GPR50

protein-coding

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

Gene summary

This gene product belongs to the G-protein coupled receptor 1 family. Even though this protein shares similarity with the melatonin receptors, it does not bind melatonin, however, it inhibits melatonin receptor 1A function through heterodimerization. Polymorphic variants of this gene have been associated with bipolar affective disorder in women. [provided by RefSeq, Jan 2010]

MANE transcript

NM_004224.3

Inheritance

—

ClinVar variants

U:84B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chrX:151,176,584-151,181,465

External References & Databases

Ensembl (ENSG00000102195)

Transcript & Mutation Effects

hg38 • Region Span ~4.9 kb

Loading mutation effect viewer...

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 GPR50 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004224.3. 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				3 clinvar	3 clinvar	6
missense			84 clinvar	6 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	9	3	96

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004224.3	RefSeq	NP_004215.2	2	MANE Select
ENST00000218316.4	Ensembl	ENSP00000218316.3	2	MANE Select
XM_011531216.3	RefSeq	XP_011529518.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuroactive ligand-receptor interaction - Homo sapiens (human)
Small Ligand GPCRs
GPCRs, Class A Rhodopsin-like

Biological Process

G protein-coupled receptor signaling pathway
cell-cell signaling

Molecular Function

G protein-coupled receptor activity
protein binding
melatonin receptor activity
identical protein binding

Cellular Component

nucleoplasm
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000218316
Coding exons: 2
Length: 4813
Individuals with no LoFs: 124792
Homozygous LoFs: 1
Heterozygous LoFs: 2
Defined: 124795
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0722	265	268	0.988	0.0000225	4067
Missense (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

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	0.000074	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Does not bind melatonin.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.152
RVIS EVS: -0.38
RVIS percentile EVS: 28.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000854

Gene Damage Prediction

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