GPR50

gene
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Also known as H9Mel1c

Summary

GPR50 (G protein-coupled receptor 50, HGNC:4506) is a protein-coding gene on chromosome Xq28, encoding Melatonin-related receptor (Q13585). G protein-coupled receptor that plays a role in numerous physiological processes including regulation of energy metabolism, neurite outgrowth or cell migration.

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.

Source: NCBI Gene 9248 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 96 total
  • Druggable target: yes
  • MANE Select transcript: NM_004224

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4506
Approved symbolGPR50
NameG protein-coupled receptor 50
LocationXq28
Locus typegene with protein product
StatusApproved
AliasesH9, Mel1c
Ensembl geneENSG00000102195
Ensembl biotypeprotein_coding
OMIM300207
Entrez9248

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000218316

RefSeq mRNA: 1 — MANE Select: NM_004224 NM_004224

CCDS: CCDS44012

Canonical transcript exons

ENST00000218316 — 2 exons

ExonStartEnd
ENSE00000677604151176584151176908
ENSE00001306006151179771151181465

Expression profiles

Bgee: expression breadth broad, 41 present calls, max score 81.66.

FANTOM5 (CAGE): breadth broad, TPM avg 5.1861 / max 578.3263, expressed in 290 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1979825.1328290
1979830.027114
1979840.026214

Top tissues by expression

267 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
adenohypophysisUBERON:000219681.66gold quality
pituitary glandUBERON:000000780.65gold quality
lower lobe of lungUBERON:000894953.41silver quality
pancreatic ductal cellCL:000207952.59silver quality
epithelial cell of pancreasCL:000008349.91gold quality
Brodmann (1909) area 46UBERON:000648349.62gold quality
deltoidUBERON:000147649.40gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
quadriceps femorisUBERON:000137749.08gold quality
olfactory bulbUBERON:000226448.92gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
vastus lateralisUBERON:000137948.39gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
upper arm skinUBERON:000426348.06gold quality
cervix epitheliumUBERON:000480148.04gold quality
oviduct epitheliumUBERON:000480448.00gold quality
tongue squamous epitheliumUBERON:000691947.92gold quality
mucosa of urinary bladderUBERON:000125947.80gold quality
metanephric glomerulusUBERON:000473647.45gold quality
thymusUBERON:000237047.42gold quality
kidney epitheliumUBERON:000481947.39gold quality
nephron tubuleUBERON:000123147.30gold quality
diaphragmUBERON:000110347.05gold quality
gluteal muscleUBERON:000200047.03gold quality
triceps brachiiUBERON:000150947.01gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 16)

