RGS9

protein-coding

regulator of G protein signaling 9, the group of Regulators of G-protein signaling

Gene summary

This gene encodes a member of the RGS family of GTPase activating proteins that function in various signaling pathways by accelerating the deactivation of G proteins. This protein is anchored to photoreceptor membranes in retinal cells and deactivates G proteins in the rod and cone phototransduction cascades. Mutations in this gene result in bradyopsia. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

MANE transcript

NM_003835.4

Inheritance

AR

ClinVar variants

P:50U:250B:174

Top phenotype

Prolonged electroretinal response suppression 1

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr17:65,100,812-65,227,703

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~126.9 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

prolonged electroretinal response suppression 1DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0958180

Submitter: G2P

bradyopsiaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012033

Submitter: ClinGen

RGS9 gene was first reported in relation to autosomal recessive Bradyopsia in 2004 (Nishiguchi et al., 2004). Bradyopsia was reported to be characterized by difficulty in adjusting to changes in luminance, difficulty in seeing moving objects, and normal to subnormal visual acuity. Routine electroretinograms showed normal responses to scotopic stimulus flashes but responses to standard high-density flashes were strikingly reduced in amplitude. At least 03 patients were evaluated for neurologic features and were found to be normal. Color vision was normal in all patients while fundus appeared normal in most of the cases except slight pigment alterations in the maculae of one patient. The ophthalmic clinical features in patients were found to be non-progressive (PMIDs: 17826834, 19818506). By far, one missense and one nonsense variant have been reported in 05 human subjects (PMIDs: 14702087, 19818506). Four (2 siblings and 2 unrelated) Dutch patients were found to be homozygous for p.Trp299Arg variant while their unaffected parents were heterozygous for this variant. One British male was compound heterozygous for p.Trp299Arg and p.Arg128Ter (PMID: 19818506). The mechanism of pathogenicity is reported to be loss of function. This gene-disease association is also supported by animal models, expression studies and in vitro assays (PMIDs: 10676965, 25257059, 10564809, 14702087). It was reported in an expression study that there are two protein isoforms of RGS9, a retina specific RGS9-1, and a brain specific RGS9-2. The reported variants seem to affect both isoforms of RGS9 however no neurological features were reported in any patients. A single-turn over transducin GTPase assay demonstrated that activity of transducin protein is reduced with the use of mutant RGS9 domains as compared to the wild type RGS9. Furthermore, in a RGS9 knock out study, the null mice showed slow recovery of photoresponse on electroretinogram as compared to the control mice (PMID: 10676965). In another RGS9 knockout study, the null mice showed delayed pupillary reflex as well as photophobia (PMID: 25257059). Both mouse knockout studies seem to recapitulate the phenotype observed in human subjects. In a co-immunoprecipitation study RGS9 was identified in a heterotetrameric complex containing RGS9-1, G5L, G_Beta5L and R9AP (RGS9BP), R9AP interacts with the N-terminal domain of RGS9-1. Mutations in R9AP has been reported to cause autosomal recessive Bradyopsia (PMIDs: 14702087, 19818506). In summary, there is moderate evidence to support the relationship between RGS9 and autosomal recessive Bradyopsia. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. The classification was approved by the ClinGen Retina GCEP on September 8th, 2021.

prolonged electroretinal response suppression 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0958180

Submitter: PanelApp Australia

bradyopsiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012033

Submitter: Orphanet

bradyopsiaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012033

Submitter: Ambry Genetics

bradyopsiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012033

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Prolonged electroretinal response suppression 1AR

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: 1790747; 14702087; 17826834Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RGS9 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 537
Inborn genetic diseasesTotal: 108
not specifiedTotal: 86
RGS9-related disorderTotal: 37
Retinal dystrophyTotal: 8
BradyopsiaTotal: 5
Prolonged electroretinal response suppression 1Total: 4
Leber congenital amaurosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003835.4. 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
146
clinvar
1
clinvar
151
missense
1
clinvar
1
clinvar
242
clinvar
24
clinvar
3
clinvar
271
nonsense
6
clinvar
12
clinvar
2
clinvar
20
start loss
0
frameshift
5
clinvar
5
clinvar
10
splice donor/acceptor (+/-2bp)
20
clinvar
2
clinvar
22
Total12382501704474

Highest pathogenic variant AF is 0.00026707118

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003835.4RefSeqNP_003826.219MANE Select
ENST00000262406.10EnsemblENSP00000262406.919MANE Select
NM_001081955.3RefSeqNP_001075424.119Standard
NM_001165933.2RefSeqNP_001159405.117Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Phototransduction - Homo sapiens (human)
  • Cocaine addiction - Homo sapiens (human)
  • Myometrial Relaxation and Contraction Pathways
  • Calcium Regulation in the Cardiac Cell
  • Signaling by GPCR

Biological Process

  • response to amphetamine
  • protein folding
  • dopamine receptor signaling pathway
  • nervous system development
  • visual perception

Molecular Function

  • GTPase activator activity

Cellular Component

  • nucleus
  • cytoplasm
  • photoreceptor disc membrane
  • postsynaptic density membrane
  • glutamatergic synapse

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000262406
Coding exons
19
Length
90273
Individuals with no LoFs
124723
Homozygous LoFs
0
Heterozygous LoFs
87
Defined
124810
p
0.000349
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.03813773790.9940.00002314398
Missense (PolyPhen)99117.030.845911355
Synonymous-1.401681461.150.000009561258
Loss of Function2.413048.00.6250.00000318473

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000260.00026rare
Latino/Admixed American0.000410.00041rare
Ashkenazi Jewish00.0absent
East Asian0.000330.00033rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000400.00040rare
South Asian0.000490.00049rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits thereby driving them into their inactive GDP-bound form. Binds to GNAT1. Involved in phototransduction; key element in the recovery phase of visual transduction (By similarity). {ECO:0000250}.;
Disease
DISEASE: Prolonged electroretinal response suppression (PERRS) [MIM:608415]: Characterized by difficulty adjusting to sudden changes in luminance levels mediated by cones. {ECO:0000269|PubMed:14702087}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.114

Intolerance Scores

LoFtool
0.948
RVIS EVS
0.27
RVIS percentile EVS
70.64

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.668

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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