RHO

rhodopsin, the group of Opsin receptors

Basic information

Region (hg38): 3:129528638-129535344

Previous symbols: [ "RP4" ]

Links

ENSG00000163914NCBI:6010OMIM:180380HGNC:10012Uniprot:P08100AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 4; Retinitis punctata albescens; Night blindness, congenital stationary, autosomal dominant 1AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic2613244; 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 ClinVar and linked to the RHO gene.

  • 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
7
clinvar
74
clinvar
3
clinvar
84
missense
54
clinvar
66
clinvar
168
clinvar
6
clinvar
2
clinvar
296
nonsense
9
clinvar
8
clinvar
1
clinvar
18
start loss
1
clinvar
1
frameshift
5
clinvar
4
clinvar
4
clinvar
13
inframe indel
2
clinvar
7
clinvar
9
splice donor/acceptor (+/-2bp)
4
clinvar
7
clinvar
11
splice region
5
4
1
10
non coding
35
clinvar
30
clinvar
14
clinvar
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)343272
3-129528708-A-G not specified • Retinitis pigmentosa • Congenital stationary night blindness autosomal dominant 1 • Pigmentary retinal dystrophy • Retinitis pigmentosa 4 Benign (Nov 07, 2021)256383
3-129528710-G-T Congenital stationary night blindness autosomal dominant 1 • Retinitis pigmentosa Uncertain significance (Jan 13, 2018)900391
3-129528734-A-G Uncertain significance (Sep 08, 2023)2796858
3-129528741-G-A Uncertain significance (Oct 25, 2021)1481299
3-129528742-C-T Likely benign (Nov 20, 2023)1429573
3-129528744-C-A Retinal dystrophy Uncertain significance (Oct 01, 2023)3027568
3-129528747-A-G Uncertain significance (Sep 12, 2022)1017489
3-129528749-G-A Retinal dystrophy Uncertain significance (Dec 26, 2017)866917
3-129528758-T-G Uncertain significance (Nov 22, 2021)1384913
3-129528760-C-A Uncertain significance (Dec 11, 2023)1022808
3-129528760-C-T Likely benign (Aug 10, 2023)2101739
3-129528763-C-T Benign (Nov 17, 2023)1556215
3-129528764-G-A Retinal dystrophy Uncertain significance (Nov 22, 2022)866329
3-129528766-GC-G Retinal dystrophy Conflicting classifications of pathogenicity (Oct 01, 2023)1456255
3-129528768-C-G Uncertain significance (Feb 07, 2020)1036590
3-129528771-T-C Retinal dystrophy Uncertain significance (Oct 01, 2023)3027569
3-129528776-A-G Uncertain significance (Apr 18, 2022)2124182
3-129528777-A-G Retinitis pigmentosa 4 • Retinitis pigmentosa Pathogenic (Jan 11, 2024)13042
3-129528777-A-T Likely pathogenic (Nov 01, 2019)872602
3-129528778-T-A Likely pathogenic (Jan 03, 2020)1067776
3-129528778-T-G Retinitis pigmentosa 4 Pathogenic/Likely pathogenic (Feb 08, 2022)802004
3-129528780-C-T Uncertain significance (Jul 17, 2023)851374
3-129528781-G-A Congenital stationary night blindness autosomal dominant 1 • Retinitis pigmentosa Conflicting classifications of pathogenicity (Jul 27, 2023)343273
3-129528783-C-A Retinitis pigmentosa 4 Likely pathogenic (Nov 15, 2022)984772

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RHOprotein_codingprotein_codingENST00000296271 56530
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001310.8601257270211257480.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2422092190.9540.00001512293
Missense in Polyphen122123.40.988641300
Synonymous-1.3511396.21.170.00000815697
Loss of Function1.35813.30.6005.87e-7150

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001410.000141
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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