)
19-3595698-CCGGAGCG-C			Uncertain significance (Oct 04, 2022)
19-3595704-C-T			Uncertain significance (Dec 21, 2022)
19-3595705-G-A		Inborn genetic diseases • not specified	Uncertain significance (Apr 16, 2024)
19-3595707-T-A			Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBXA2R	protein_coding	protein_coding	ENST00000411851	3	12335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000128	0.646	124197	0	27	124224	0.000109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	239	290	0.823	0.0000223	2506
Missense in Polyphen		91	116.5	0.7811		1057
Synonymous	-0.426	141	135	1.05	0.0000107	946
Loss of Function	0.784	7	9.62	0.727	5.01e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000444
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000116	0.000107
Middle Eastern	0.000113	0.000111
South Asian	0.0000658	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for thromboxane A2 (TXA2), a potent stimulator of platelet aggregation. The activity of this receptor is mediated by a G-protein that activates a phosphatidylinositol-calcium second messenger system. In the kidney, the binding of TXA2 to glomerular TP receptors causes intense vasoconstriction. Activates phospholipase C. Isoform 1 activates adenylyl cyclase. Isoform 2 inhibits adenylyl cyclase. {ECO:0000269|PubMed:8613548}.
• Disease: DISEASE: Bleeding disorder, platelet-type 13 (BDPLT13) [MIM:614009]: A disorder characterized by reduced platelet aggregation and a tendency to mild mucocutaneous bleeding. {ECO:0000269|PubMed:7929844, ECO:0000269|PubMed:8613548}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Platelet activation - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Small Ligand GPCRs;GPCRs, Class A Rhodopsin-like;Prostaglandin Synthesis and Regulation;Signaling by GPCR;Signal Transduction;eicosanoid metabolism;Thromboxane signalling through TP receptor;Signal amplification;Prostanoid ligand receptors;Eicosanoid ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Platelet activation, signaling and aggregation;Hemostasis;Thromboxane A2 receptor signaling;G alpha (12/13) signalling events;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.313

Intolerance Scores

• loftool: 0.348
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.0678
• hipred: N
• hipred_score: 0.358
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.767

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tbxa2r
• Phenotype: immune system phenotype; respiratory system phenotype; 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); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: inflammatory response;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;response to nutrient;positive regulation of blood coagulation;response to testosterone;thromboxane A2 signaling pathway;response to ethanol;positive regulation of angiogenesis;positive regulation of blood pressure;positive regulation of vasoconstriction;positive regulation of smooth muscle contraction;cellular response to lipopolysaccharide;negative regulation of cell migration involved in sprouting angiogenesis
• Cellular component: acrosomal vesicle;plasma membrane;integral component of plasma membrane;nuclear speck
• Molecular function: thromboxane A2 receptor activity;guanyl-nucleotide exchange factor activity;protein binding