P2RX4

purinergic receptor P2X 4, the group of Purinergic receptors P2X

Basic information

Region (hg38): 12:121210065-121234106

Links

ENSG00000135124 ∙ NCBI:5025 ∙ OMIM:600846 ∙ HGNC:8535 ∙ Uniprot:Q99571 ∙ 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 P2RX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P2RX4 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				1		1
missense			31	4	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	31	5	2

Variants in P2RX4

This is a list of pathogenic ClinVar variants found in the P2RX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121210171-G-T			Benign (Jul 20, 2018)
12-121210197-C-T			Likely benign (Apr 04, 2018)
12-121210276-C-T		not specified	Uncertain significance (Feb 02, 2022)
12-121210291-G-C		not specified	Uncertain significance (Nov 27, 2023)
12-121210295-T-C		not specified	Uncertain significance (Aug 08, 2023)
12-121217189-G-C		not specified	Uncertain significance (Feb 27, 2024)
12-121217189-G-T		not specified	Uncertain significance (Mar 11, 2024)
12-121217190-T-A		not specified	Uncertain significance (Feb 01, 2023)
12-121217193-C-T			Likely benign (May 14, 2018)
12-121217210-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-121217234-C-T		not specified	Uncertain significance (Mar 04, 2024)
12-121217244-G-A		not specified	Uncertain significance (Jun 05, 2023)
12-121217259-C-G		not specified	Uncertain significance (Feb 17, 2023)
12-121217279-C-A		not specified	Uncertain significance (Feb 05, 2024)
12-121221931-G-A		not specified	Likely benign (May 24, 2024)
12-121221960-C-A		not specified	Uncertain significance (Sep 16, 2021)
12-121221961-C-G		not specified	Uncertain significance (Dec 08, 2023)
12-121221976-T-A		not specified	Uncertain significance (Aug 16, 2021)
12-121222134-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-121222171-G-C			Benign (Aug 05, 2018)
12-121222967-G-A		not specified	Uncertain significance (May 01, 2024)
12-121223016-C-T		not specified	Uncertain significance (Nov 10, 2024)
12-121223022-A-G		not specified	Uncertain significance (Nov 10, 2024)
12-121223039-C-T		not specified	Uncertain significance (Mar 07, 2023)
12-121228595-C-G		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P2RX4	protein_coding	protein_coding	ENST00000359949	13	24250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.98e-12	0.106	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	209	243	0.859	0.0000150	2646
Missense in Polyphen		82	100.26	0.81786		1125
Synonymous	0.122	95	96.5	0.984	0.00000670	761
Loss of Function	0.545	19	21.7	0.874	9.29e-7	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00149
Ashkenazi Jewish	0.00150	0.00149
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000381	0.000381
South Asian	0.000231	0.000229
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for ATP that acts as a ligand-gated ion channel. This receptor is insensitive to the antagonists PPADS and suramin. {ECO:0000269|PubMed:10515189, ECO:0000269|PubMed:22068874, ECO:0000269|PubMed:28326637}.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Hemostasis;Elevation of cytosolic Ca2+ levels;Platelet calcium homeostasis;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• loftool: 0.834
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.239
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: P2rx4
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; hematopoietic 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); 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); skeleton phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: tissue homeostasis;regulation of sodium ion transport;response to ischemia;cation transport;signal transduction;blood coagulation;regulation of blood pressure;positive regulation of calcium ion transport into cytosol;negative regulation of cardiac muscle hypertrophy;neuronal action potential;sensory perception of pain;calcium-mediated signaling;positive regulation of prostaglandin secretion;response to ATP;ion transmembrane transport;response to fluid shear stress;purinergic nucleotide receptor signaling pathway;endothelial cell activation;positive regulation of blood vessel endothelial cell migration;positive regulation of nitric oxide biosynthetic process;behavioral response to pain;response to axon injury;positive regulation of calcium-mediated signaling;regulation of chemotaxis;sensory perception of touch;protein homooligomerization;positive regulation of protein kinase B signaling;membrane depolarization;positive regulation of calcium ion transport;regulation of cardiac muscle contraction;relaxation of cardiac muscle;excitatory postsynaptic potential;calcium ion transmembrane transport;cellular response to zinc ion;cellular response to ATP;apoptotic signaling pathway;regulation of ruffle assembly;positive regulation of microglial cell migration;positive regulation of endothelial cell chemotaxis
• Cellular component: integral component of nuclear inner membrane;lysosomal membrane;plasma membrane;integral component of plasma membrane;postsynaptic density;membrane;integral component of membrane;cell junction;neuronal cell body;terminal bouton;dendritic spine;cell body;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: purinergic nucleotide receptor activity;extracellularly ATP-gated cation channel activity;signaling receptor binding;copper ion binding;protein binding;ATP binding;zinc ion binding;ATP-gated ion channel activity;protein homodimerization activity;cadherin binding;ligand-gated calcium channel activity