GPR3

G protein-coupled receptor 3, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 1:27392622-27395814

Links

ENSG00000181773 ∙ NCBI:2827 ∙ OMIM:600241 ∙ HGNC:4484 ∙ Uniprot:P46089 ∙ 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 GPR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR3 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in GPR3

This is a list of pathogenic ClinVar variants found in the GPR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27393874-C-T		not specified	Likely benign (Oct 16, 2024)
1-27393901-G-A		not specified	Uncertain significance (Oct 24, 2023)
1-27393905-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-27393923-C-T		not specified	Uncertain significance (Sep 09, 2024)
1-27393965-G-A		not specified	Uncertain significance (May 10, 2024)
1-27393980-T-C		not specified	Uncertain significance (May 06, 2022)
1-27394048-G-A		not specified	Uncertain significance (Jun 05, 2024)
1-27394100-T-A		not specified	Uncertain significance (Aug 26, 2024)
1-27394105-A-C		not specified	Uncertain significance (Nov 21, 2022)
1-27394115-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-27394198-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-27394286-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-27394504-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-27394514-A-G		not specified	Uncertain significance (Aug 20, 2024)
1-27394673-T-A		not specified	Uncertain significance (Sep 09, 2024)
1-27394709-T-C		not specified	Uncertain significance (Jul 11, 2023)
1-27394725-G-C		not specified	Uncertain significance (Jul 11, 2023)
1-27394766-G-A		not specified	Uncertain significance (Dec 05, 2024)
1-27394782-T-A		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR3	protein_coding	protein_coding	ENST00000374024	1	3171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000263	0.559	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.944	161	198	0.811	0.0000121	2069
Missense in Polyphen		38	55.772	0.68135		635
Synonymous	-0.361	93	88.7	1.05	0.00000552	780
Loss of Function	0.512	6	7.52	0.798	3.26e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor with constitutive G(s) signaling activity that activate cyclic AMP. Has a potential role in modulating a number of brain functions, including behavioral responses to stress (By similarity), amyloid-beta peptide generation in neurons and neurite outgrowth (By similarity). Maintains also meiotic arrest in oocytes (By similarity). {ECO:0000250, ECO:0000269|PubMed:19213921}.
• Pathway: GPCRs, Class A Rhodopsin-like (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.439
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.641
• hipred: N
• hipred_score: 0.459
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.556

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr3
• Phenotype: homeostasis/metabolism phenotype; 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: adenylate cyclase-activating G protein-coupled receptor signaling pathway;regulation of meiotic nuclear division;positive regulation of cold-induced thermogenesis
• Cellular component: integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;protein binding