P2RY4

protein-coding

pyrimidinergic receptor P2Y4, the group of P2Y receptors

Gene summary

The product of this gene belongs to the family of G-protein coupled receptors. This family has several receptor subtypes with different pharmacological selectivity, which overlaps in some cases, for various adenosine and uridine nucleotides. This receptor is responsive to uridine nucleotides, partially responsive to ATP, and not responsive to ADP. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002565.4

Inheritance

—

ClinVar variants

U:53B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chrX:70,258,166-70,260,204

External References & Databases

Ensembl (ENSG00000186912)

Transcript & Mutation Effects

hg38 • Region Span ~2.0 kb

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GenCC 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 P2RY4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002565.4. 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						0
missense			52 clinvar	1 clinvar	2 clinvar	55
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	1	2	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002565.4	RefSeq	NP_002556.1	1	MANE Select
ENST00000374519.4	Ensembl	ENSP00000363643.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuroactive ligand-receptor interaction - Homo sapiens (human)
Taste transduction - Homo sapiens (human)
GPCRs, Class A Rhodopsin-like
Nucleotide GPCRs
Signaling by GPCR

Biological Process

G protein-coupled receptor signaling pathway
phospholipase C-activating G protein-coupled receptor signaling pathway
positive regulation of cytosolic calcium ion concentration
transepithelial chloride transport
G protein-coupled purinergic nucleotide receptor signaling pathway

Molecular Function

ATP binding
uridine nucleotide receptor activity
G protein-coupled purinergic nucleotide receptor activity
UTP-activated nucleotide receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
basolateral plasma membrane
apical plasma membrane
glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374519
Coding exons: 1
Length: 1639
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.317	174	163	1.07	0.0000144	2323
Missense (PolyPhen)		44	37.428	1.1756		686
Synonymous	0.601	62	68.3	0.908	0.00000569	821
Loss of Function	1.58	2	6.29	0.318	5.46e-7	90

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for UTP and UDP coupled to G-proteins that activate a phosphatidylinositol-calcium second messenger system. Not activated by ATP or ADP.;

Recessive Scores

pRec: 0.168

Intolerance Scores

LoFtool: 0.445
RVIS EVS: 1.46
RVIS percentile EVS: 95.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0736

Gene Damage Prediction

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