  • Polymorphisms in GPR50 were compared in bipolar affective disorder (BD), major depressive disorder (MDD), schizophrenia (SCZ) and controls. GPR50(Delta502-505) or a variant is a sex-specific risk factor for susceptibility to BD and SCZ. (PMID:15452587)
  • Results describe sequence variants in the melatonin-related receptor gene (GPR50) that associate with circulating triglyceride and HDL levels. (PMID:16436372)
  • GPR50, an orphan GPCR, heterodimerizes constitutively and specifically with MT(1) and MT(2) melatonin receptors (PMID:16778767)
  • No evidence for an association for this gene with mood disorders in a Hungarian population. (PMID:18075476)
  • Results identify neurite outgrowth inhibitor NOGO-A as an interacting partner of GPR50 and found an enrichment of both Gpr50 and neuronal Nogo-A at the synapse. (PMID:19699797)
  • Antibodies were used to study the expression of GPR50 in mouse, rat and human hypothalamus.GPR50 immunoreactivity (ir) was observed in dorsomedial hypothalamic (DMH) cells and in cells of the ependymal layer of the third ventricle of the hypothalamus. (PMID:20210849)
  • This is the first association of rs1202874 with BD and is the second positive association at the GPR50 locus. (PMID:20371266)
  • we found 2 polymorphisms in the GPR50 receptor of patients with adolescent idiopathic scoliosis, but they were not present at a highly significant frequency when compared with controls (PMID:20733416)
  • Positive expression of melatonin receptor can be found in human hypertrophic scar and normal skin, but it is higher in scar. (PMID:20737950)
  • study found an association between Seasonal Affective Disorder (SAD) and a single nucleotide polymorphism (intronic rs2072621) of the gene encoding GPR50 in females. (PMID:21565467)
  • The results provide deeper insight into the functional evolution of GPR50 in mammals at the molecular level (PMID:25730005)
  • There was only weak female-specific association between GPR50 variants in late-life depression. No significant associations were observed in men. (PMID:25798330)
  • Pre-eclampsia (PE) plasma IgG1 anti-Epstein-Barr virus nuclear antigen 1 (EBNA-1) antibody cross-reacts with placental protein G protein-coupled receptor 50 (GPR50). (PMID:27181993)
  • GPR50 is a TbetaRI co-receptor with potential impact on cancer development (PMID:29572483)
  • GPR50 promoter methylation level was decreased in the male Alzheimer’s disease group compared with the male control group. (PMID:31173244)
  • GPR50-Ctail cleavage and nuclear translocation: a new signal transduction mode for G protein-coupled receptors. (PMID:31900622)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriomtnr1cENSDARG00000035609
mus_musculusGpr50ENSMUSG00000056380
rattus_norvegicusGpr50ENSRNOG00000011335

Paralogs (33): TACR2 (ENSG00000075073), PROKR2 (ENSG00000101292), TACR1 (ENSG00000115353), GPR75 (ENSG00000119737), PRLHR (ENSG00000119973), GPR83 (ENSG00000123901), MCHR1 (ENSG00000128285), OR11H1 (ENSG00000130538), MTNR1B (ENSG00000134640), MCHR2 (ENSG00000152034), NPY1R (ENSG00000164128), NPY5R (ENSG00000164129), MTNR1A (ENSG00000168412), PROKR1 (ENSG00000169618), TACR3 (ENSG00000169836), OR9G1 (ENSG00000174914), OR11H4 (ENSG00000176198), OR11H6 (ENSG00000176219), OR9A2 (ENSG00000179468), GPR88 (ENSG00000181656), GPR19 (ENSG00000183150), NPY2R (ENSG00000185149), OR11G2 (ENSG00000196832), NPY4R (ENSG00000204174), OR11A1 (ENSG00000204694), OR9A1P (ENSG00000237621), OR11H12 (ENSG00000257115), OR9A4 (ENSG00000258083), OR11H2 (ENSG00000258453), OR11H7 (ENSG00000258806), NPY4R2 (ENSG00000264717), OR10X1 (ENSG00000279111), OR51F1 (ENSG00000280021)

Protein

Protein identifiers

Melatonin-related receptorQ13585 (reviewed: Q13585)

Alternative names: G protein-coupled receptor 50, H9

All UniProt accessions (1): Q13585

UniProt curated annotations — full annotation on UniProt →

Function. G protein-coupled receptor that plays a role in numerous physiological processes including regulation of energy metabolism, neurite outgrowth or cell migration. Promotes self-renewal and neuronal differentiation of neural progenitor cells through activation of the NOTCH and WNT/beta-catenin signaling pathways. Modulates the KAT5-dependent glucocorticoid receptor signaling by modulating KAT5 subcellular compartmentalisation. Also plays a role in the activation TGFBR1 in the absence of TGFBR2 by interfering with FKBP1A binding to TGFBR1, leading to induction of both canonical and non-canonical SMAD signaling pathways resulting in inhibition of proliferation or promotion of migration. Upon cleavage by CAPN1, functions as a scaffold in the nucleus for interacting partners such as GTF2I to promote FOS promoter activation.

