RGR

retinal G protein coupled receptor, the group of Opsin receptors

Basic information

Region (hg38): 10:84230666-84259960

Links

ENSG00000148604 ∙ NCBI:5995 ∙ OMIM:600342 ∙ HGNC:9990 ∙ Uniprot:P47804 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD
• retinitis pigmentosa 44 (Limited), mode of inheritance: Semidominant
• retinitis pigmentosa 44 (Limited), mode of inheritance: AD
• retinitis pigmentosa 44 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 44	AD/AR	General	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	Ophthalmologic	10581022

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RGR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGR 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			4	63	6	73
missense			110	1	1	112
nonsense			7			7
start loss						0
frameshift		1	8			9
inframe indel						0
splice donor/acceptor (+/-2bp)			5			5
splice region			7	9		16
non coding			72	30	3	105
Total	0	1	206	94	10

Variants in RGR

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

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

Position	Type	Phenotype	Significance	ClinVar
10-84231959-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-84232034-G-A		not specified	Uncertain significance (Oct 27, 2023)
10-84232056-C-G		not specified	Uncertain significance (Sep 26, 2022)
10-84232082-T-C		not specified	Uncertain significance (Jan 29, 2024)
10-84232112-C-A		not specified	Uncertain significance (Aug 13, 2021)
10-84232190-T-C		not specified	Likely benign (Sep 27, 2021)
10-84232205-C-A		not specified	Uncertain significance (Mar 07, 2023)
10-84232252-T-C		not specified	Uncertain significance (May 18, 2022)
10-84232270-C-T		not specified	Uncertain significance (Mar 08, 2024)
10-84232282-C-T		not specified	Uncertain significance (Mar 25, 2022)
10-84232318-T-G		not specified	Uncertain significance (Nov 20, 2023)
10-84232349-T-A		not specified	Uncertain significance (Apr 25, 2023)
10-84232352-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-84232354-C-G		not specified	Uncertain significance (Mar 17, 2023)
10-84232385-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-84232422-G-C		not specified	Uncertain significance (Dec 17, 2023)
10-84232439-T-C		not specified	Uncertain significance (May 04, 2022)
10-84232510-A-G		not specified	Uncertain significance (Nov 08, 2022)
10-84232541-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-84232549-T-C		not specified	Uncertain significance (May 04, 2022)
10-84232550-C-G		not specified	Uncertain significance (Jan 23, 2023)
10-84232631-C-G		not specified	Uncertain significance (Nov 08, 2022)
10-84232654-T-G		not specified	Uncertain significance (Mar 20, 2023)
10-84232666-A-G		not specified	Uncertain significance (Apr 15, 2024)
10-84232753-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RGR	protein_coding	protein_coding	ENST00000359452	7	14908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-10	0.0406	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.284	182	172	1.06	0.0000107	1894
Missense in Polyphen		65	55.344	1.1745		650
Synonymous	-2.33	101	75.3	1.34	0.00000538	618
Loss of Function	-0.352	14	12.7	1.11	6.50e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000272	0.000272
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000272	0.000272
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

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.
• Pathway: Signaling by GPCR;Signal Transduction;Opsins;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.566
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.282
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rgr
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;visual perception;phototransduction;detection of visible light;protein-chromophore linkage;cellular response to light stimulus
• Cellular component: integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;protein binding;G protein-coupled photoreceptor activity