GPR50

G protein-coupled receptor 50, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): X:151176583-151181465

Links

ENSG00000102195 ∙ NCBI:9248 ∙ OMIM:300207 ∙ HGNC:4506 ∙ Uniprot:Q13585 ∙ 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 GPR50 gene.

• Inborn genetic diseases (27 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR50 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				3	3	6
missense			23	4		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	7	3

Variants in GPR50

This is a list of pathogenic ClinVar variants found in the GPR50 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-151176738-C-T		not specified	Uncertain significance (Jun 23, 2023)
X-151176776-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-151176782-C-G		not specified	Uncertain significance (Dec 21, 2023)
X-151176813-T-C		not specified	Uncertain significance (Feb 16, 2023)
X-151176819-G-C		not specified	Uncertain significance (Jun 23, 2023)
X-151176889-C-G		not specified	Uncertain significance (Mar 21, 2023)
X-151176899-C-T			Likely benign (Feb 01, 2023)
X-151176900-G-A		not specified	Uncertain significance (Mar 17, 2023)
X-151179855-T-C		not specified	Likely benign (Dec 07, 2021)
X-151179870-T-C		not specified	Uncertain significance (Aug 03, 2022)
X-151179882-A-C		not specified	Uncertain significance (Jan 31, 2024)
X-151179894-T-G		not specified	Uncertain significance (Jan 23, 2024)
X-151179923-G-A		not specified	Likely benign (May 18, 2023)
X-151180011-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-151180090-C-T			Benign (Aug 20, 2018)
X-151180091-G-A		not specified	Uncertain significance (Mar 01, 2023)
X-151180098-A-G		not specified	Uncertain significance (May 17, 2023)
X-151180104-G-A		not specified	Uncertain significance (Apr 06, 2022)
X-151180138-C-T			Benign (Jun 23, 2018)
X-151180141-T-C			Likely benign (Jun 01, 2022)
X-151180152-T-C		not specified	Uncertain significance (Oct 25, 2023)
X-151180167-T-C		not specified	Uncertain significance (Nov 13, 2023)
X-151180169-C-A		not specified	Uncertain significance (Jul 28, 2021)
X-151180238-C-A		not specified	Uncertain significance (Jan 26, 2022)
X-151180446-G-C		not specified	Uncertain significance (Nov 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR50	protein_coding	protein_coding	ENST00000218316	2	4813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.646	0.348	124792	1	2	124795	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0722	265	268	0.988	0.0000225	4067
Missense in Polyphen		30	40.887	0.73372		661
Synonymous	-0.818	119	108	1.10	0.00000934	1298
Loss of Function	2.22	1	7.62	0.131	5.57e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000738	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000256	0.0000177
Middle Eastern	0.0000738	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not bind melatonin.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;GPCRs, Class A Rhodopsin-like (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.152
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.0861
• hipred: N
• hipred_score: 0.212
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr50
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;cell-cell signaling
• Cellular component: nucleoplasm;plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;protein binding;melatonin receptor activity;identical protein binding