Subunit / interactions. Homodimer, and heterodimer with MTNR1A and MTNR1B. Interacts with KAT5. Interacts with RTN4 isoform A/NOGO-A. Interacts with TGFBR1. Interacts with GTF2I.

Subcellular location. Cell membrane. Postsynaptic density Nucleus.

Tissue specificity. Hypothalamus and pituitary.

Post-translational modifications. Cleaved by CAPN1 in a calcium-dependent manner.

Induction. By TGFB.

Similarity. Belongs to the G-protein coupled receptor 1 family.

RefSeq proteins (1): NP_004215* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000025Melatonin_rcptFamily
IPR000276GPCR_RhodpsnFamily
IPR002280Mel_rcpt_1XFamily
IPR017452GPCR_Rhodpsn_7TMDomain

Pfam: PF00001

UniProt features (28 total): topological domain 8, transmembrane region 7, sequence variant 3, chain 2, region of interest 2, compositionally biased region 2, sequence conflict 2, site 1, disulfide bond 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9L9OELECTRON MICROSCOPY2.98

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13585-F167.350.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 408–409 (cleavage; by calpain-1/capn1)

Disulfide bonds (1): 101–178

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): RACCACAR_AML_Q6, GOBP_CELL_CELL_SIGNALING, KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION, TATA_C, AACTTT_UNKNOWN, TTCNRGNNNNTTC_HSF_Q6, GOCC_POSTSYNAPSE, GOCC_SYNAPSE, GOMF_TRANSMEMBRANE_SIGNALING_RECEPTOR_ACTIVITY, CHENG_IMPRINTED_BY_ESTRADIOL, GOMF_G_PROTEIN_COUPLED_RECEPTOR_ACTIVITY, MEISSNER_BRAIN_HCP_WITH_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, chrXq28

GO Biological Process (3): G protein-coupled receptor signaling pathway (GO:0007186), cell-cell signaling (GO:0007267), signal transduction (GO:0007165)

GO Molecular Function (3): G protein-coupled receptor activity (GO:0004930), melatonin receptor activity (GO:0008502), protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), plasma membrane (GO:0005886), postsynaptic density (GO:0014069), nucleus (GO:0005634), membrane (GO:0016020), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
G protein-coupled receptor activity2
cell communication2
signaling2
cellular anatomical structure2
signal transduction1
cellular process1
regulation of cellular process1
cellular response to stimulus1
transmembrane signaling receptor activity1
G protein-coupled receptor signaling pathway1
binding1
nuclear lumen1
membrane1
cell periphery1
asymmetric synapse1
postsynaptic specialization1
intracellular membrane-bounded organelle1
cell junction1

Protein interactions and networks

STRING

822 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPR50ASMTP46597598
GPR50AANATQ16613577
GPR50F9P00740548
GPR50QRFPP83859533
GPR50GPR62Q9BZJ7497
GPR50PRLP01236490
GPR50NQO2P16083479
GPR50KAT5Q92993467
GPR50RARRES2Q99969446
GPR50GPR88Q9GZN0445
GPR50GPR26Q8NDV2441
GPR50CAND2O75155438
GPR50NPVFQ9HCQ7438
GPR50KRT74Q7RTS7434
GPR50FKBP1AP20071426

IntAct

73 interactions, top by confidence:

ABTypeScore
IFT27IFT56psi-mi:“MI:0914”(association)0.690
HLA-CHLA-Apsi-mi:“MI:0914”(association)0.670
ATP5F1BATP5PDpsi-mi:“MI:0914”(association)0.670
GPR50ZNF572psi-mi:“MI:0915”(physical association)0.560
ZNF572GPR50psi-mi:“MI:0915”(physical association)0.560
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
IPPKTMEM223psi-mi:“MI:0914”(association)0.530
HTR2CKLRG2psi-mi:“MI:0914”(association)0.530
ADGRG5KLRG2psi-mi:“MI:0914”(association)0.530
MAS1POTEFpsi-mi:“MI:0914”(association)0.530
TMEM171THAP12psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
TMEM9ESYT2psi-mi:“MI:0914”(association)0.530
GPR21TMEM120Bpsi-mi:“MI:0914”(association)0.530
GPR50MT1Apsi-mi:“MI:0915”(physical association)0.520
GPR50MT1Apsi-mi:“MI:2364”(proximity)0.520
GPR50MT1Apsi-mi:“MI:0403”(colocalization)0.520
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
GPR50GPR50psi-mi:“MI:0915”(physical association)0.470
GPR50MT2Apsi-mi:“MI:0915”(physical association)0.470
GPR50GPR50psi-mi:“MI:2364”(proximity)0.470
GPR50MT2Apsi-mi:“MI:2364”(proximity)0.470
GPR50H2BC21psi-mi:“MI:0915”(physical association)0.400
ADAM17GPR50psi-mi:“MI:0915”(physical association)0.400

BioGRID (83): ZNF572 (Two-hybrid), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), GPR50 (Affinity Capture-MS)

ESM2 similar proteins: A9RZ57, E7EM37, F5HET1, O01670, O12000, O57422, O75121, O77408, O88495, O95800, P09256, P11322, P15792, P16751, P16849, P20905, P22270, P34590, P49219, Q03613, Q10042, Q13585, Q14439, Q16950, Q18775, Q18LE5, Q25190, Q25414, Q28558, Q2KNE5, Q4R1I4, Q61H86, Q64017, Q6AYF7, Q6RYS9, Q6SW98, Q6X632, Q7Z2Y5, Q804Q2, Q804X9

Diamond homologs: A5A4K9, A5A4L1, C3ZQF9, F1MV99, G4WMX4, O02835, O02836, O08725, O42179, O43614, O54799, O62729, O62809, O70342, O77408, P0DQD5, P11617, P20288, P22270, P24053, P24628, P25929, P25931, P28336, P29274, P30731, P30938, P30975, P32251, P35346, P35371, P41143, P47211, P47751, P49146, P49219, P49285, P49288, P49683, P50391

SIGNOR signaling

1 interactions.

AEffectBMechanism
GPR50“up-regulates activity”ADAM17binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 89 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
G alpha (q) signalling events88.3×3e-04
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell57.9×3e-03
Peptide ligand-binding receptors56.7×6e-03

GO biological processes:

GO termPartnersFoldFDR
adenylate cyclase-activating G protein-coupled receptor signaling pathway1014.9×8e-07
phospholipase C-activating G protein-coupled receptor signaling pathway712.1×4e-04
cell surface receptor signaling pathway86.7×4e-03
G protein-coupled receptor signaling pathway136.2×5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

96 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance80
Likely benign8
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

267 predictions. Top by Δscore:

VariantEffectΔscore
X:151179761:T:Gacceptor_gain1.0000
X:151179766:TTCA:Tacceptor_loss1.0000
X:151179768:CA:Cacceptor_loss1.0000
X:151179769:A:AGacceptor_gain1.0000
X:151179769:A:Cacceptor_loss1.0000
X:151179770:G:GGacceptor_gain1.0000
X:151179756:C:Aacceptor_gain0.9900
X:151179760:A:AGacceptor_gain0.9900
X:151179760:AT:Aacceptor_gain0.9900
X:151179761:T:TAacceptor_gain0.9900
X:151179769:AG:Aacceptor_gain0.9900
X:151179770:GG:Gacceptor_gain0.9900
X:151179770:GGC:Gacceptor_gain0.9900
X:151179770:GGCA:Gacceptor_gain0.9900
X:151179770:GGCAA:Gacceptor_gain0.9900
X:151177634:GTCC:Gdonor_gain0.9800
X:151177630:CAAG:Cdonor_loss0.9700
X:151177631:AAG:Adonor_loss0.9700
X:151177638:G:GGdonor_gain0.9700
X:151177632:AGGTC:Adonor_gain0.9600
X:151177346:T:Gdonor_gain0.9500
X:151177637:C:CGdonor_gain0.9500
X:151179013:C:Tdonor_gain0.9500
X:151176909:G:GGdonor_gain0.9400
X:151177631:AAGGT:Adonor_gain0.9400
X:151177633:GGTC:Gdonor_gain0.9400
X:151176905:TCTGG:Tdonor_loss0.9300
X:151176909:GTAA:Gdonor_loss0.9300
X:151176910:T:Adonor_loss0.9300
X:151177635:T:Adonor_gain0.9300

AlphaMissense

4093 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:151179788:A:CS69R0.999
X:151179790:T:AS69R0.999
X:151179790:T:GS69R0.999
X:151180484:T:CF301L0.998
X:151180486:C:AF301L0.998
X:151180486:C:GF301L0.998
X:151180485:T:CF301S0.997
X:151179960:G:CR126P0.996
X:151180442:A:CS287R0.996
X:151180444:C:AS287R0.996
X:151180444:C:GS287R0.996
X:151180467:G:AG295E0.996
X:151180485:T:GF301C0.996
X:151176876:C:AA52D0.994
X:151180040:T:AW153R0.994
X:151180040:T:CW153R0.994
X:151180115:T:CC178R0.994
X:151180117:C:GC178W0.994
X:151180319:T:CF246L0.994
X:151180321:T:AF246L0.994
X:151180321:T:GF246L0.994
X:151180488:G:CR302P0.994
X:151176854:G:CG45R0.993
X:151176855:G:AG45D0.993
X:151176859:C:AN46K0.993
X:151176859:C:GN46K0.993
X:151179884:T:AC101S0.993
X:151179885:G:CC101S0.993
X:151179951:C:AA123D0.993
X:151180116:G:AC178Y0.993

dbSNP variants (sampled 300 via entrez): RS1000717126 (X:151177236 C>T), RS1000864690 (X:151179502 A>G), RS1001255852 (X:151174808 G>C), RS1001355813 (X:151182230 A>G), RS1001623658 (X:151175153 T>C), RS1002895906 (X:151176821 G>A), RS1003331674 (X:151180781 G>A), RS1003337508 (X:151176428 T>C,G), RS1004841500 (X:151181744 CTT>C), RS1005337522 (X:151175984 C>G), RS1006170655 (X:151182301 A>G), RS1006513049 (X:151182621 C>G,T), RS1006904065 (X:151183331 C>A,G,T), RS1007142279 (X:151177134 A>G,T), RS1007729245 (X:151174783 C>G)

Disease associations

OMIM: gene MIM:300207 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3341577 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: gpcr — Class A Orphans with no pharmacology

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
LittleLENAgonist7.32pEC50

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression2
methylmercuric chlorideincreases expression1
decabromobiphenyl etherincreases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
tetrabromobisphenol Aincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
tetrachlorodianincreases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
(+)-JQ1 compoundincreases expression1
Calcitriolincreases expression1
Doxorubicinincreases expression1
Estradiolincreases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Nicotineincreases expression, increases splicing1
Valproic Acidincreases expression1
Okadaic Acidincreases expression1
Acrylamideincreases expression1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3383679BindingDisplacement of [125I]2-Iodomelatonin from human MT1 receptor at 10 uMDevelopment of (E)-2-((1,4-dimethylpiperazin-2-ylidene)amino)-5-nitro-N-phenylbenzamide, ML336: Novel 2-amidinophenylbenzamides as potent inhibitors of venezuelan equine encephalitis virus. — J Med Chem

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D7GKUbigene HEK293T GPR50 KOTransformed cell lineFemale
CVCL_KX65PathHunter CHO-K1 GPR50 beta-arrestinSpontaneously immortalized cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.