P2RX4
protein-codingpurinergic receptor P2X 4, the group of Purinergic receptors P2X
Gene summary
The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel with high calcium permeability. The main pharmacological distinction between the members of the purinoceptor family is the relative sensitivity to the antagonists suramin and PPADS. The product of this gene has the lowest sensitivity for these antagonists. Multiple alternatively spliced transcript variants, some protein-coding and some not protein-coding, have been found for this gene. [provided by RefSeq, Feb 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to P2RX4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002560.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 56 | 4 | 1 | 61 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 61 | 5 | 1 | 67 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002551.2 | 12 | MANE Select | |
| Ensembl | ENSP00000336607.4 | 12 | MANE Select | |
| RefSeq | NP_001243725.1 | 13 | Standard | |
| RefSeq | NP_001248326.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Calcium signaling pathway - Homo sapiens (human)
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
- Hemostasis
- Elevation of cytosolic Ca2+ levels
- Platelet calcium homeostasis
Biological Process
- tissue homeostasis
- regulation of sodium ion transport
- response to ischemia
- cation transport
- signal transduction
Molecular Function
- purinergic nucleotide receptor activity
- extracellularly ATP-gated cation channel activity
- signaling receptor binding
- copper ion binding
- protein binding
Cellular Component
- integral component of nuclear inner membrane
- lysosomal membrane
- plasma membrane
- integral component of plasma membrane
- postsynaptic density
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359949
- Coding exons
- 13
- Length
- 24250
- Individuals with no LoFs
- 125661
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 87
- Defined
- 125748
- p
- 0.000346
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.779 | 209 | 243 | 0.859 | 0.0000150 | 2646 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0.00069 | 0.00069 | rare |
| Ashkenazi Jewish | 0.0015 | 0.0015 | notable |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- LoFtool
- 0.834
- RVIS EVS
- -0.04
- RVIS percentile EVS
- 50.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.777
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |