P2RX3

purinergic receptor P2X 3, the group of Purinergic receptors P2X

Basic information

Region (hg38): 11:57338351-57372396

Links

ENSG00000109991 ∙ NCBI:5024 ∙ OMIM:600843 ∙ HGNC:8534 ∙ Uniprot:P56373 ∙ 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 P2RX3 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P2RX3 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			13	2	1	16
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	3	2

Variants in P2RX3

This is a list of pathogenic ClinVar variants found in the P2RX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57338557-T-C		not specified	Uncertain significance (Nov 03, 2023)
11-57338558-GC-G			Likely benign (Jun 20, 2018)
11-57338633-G-T		not specified	Uncertain significance (Jun 30, 2023)
11-57346560-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-57346575-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-57346584-A-G		not specified	Uncertain significance (May 05, 2022)
11-57346600-C-T		not specified	Uncertain significance (Feb 17, 2022)
11-57346626-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-57346653-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-57347431-G-A		not specified	Uncertain significance (May 04, 2022)
11-57348211-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-57348212-G-A			Benign (May 21, 2018)
11-57348223-A-G		not specified	Uncertain significance (Jun 16, 2023)
11-57348234-G-T		not specified	Uncertain significance (Feb 09, 2023)
11-57348664-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-57348695-A-G		not specified	Uncertain significance (Nov 21, 2023)
11-57349779-A-T		not specified	Uncertain significance (Dec 08, 2023)
11-57350762-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-57350789-T-A		not specified	Uncertain significance (May 25, 2022)
11-57350820-A-G		not specified	Uncertain significance (Mar 29, 2023)
11-57368071-G-T		not specified	Uncertain significance (Aug 19, 2021)
11-57368073-A-T		not specified	Uncertain significance (Dec 09, 2023)
11-57368415-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-57369351-C-A			Benign (Jul 06, 2018)
11-57369893-A-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P2RX3	protein_coding	protein_coding	ENST00000263314	12	32226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000103	0.939	125604	1	143	125748	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	186	242	0.770	0.0000141	2600
Missense in Polyphen		79	112.23	0.70394		1223
Synonymous	0.342	90	94.2	0.955	0.00000619	733
Loss of Function	1.81	13	22.2	0.586	0.00000103	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00633	0.00628
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.000462	0.000462
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.000329	0.000326
South Asian	0.0000990	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for ATP that acts as a ligand-gated cation channel (PubMed:27626375). Plays a role in sensory perception. Required for normal perception of pain. Required for normal taste perception (By similarity). {ECO:0000250|UniProtKB:Q3UR32, ECO:0000269|PubMed:27626375}.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - Homo sapiens (human);Hemostasis;Elevation of cytosolic Ca2+ levels;Platelet calcium homeostasis;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.700
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.317
• hipred: N
• hipred_score: 0.480
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: P2rx3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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)

Zebrafish Information Network

• Gene name: p2rx3a
• Affected structure: pharyngeal arch 1
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: response to hypoxia;cation transport;signal transduction;neuromuscular synaptic transmission;blood coagulation;response to heat;response to cold;response to mechanical stimulus;response to carbohydrate;positive regulation of calcium ion transport into cytosol;urinary bladder smooth muscle contraction;monovalent inorganic cation transport;neuronal action potential;peristalsis;ion transmembrane transport;purinergic nucleotide receptor signaling pathway;regulation of synaptic plasticity;positive regulation of calcium-mediated signaling;sensory perception of taste;excitatory postsynaptic potential;behavioral response to formalin induced pain;protein homotrimerization;cellular response to ATP;cation transmembrane transport;positive regulation of sensory perception of pain
• Cellular component: integral component of nuclear inner membrane;rough endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;integral component of membrane;neuronal cell body;terminal bouton;dendritic spine;receptor complex;membrane raft;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;integral component of presynaptic membrane
• Molecular function: purinergic nucleotide receptor activity;extracellularly ATP-gated cation channel activity;ATP binding;ATP-gated ion channel activity