P2RX1

purinergic receptor P2X 1, the group of Purinergic receptors P2X

Basic information

Region (hg38): 17:3896592-3916476

Links

ENSG00000108405 ∙ NCBI:5023 ∙ OMIM:600845 ∙ HGNC:8533 ∙ Uniprot:P51575 ∙ 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 P2RX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P2RX1 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				5	2	7
missense			27	3	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding					10	10
Total	0	0	27	8	13

Variants in P2RX1

This is a list of pathogenic ClinVar variants found in the P2RX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3897701-T-C			Benign (Nov 12, 2018)
17-3897729-G-A			Benign (Jun 21, 2021)
17-3897786-C-T			Benign (Nov 12, 2018)
17-3897828-T-C			Benign (Nov 30, 2017)
17-3897863-G-A		not specified	Uncertain significance (Jan 20, 2023)
17-3897865-G-A		P2RX1-related disorder	Likely benign (Jul 08, 2024)
17-3897872-C-T		P2RX1-related disorder	Likely benign (Aug 14, 2019)
17-3897888-G-A			Benign (Dec 31, 2019)
17-3898033-G-A		P2RX1-related disorder	Benign (Aug 16, 2017)
17-3898071-G-A		not specified	Uncertain significance (Nov 29, 2021)
17-3898081-AAGC-A		Platelet-type bleeding disorder 8	Uncertain significance (Jul 28, 2000)
17-3898140-G-A			Benign (Jun 21, 2021)
17-3898511-G-A		P2RX1-related disorder	Benign (Jul 15, 2019)
17-3898939-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-3898981-G-A		not specified	Uncertain significance (Jul 27, 2021)
17-3899001-T-A		P2RX1-related disorder	Uncertain significance (Aug 31, 2024)
17-3899008-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-3899649-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-3899669-G-A		P2RX1-related disorder	Likely benign (Aug 09, 2019)
17-3899710-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-3899769-G-T			Likely benign (Aug 22, 2018)
17-3903230-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-3903235-C-T		P2RX1-related disorder	Likely benign (Jan 13, 2021)
17-3903309-T-C		not specified	Uncertain significance (Jun 23, 2023)
17-3903370-T-A			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P2RX1	protein_coding	protein_coding	ENST00000225538	12	19909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.76e-11	0.240	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	197	242	0.815	0.0000158	2626
Missense in Polyphen		72	107.13	0.67206		1256
Synonymous	0.135	96	97.7	0.983	0.00000678	768
Loss of Function	0.813	18	22.1	0.813	0.00000114	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00160
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000497	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000497	0.000489
South Asian	0.000817	0.000817
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand-gated ion channel with relatively high calcium permeability. Binding to ATP mediates synaptic transmission between neurons and from neurons to smooth muscle. Seems to be linked to apoptosis, by increasing the intracellular concentration of calcium in the presence of ATP, leading to programmed cell death (By similarity). {ECO:0000250}.
• Pathway: Platelet activation - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Neutrophil degranulation;Innate Immune System;Immune System;Hemostasis;Elevation of cytosolic Ca2+ levels;Platelet calcium homeostasis;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.872
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.0840
• hipred: N
• hipred_score: 0.239
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.157

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: P2rx1
• 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); reproductive system phenotype

Gene ontology

• Biological process: serotonin secretion by platelet;regulation of vascular smooth muscle contraction;ion transport;cation transport;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;signal transduction;insemination;blood coagulation;regulation of blood pressure;neuronal action potential;platelet activation;response to ATP;ion transmembrane transport;synaptic transmission, glutamatergic;purinergic nucleotide receptor signaling pathway;positive regulation of ion transport;neutrophil degranulation;ceramide biosynthetic process;protein homooligomerization;protein heterooligomerization;regulation of calcium ion transport;excitatory postsynaptic potential;cation transmembrane transport;ATP hydrolysis coupled ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport;regulation of presynaptic cytosolic calcium ion concentration;regulation of synaptic vesicle exocytosis
• Cellular component: integral component of nuclear inner membrane;plasma membrane;integral component of plasma membrane;external side of plasma membrane;integral component of membrane;secretory granule membrane;protein-containing complex;specific granule membrane;neuron projection;membrane raft;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic active zone membrane
• Molecular function: purinergic nucleotide receptor activity;extracellularly ATP-gated cation channel activity;cation channel activity;ATP binding;zinc ion binding;ATP-gated ion channel activity