RHO
rhodopsin, the group of Opsin receptors
Basic information
Region (hg38): 3:129528639-129535344
Previous symbols: [ "RP4" ]
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa 4 (Definitive), mode of inheritance: Semidominant
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- congenital stationary night blindness (Supportive), mode of inheritance: AD
- congenital stationary night blindness autosomal dominant 1 (Definitive), mode of inheritance: AD
- congenital stationary night blindness autosomal dominant 1 (Strong), mode of inheritance: AD
- retinitis pigmentosa 4 (Strong), mode of inheritance: AD
- retinitis pigmentosa 4 (Strong), mode of inheritance: AR
- fundus albipunctatus (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Retinitis pigmentosa 4; Retinitis punctata albescens; Night blindness, congenital stationary, autosomal dominant 1 | 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 | 2613244; 2137202; 2215617; 2333895; 1882937; 1302614; 1301135; 8512476; 8358437; 7846071; 8841304; 9197578; 9888392; 10980774; 20301590; 20555336; 21174529; 22419850 |
| Oral vitamin A may slow retinal degeneration in some forms of retinitis pigmentosa |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (68 variants)
- Retinitis pigmentosa 4 (28 variants)
- Retinitis pigmentosa (15 variants)
- Retinal dystrophy (14 variants)
- Pigmentary retinal dystrophy (3 variants)
- Congenital stationary night blindness autosomal dominant 1 (2 variants)
- RHO-related disorder (1 variants)
- not specified (1 variants)
- Retinitis punctata albescens (1 variants)
- 11 conditions (1 variants)
- Congenital stationary night blindness autosomal dominant 1;Pigmentary retinal dystrophy;Retinitis pigmentosa 4 (1 variants)
- Retinitis pigmentosa 4, autosomal recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHO 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 | 74 | 84 | ||||
| missense | 54 | 66 | 168 | 296 | ||
| nonsense | 18 | |||||
| start loss | 1 | |||||
| frameshift | 13 | |||||
| inframe indel | 9 | |||||
| splice donor/acceptor (+/-2bp) | 11 | |||||
| splice region | 5 | 4 | 1 | 10 | ||
| non coding | 35 | 30 | 14 | 79 | ||
| Total | 72 | 87 | 223 | 110 | 19 |
Highest pathogenic variant AF is 0.0000329
Variants in RHO
This is a list of pathogenic ClinVar variants found in the RHO region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-129528683-G-A | Retinitis pigmentosa • Congenital stationary night blindness autosomal dominant 1 | Benign (Jan 13, 2018) | ||
| 3-129528708-A-G | not specified • Retinitis pigmentosa • Congenital stationary night blindness autosomal dominant 1 • Retinitis pigmentosa 4 • Pigmentary retinal dystrophy | Benign (Nov 07, 2021) | ||
| 3-129528710-G-T | Congenital stationary night blindness autosomal dominant 1 • Retinitis pigmentosa | Uncertain significance (Jan 13, 2018) | ||
| 3-129528734-A-G | Uncertain significance (Sep 08, 2023) | |||
| 3-129528741-G-A | Uncertain significance (Oct 25, 2021) | |||
| 3-129528742-C-T | Likely benign (Nov 20, 2023) | |||
| 3-129528744-C-A | Retinal dystrophy | Uncertain significance (Oct 01, 2023) | ||
| 3-129528747-A-G | Uncertain significance (Sep 12, 2022) | |||
| 3-129528749-G-A | Retinal dystrophy | Uncertain significance (Dec 26, 2017) | ||
| 3-129528758-T-G | Uncertain significance (Jun 26, 2023) | |||
| 3-129528760-C-A | Uncertain significance (Dec 11, 2023) | |||
| 3-129528760-C-T | Likely benign (Aug 10, 2023) | |||
| 3-129528763-C-T | Benign (Nov 17, 2023) | |||
| 3-129528764-G-A | Retinal dystrophy | Uncertain significance (Nov 22, 2022) | ||
| 3-129528766-GC-G | Retinal dystrophy | Conflicting classifications of pathogenicity (Oct 01, 2023) | ||
| 3-129528768-C-G | Uncertain significance (Feb 07, 2020) | |||
| 3-129528771-T-C | Retinal dystrophy | Uncertain significance (Oct 01, 2023) | ||
| 3-129528776-A-G | Uncertain significance (Apr 18, 2022) | |||
| 3-129528777-A-G | Retinitis pigmentosa 4 • Retinitis pigmentosa | Pathogenic (Jan 11, 2024) | ||
| 3-129528777-A-T | Likely pathogenic (Nov 01, 2019) | |||
| 3-129528778-T-A | Likely pathogenic (Jan 03, 2020) | |||
| 3-129528778-T-G | Retinitis pigmentosa 4 | Pathogenic/Likely pathogenic (Feb 08, 2022) | ||
| 3-129528780-C-T | Uncertain significance (Jul 17, 2023) | |||
| 3-129528781-G-A | Retinitis pigmentosa • Congenital stationary night blindness autosomal dominant 1 | Conflicting classifications of pathogenicity (Jul 27, 2023) | ||
