RGS9
protein-codingregulator 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~126.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0958180
Submitter: G2P
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.
Inheritance Pattern: AR
Disease ID:MONDO:0958180
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012033
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012033
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0012033
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RGS9 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 146 | 1 | 151 | ||
| missense | 1 | 1 | 242 | 24 | 3 | 271 |
| nonsense | 6 | 12 | 2 | 20 | ||
| start loss | 0 | |||||
| frameshift | 5 | 5 | 10 | |||
| splice donor/acceptor (+/-2bp) | 20 | 2 | 22 | |||
| Total | 12 | 38 | 250 | 170 | 4 | 474 |
Highest pathogenic variant AF is 0.00026707118
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003826.2 | 19 | MANE Select | |
| Ensembl | ENSP00000262406.9 | 19 | MANE Select | |
| RefSeq | NP_001075424.1 | 19 | Standard | |
| RefSeq | NP_001159405.1 | 17 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0381 | 377 | 379 | 0.994 | 0.0000231 | 4398 |
| Missense (PolyPhen) | 99 | 117.03 | 0.84591 | 1355 | ||
| Synonymous | -1.40 | 168 | 146 | 1.15 | 0.00000956 | 1258 |
| Loss of Function | 2.41 | 30 | 48.0 | 0.625 | 0.00000318 | 473 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.00041 | 0.00041 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00040 | 0.00040 | rare |
| South Asian | 0.00049 | 0.00049 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |