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GRK1

G protein-coupled receptor kinase 1, the group of AGC family kinases

Basic information

Region (hg38): 13:113667218-113737736

Previous symbols: [ "RHOK" ]

Links

ENSG00000185974NCBI:6011OMIM:180381HGNC:10013Uniprot:Q15835AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Oguchi disease (Supportive), mode of inheritance: AR
  • Oguchi disease-2 (Strong), mode of inheritance: AR
  • Oguchi disease (Definitive), mode of inheritance: AR
  • Oguchi disease-2 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Oguchi disease 2ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic14281981; 9020843; 17070587; 17765441; 19753316; 22959359

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GRK1 gene.

  • Inborn genetic diseases (16 variants)
  • not provided (11 variants)
  • Oguchi disease-2 (3 variants)
  • not specified (1 variants)
  • Oguchi disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRK1 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
1
clinvar
1
missense
1
clinvar
18
clinvar
3
clinvar
22
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
4
clinvar
4
Total 1 1 18 4 4

Highest pathogenic variant AF is 0.0000396

Variants in GRK1

This is a list of pathogenic ClinVar variants found in the GRK1 region.

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

Position Type Phenotype Significance ClinVar
13-113667441-C-T Oguchi disease-2 Likely pathogenic (Dec 19, 2019)870441
13-113667478-G-A Oguchi disease Uncertain significance (Apr 27, 2019)638310
13-113667525-TGTGA-T Oguchi disease-2 Likely pathogenic (Feb 20, 2019)870427
13-113667537-C-T Inborn genetic diseases Uncertain significance (Apr 07, 2022)2352391
13-113667548-C-T Oguchi disease-2 • not specified Likely benign (Jun 28, 2017)522307
13-113667564-A-C Inborn genetic diseases Uncertain significance (Feb 04, 2022)2227223
13-113667675-A-C Inborn genetic diseases Uncertain significance (Jul 15, 2021)2237806
13-113667683-C-G Inborn genetic diseases Uncertain significance (Apr 05, 2023)2533287
13-113667748-T-C Inborn genetic diseases Uncertain significance (Jun 18, 2021)2233589
13-113667754-G-A Inborn genetic diseases Uncertain significance (Jul 09, 2021)2354093
13-113667781-C-T Inborn genetic diseases Likely benign (May 09, 2022)2228238
13-113667798-C-A Inborn genetic diseases Uncertain significance (Sep 16, 2021)2217593
13-113667816-G-T Inborn genetic diseases Uncertain significance (Apr 26, 2023)2540913
13-113667849-G-T Inborn genetic diseases Uncertain significance (Feb 24, 2022)2365979
13-113667850-C-T Inborn genetic diseases Uncertain significance (Apr 19, 2023)2538849
13-113667853-A-T Inborn genetic diseases Uncertain significance (Oct 25, 2022)2408765
13-113667856-T-C Oguchi disease-2 Likely pathogenic (Dec 17, 2019)870428
13-113667889-GCCTGTACTT-G Oguchi disease-2 Likely pathogenic (Sep 01, 2022)1710125
13-113667958-T-A Inborn genetic diseases Uncertain significance (Mar 22, 2023)2525644
13-113667981-G-C Oguchi disease-2 Likely pathogenic (Feb 20, 2019)870429
13-113668000-C-A Oguchi disease-2 Likely pathogenic (Feb 20, 2019)870430
13-113668007-C-G Inborn genetic diseases Uncertain significance (Jan 18, 2022)2374105
13-113668041-A-C Uncertain significance (Sep 01, 2023)2582915
13-113669574-C-T Benign (May 12, 2021)1288366
13-113669682-T-C Benign (May 04, 2021)1253118

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GRK1protein_codingprotein_codingENST00000335678 7119239
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003070.9871246321411246740.000168
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4323143360.9340.00002103702
Missense in Polyphen125149.790.834481572
Synonymous0.2751541580.9720.00001161088
Loss of Function2.221122.30.4930.00000111254

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003920.000380
Ashkenazi Jewish0.000.00
East Asian0.0001110.000111
Finnish0.000.00
European (Non-Finnish)0.00005450.0000531
Middle Eastern0.0001110.000111
South Asian0.0008660.000817
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade. This rapid desensitization is essential for scotopic vision and permits rapid adaptation to changes in illumination. {ECO:0000269|PubMed:15946941}.;
Disease
DISEASE: Night blindness, congenital stationary, Oguchi type 2 (CSNBO2) [MIM:613411]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:17070587, ECO:0000269|PubMed:9020843}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Endocytosis - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Phototransduction - Homo sapiens (human);Chemokine signaling pathway;Signaling by GPCR;Signal Transduction;visual signal transduction;Visual signal transduction: Rods;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling;Visual signal transduction: Cones (Consensus)

Recessive Scores

pRec
0.180

Haploinsufficiency Scores

pHI
0.178
hipred
N
hipred_score
0.322
ghis
0.461

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.809

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Grk1
Phenotype
cellular 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
visual perception;regulation of G protein-coupled receptor signaling pathway;rhodopsin mediated signaling pathway;regulation of rhodopsin mediated signaling pathway;protein autophosphorylation
Cellular component
photoreceptor disc membrane
Molecular function
protein kinase activity;G protein-coupled receptor kinase activity;ATP binding;rhodopsin kinase activity