| 3-129528783-C-A | Retinitis pigmentosa 4 | Likely pathogenic (Nov 15, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RHO | protein_coding | protein_coding | ENST00000296271 | 5 | 6530 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000131 | 0.860 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.242 | 209 | 219 | 0.954 | 0.0000151 | 2293 |
| Missense in Polyphen | 122 | 123.4 | 0.98864 | 1300 | ||
| Synonymous | -1.35 | 113 | 96.2 | 1.17 | 0.00000815 | 697 |
| Loss of Function | 1.35 | 8 | 13.3 | 0.600 | 5.87e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000141 | 0.000141 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Photoreceptor required for image-forming vision at low light intensity (PubMed:8107847, PubMed:7846071). Required for photoreceptor cell viability after birth (PubMed:2215617, PubMed:12566452). Light-induced isomerization of the chromophore 11-cis-retinal to all-trans-retinal triggers a conformational change that activates signaling via G-proteins (PubMed:8107847, PubMed:28524165, PubMed:26200343, PubMed:28753425). Subsequent receptor phosphorylation mediates displacement of the bound G- protein alpha subunit by the arrestin SAG and terminates signaling (PubMed:28524165, PubMed:26200343). {ECO:0000269|PubMed:12566452, ECO:0000269|PubMed:2215617, ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425, ECO:0000269|PubMed:7846071, ECO:0000269|PubMed:8107847, ECO:0000305|PubMed:28524165}.;
- Disease
- DISEASE: Retinitis pigmentosa 4 (RP4) [MIM:613731]: 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:12566452, ECO:0000269|PubMed:1302614, ECO:0000269|PubMed:1391967, ECO:0000269|PubMed:1833777, ECO:0000269|PubMed:1840561, ECO:0000269|PubMed:1862076, ECO:0000269|PubMed:1897520, ECO:0000269|PubMed:1985460, ECO:0000269|PubMed:19934218, ECO:0000269|PubMed:19960070, ECO:0000269|PubMed:2137202, ECO:0000269|PubMed:2215617, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:2239971, ECO:0000269|PubMed:7633434, ECO:0000269|PubMed:7981701, ECO:0000269|PubMed:7987326, ECO:0000269|PubMed:7987331, ECO:0000269|PubMed:8045708, ECO:0000269|PubMed:8076945, ECO:0000269|PubMed:8081400, ECO:0000269|PubMed:8088850, ECO:0000269|PubMed:8317502, ECO:0000269|PubMed:8353500, ECO:0000269|PubMed:8554077, ECO:0000269|PubMed:9452035}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Night blindness, congenital stationary, autosomal dominant 1 (CSNBAD1) [MIM:610445]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:7846071, ECO:0000269|PubMed:8107847, ECO:0000269|PubMed:8358437, ECO:0000269|PubMed:9888392}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Phototransduction - Homo sapiens (human);Integrated Breast Cancer Pathway;Integrin-mediated Cell Adhesion;Regulation of Microtubule Cytoskeleton;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;visual signal transduction;The canonical retinoid cycle in rods (twilight vision);Opsins;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Visual signal transduction: Rods;G alpha (i) signalling events;Activation of the phototransduction cascade;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling;VxPx cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.833
Intolerance Scores
- loftool
- 0.388
- rvis_EVS
- -0.89
- rvis_percentile_EVS
- 10.37
Haploinsufficiency Scores
- pHI
- 0.496
- hipred
- Y
- hipred_score
- 0.732
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.881
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rho
- Phenotype
- immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- rho
- Affected structure
- retinal rod cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased thickness
Gene ontology
- Biological process
- retinoid metabolic process;protein phosphorylation;G protein-coupled receptor signaling pathway;visual perception;phototransduction;phototransduction, visible light;absorption of visible light;rhodopsin mediated signaling pathway;protein-chromophore linkage;regulation of rhodopsin mediated signaling pathway;photoreceptor cell maintenance;retina development in camera-type eye;cellular response to light stimulus
- Cellular component
- Golgi membrane;photoreceptor outer segment;photoreceptor inner segment;Golgi apparatus;plasma membrane;integral component of plasma membrane;cell-cell junction;integral component of membrane;Golgi-associated vesicle membrane;photoreceptor outer segment membrane;ciliary membrane;photoreceptor inner segment membrane;photoreceptor disc membrane
- Molecular function
- G protein-coupled receptor activity;11-cis retinal binding;protein binding;G protein-coupled photoreceptor activity;metal ion binding