GPR4

G protein-coupled receptor 4, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 19:45589764-45602212

Links

ENSG00000177464 ∙ NCBI:2828 ∙ OMIM:600551 ∙ HGNC:4497 ∙ Uniprot:P46093 ∙ 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 GPR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR4 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in GPR4

This is a list of pathogenic ClinVar variants found in the GPR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45590792-G-A		not specified	Uncertain significance (Apr 13, 2023)
19-45590845-C-T		not specified	Uncertain significance (Dec 31, 2024)
19-45590855-T-A		not specified	Uncertain significance (Jun 03, 2022)
19-45590866-G-T		not specified	Uncertain significance (Jan 22, 2024)
19-45590906-G-T		not specified	Uncertain significance (Nov 10, 2024)
19-45590951-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-45590979-A-T		not specified	Uncertain significance (Sep 03, 2024)
19-45590982-G-C		not specified	Uncertain significance (Nov 13, 2024)
19-45591052-A-G		not specified	Uncertain significance (Jan 18, 2025)
19-45591073-A-C		not specified	Uncertain significance (Oct 28, 2023)
19-45591080-G-A		not specified	Uncertain significance (Apr 10, 2023)
19-45591106-C-T		not specified	Uncertain significance (May 14, 2024)
19-45591234-G-T		not specified	Uncertain significance (Dec 19, 2022)
19-45591283-G-A		not specified	Uncertain significance (Jan 19, 2024)
19-45591284-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-45591301-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-45591436-G-T		not specified	Uncertain significance (Jun 23, 2023)
19-45591464-C-T		not specified	Uncertain significance (Dec 17, 2024)
19-45591560-T-C		not specified	Uncertain significance (Jul 13, 2022)
19-45591707-C-T		not specified	Uncertain significance (Oct 16, 2023)
19-45591721-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-45591727-T-C		not specified	Likely benign (Sep 10, 2024)
19-45591737-G-A		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR4	protein_coding	protein_coding	ENST00000323040	1	12445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.100	0.869	125717	0	15	125732	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	138	251	0.550	0.0000166	2344
Missense in Polyphen		36	104.33	0.34507		1021
Synonymous	1.78	96	121	0.794	0.00000875	777
Loss of Function	1.85	3	9.00	0.333	3.86e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000891	0.0000891
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000937	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-sensing receptor coupled to several G-proteins, including G(s), G(13) and G(q)/G(11) proteins, leading to cAMP production. {ECO:0000269|PubMed:12955148, ECO:0000269|PubMed:17462861}.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.256
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.646
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr4
• 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); 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); neoplasm; respiratory system phenotype; renal/urinary system phenotype; 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;response to acidic pH;negative regulation of angiogenesis;positive regulation of Rho protein signal transduction;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;angiogenesis involved in wound healing;glomerular mesangial cell development
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity