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GeneBe

RGS9

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

Basic information

Region (hg38): 17:65100811-65227703

Links

ENSG00000108370NCBI:8787OMIM:604067HGNC:10004Uniprot:O75916AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • bradyopsia (Strong), mode of inheritance: AR
  • bradyopsia (Strong), mode of inheritance: AR
  • bradyopsia (Supportive), mode of inheritance: AR
  • bradyopsia (Moderate), mode of inheritance: AR
  • bradyopsia (Moderate), mode of inheritance: AR
  • bradyopsia (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Prolonged electroretinal response suppression 1ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic1790747; 14702087; 17826834

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RGS9 gene.

  • not provided (455 variants)
  • Inborn genetic diseases (37 variants)
  • not specified (6 variants)
  • Bradyopsia (5 variants)
  • Leber congenital amaurosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RGS9 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
clinvar
96
clinvar
6
clinvar
106
missense
1
clinvar
1
clinvar
204
clinvar
5
clinvar
6
clinvar
217
nonsense
11
clinvar
1
clinvar
12
start loss
0
frameshift
5
clinvar
5
inframe indel
4
clinvar
4
splice donor/acceptor (+/-2bp)
12
clinvar
1
clinvar
13
splice region
14
24
38
non coding
4
clinvar
52
clinvar
7
clinvar
63
Total 17 13 218 153 19

Highest pathogenic variant AF is 0.000184

Variants in RGS9

This is a list of pathogenic ClinVar variants found in the RGS9 region.

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

Position Type Phenotype Significance ClinVar
17-65137551-G-T Uncertain significance (Jan 02, 2022)2070865
17-65137555-C-T Likely benign (Feb 09, 2023)1539417
17-65137556-C-A Inborn genetic diseases Uncertain significance (Oct 25, 2022)1917832
17-65137559-G-C Uncertain significance (May 20, 2020)1062407
17-65137561-C-G Likely benign (Mar 31, 2020)1111381
17-65137563-A-G Uncertain significance (Nov 20, 2019)839492
17-65137575-C-G Uncertain significance (Dec 08, 2021)1359815
17-65137577-A-G Uncertain significance (Feb 04, 2022)1930078
17-65137579-G-A Likely benign (May 19, 2023)2811118
17-65137586-T-C Uncertain significance (Oct 15, 2019)969280
17-65137603-C-T Uncertain significance (Jul 27, 2019)936024
17-65137607-G-A Likely benign (Dec 13, 2021)1088309
17-65137611-C-T Likely benign (Jul 18, 2022)1655308
17-65153410-T-C Likely benign (Aug 19, 2020)1107812
17-65153416-T-C Likely benign (Aug 22, 2023)2789740
17-65153421-G-T Likely pathogenic (Feb 25, 2022)1009429
17-65153429-C-T Uncertain significance (Aug 23, 2022)1055229
17-65153430-G-A not specified Likely benign (Jan 14, 2024)775332
17-65153433-C-T Conflicting classifications of pathogenicity (Sep 08, 2023)286373
17-65153434-G-A Uncertain significance (Aug 28, 2021)1475188
17-65153442-C-T Likely benign (Jun 03, 2021)1108111
17-65153443-A-G Uncertain significance (Dec 11, 2023)858339
17-65153446-C-T Pathogenic (Feb 29, 2020)962370
17-65153450-A-T Uncertain significance (Mar 20, 2021)1517845
17-65153451-C-G Uncertain significance (Jul 05, 2022)1939591

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RGS9protein_codingprotein_codingENST00000262406 1990273
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.13e-140.9711247230871248100.000349
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.03813773790.9940.00002314398
Missense in Polyphen99117.030.845911355
Synonymous-1.401681461.150.000009561258
Loss of Function2.413048.00.6250.00000318473

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006680.000664
Ashkenazi Jewish0.000.00
East Asian0.0003340.000334
Finnish0.00004640.0000464
European (Non-Finnish)0.0003980.000397
Middle Eastern0.0003340.000334
South Asian0.0004930.000490
Other0.0003310.000330

dbNSFP

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.;
Pathway
Phototransduction - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Calcium Regulation in the Cardiac Cell;Signaling by GPCR;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signal Transduction;Metabolism of proteins;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Chaperonin-mediated protein folding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Visual signal transduction: Rods;Protein folding;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR signaling-G alpha i;GPCR downstream signalling;Visual signal transduction: Cones (Consensus)

Recessive Scores

pRec
0.114

Intolerance Scores

loftool
0.948
rvis_EVS
0.27
rvis_percentile_EVS
70.64

Haploinsufficiency Scores

pHI
0.0953
hipred
N
hipred_score
0.422
ghis
0.425

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.668

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rgs9
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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);

Gene ontology

Biological process
response to amphetamine;protein folding;dopamine receptor signaling pathway;nervous system development;visual perception;regulation of G protein-coupled receptor signaling pathway;negative regulation of signal transduction;response to estradiol;intracellular signal transduction;positive regulation of GTPase activity;positive regulation of NMDA glutamate receptor activity;regulation of calcium ion export across plasma membrane
Cellular component
nucleus;cytoplasm;photoreceptor disc membrane;postsynaptic density membrane;glutamatergic synapse
Molecular function
GTPase activator activity