GeneBe

RGR

protein-coding

retinal G protein coupled receptor, the group of Opsin receptors

Gene summary

This gene encodes a putative retinal G-protein coupled receptor. The gene is a member of the opsin subfamily of the 7 transmembrane, G-protein coupled receptor 1 family. Like other opsins which bind retinaldehyde, it contains a conserved lysine residue in the seventh transmembrane domain. The protein acts as a photoisomerase to catalyze the conversion of all-trans-retinal to 11-cis-retinal. The reverse isomerization occurs with rhodopsin in retinal photoreceptor cells. The protein is exclusively expressed in tissue adjacent to retinal photoreceptor cells, the retinal pigment epithelium and Mueller cells. This gene may be associated with autosomal recessive and autosomal dominant retinitis pigmentosa (arRP and adRP, respectively). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001012720.2

Inheritance

AD, AR, SD

ClinVar variants

P:3U:176B:88

Top phenotype

Retinitis pigmentosa 44

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr10:84,230,666-84,259,960

External References & Databases

Ensembl (ENSG00000148604)NCBI Gene (5995)OMIM (600342)HGNC:9990GenCCUniProt (P47804)AlphaFoldClinVar (RGR)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~29.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa 44LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013414

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 44LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0013414

Submitter: PanelApp Australia

retinitis pigmentosa 44LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013414

Submitter: PanelApp Australia

retinitis pigmentosa 44LIMITED

Inheritance Pattern: SD

Disease ID:MONDO:0013414

Submitter: Ambry Genetics

retinitis pigmentosa 44LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013414

Submitter: G2P

Clinical Genomic Database (CGD)

Retinitis pigmentosa 44AD/AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 10581022Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RGR variants in ClinVar

8 Conditions Cataloged
not providedTotal: 296
not specifiedTotal: 83
Retinal dystrophyTotal: 18
Retinitis pigmentosaTotal: 17
Retinitis pigmentosa 44Total: 13
RGR-related disorderTotal: 8
Optic atrophyTotal: 1
Cone dystrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012720.2. 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
83
clinvar
1
clinvar
 88
missense
1
clinvar
147
clinvar
4
clinvar
 152
nonsense
8
clinvar
 8
start loss
0
frameshift
2
clinvar
9
clinvar
 11
splice donor/acceptor (+/-2bp)
8
clinvar
 8
Total03176871267

Highest pathogenic variant AF is 0.00003965353

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001012720.2RefSeqNP_001012738.17MANE Select
ENST00000652092.2EnsemblENSP00000498299.17MANE Select
NM_001012722.2RefSeqNP_001012740.16Standard
NM_002921.4RefSeqNP_002912.27Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Signaling by GPCR
  • Signal Transduction
  • Opsins
  • Class A/1 (Rhodopsin-like receptors)
  • GPCR ligand binding

Biological Process

  • G protein-coupled receptor signaling pathway
  • visual perception
  • phototransduction
  • detection of visible light
  • protein-chromophore linkage

Molecular Function

  • G protein-coupled receptor activity
  • protein binding
  • G protein-coupled photoreceptor activity

Cellular Component

  • integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000359452
Coding exons
7
Length
14908
Individuals with no LoFs
125706
Homozygous LoFs
0
Heterozygous LoFs
42
Defined
125748
p
0.000167
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2841821721.060.00001071894
Missense (PolyPhen)6555.3441.1745650
Synonymous-2.3310175.31.340.00000538618
Loss of Function-0.3521412.71.116.50e-7127

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000270.00027rare
Finnish0.000280.00028rare
European (Non-Finnish)0.000160.00016rare
South Asian0.000160.00016rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Receptor for all-trans- and 11-cis-retinal. Binds preferentially to the former and may catalyze the isomerization of the chromophore by a retinochrome-like mechanism.;
Disease
DISEASE: Retinitis pigmentosa 44 (RP44) [MIM:613769]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10581022}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.125

Intolerance Scores

LoFtool
0.566
RVIS EVS
-0.47
RVIS percentile EVS
23.43

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.670

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.