P2RY4

pyrimidinergic receptor P2Y4, the group of P2Y receptors

Basic information

Region (hg38): X:70258165-70260204

Links

ENSG00000186912 ∙ NCBI:5030 ∙ OMIM:300038 ∙ HGNC:8542 ∙ Uniprot:P51582 ∙ 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 P2RY4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the P2RY4 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			26	1	2	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in P2RY4

This is a list of pathogenic ClinVar variants found in the P2RY4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70258565-C-A		not specified	Uncertain significance (Jul 15, 2021)
X-70258636-G-A		not specified	Uncertain significance (Mar 19, 2024)
X-70258663-C-T		not specified	Uncertain significance (Feb 27, 2024)
X-70258672-C-T			Benign (Jan 19, 2018)
X-70258681-C-T		not specified	Uncertain significance (Jan 24, 2024)
X-70258748-G-C		not specified	Uncertain significance (Sep 06, 2022)
X-70258789-C-T		not specified	Likely benign (Dec 28, 2023)
X-70258831-C-A		not specified	Uncertain significance (Apr 05, 2023)
X-70258876-A-G		not specified	Uncertain significance (Feb 13, 2024)
X-70258891-C-T		not specified	Uncertain significance (Apr 15, 2024)
X-70258900-C-T		not specified	Uncertain significance (Sep 29, 2022)
X-70258906-C-T		not specified	Uncertain significance (Dec 18, 2023)
X-70258915-G-A		not specified	Uncertain significance (Jun 27, 2023)
X-70258968-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-70259132-C-T		not specified	Uncertain significance (Oct 12, 2022)
X-70259138-C-G		not specified	Uncertain significance (Nov 22, 2021)
X-70259138-C-T		not specified	Uncertain significance (Feb 07, 2023)
X-70259177-G-A		not specified	Uncertain significance (Jun 29, 2023)
X-70259183-G-A		not specified	Uncertain significance (Feb 15, 2023)
X-70259227-C-T		not specified	Uncertain significance (Jun 29, 2022)
X-70259242-C-G		not specified	Uncertain significance (Feb 05, 2024)
X-70259255-G-A		not specified	Uncertain significance (Jun 02, 2023)
X-70259291-G-A		not specified	Uncertain significance (Nov 03, 2022)
X-70259437-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-70259438-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
P2RY4	protein_coding	protein_coding	ENST00000374519	1	1639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.169	0.777	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.317	174	163	1.07	0.0000144	2323
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - Homo sapiens (human);GPCRs, Class A Rhodopsin-like;Nucleotide GPCRs;Signaling by GPCR;Signal Transduction;P2Y receptors;Nucleotide-like (purinergic) receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.445
• rvis_EVS: 1.46
• rvis_percentile_EVS: 95.21

Haploinsufficiency Scores

• pHI: 0.0960
• hipred: N
• hipred_score: 0.292

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0736

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: P2ry4
• Phenotype: digestive/alimentary phenotype; 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)

Gene ontology

• 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;cellular response to ATP;cellular response to prostaglandin E stimulus;regulation of presynaptic cytosolic calcium ion concentration;regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane;apical plasma membrane;glutamatergic synapse;integral component of presynaptic active zone membrane
• Molecular function: ATP binding;uridine nucleotide receptor activity;G protein-coupled purinergic nucleotide receptor activity;UTP-activated nucleotide receptor activity