RACK1
receptor for activated C kinase 1, the group of WD repeat domain containing|SSU processome|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 5:181236897-181248096
Previous symbols: [ "GNB2L1" ]
Links
Phenotypes
GenCC
Source:
- Tourette syndrome (Limited), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RACK1 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 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 1 |
Variants in RACK1
This is a list of pathogenic ClinVar variants found in the RACK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-181241646-G-A | Benign (Dec 31, 2019) | |||
| 5-181242275-C-T | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RACK1 | protein_coding | protein_coding | ENST00000512805 | 8 | 11188 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00164 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.58 | 49 | 186 | 0.263 | 0.00000988 | 2064 |
| Missense in Polyphen | 12 | 76.944 | 0.15596 | 883 | ||
| Synonymous | -0.0138 | 72 | 71.9 | 1.00 | 0.00000377 | 639 |
| Loss of Function | 4.01 | 0 | 18.7 | 0.00 | 9.56e-7 | 182 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Scaffolding protein involved in the recruitment, assembly and/or regulation of a variety of signaling molecules. Interacts with a wide variety of proteins and plays a role in many cellular processes. Component of the 40S ribosomal subunit involved in translational repression (PubMed:23636399). Involved in the initiation of the ribosome quality control (RQC), a pathway that takes place when a ribosome has stalled during translation, by promoting ubiquitination of a subset of 40S ribosomal subunits (PubMed:28132843). Binds to and stabilizes activated protein kinase C (PKC), increasing PKC-mediated phosphorylation. May recruit activated PKC to the ribosome, leading to phosphorylation of EIF6. Inhibits the activity of SRC kinases including SRC, LCK and YES1. Inhibits cell growth by prolonging the G0/G1 phase of the cell cycle. Enhances phosphorylation of BMAL1 by PRKCA and inhibits transcriptional activity of the BMAL1-CLOCK heterodimer. Facilitates ligand-independent nuclear translocation of AR following PKC activation, represses AR transactivation activity and is required for phosphorylation of AR by SRC. Modulates IGF1R- dependent integrin signaling and promotes cell spreading and contact with the extracellular matrix. Involved in PKC-dependent translocation of ADAM12 to the cell membrane. Promotes the ubiquitination and proteasome-mediated degradation of proteins such as CLEC1B and HIF1A. Required for VANGL2 membrane localization, inhibits Wnt signaling, and regulates cellular polarization and oriented cell division during gastrulation. Required for PTK2/FAK1 phosphorylation and dephosphorylation. Regulates internalization of the muscarinic receptor CHRM2. Promotes apoptosis by increasing oligomerization of BAX and disrupting the interaction of BAX with the anti-apoptotic factor BCL2L. Inhibits TRPM6 channel activity. Regulates cell surface expression of some GPCRs such as TBXA2R. Plays a role in regulation of FLT1-mediated cell migration. Involved in the transport of ABCB4 from the Golgi to the apical bile canalicular membrane (PubMed:19674157). Promotes migration of breast carcinoma cells by binding to and activating RHOA (PubMed:20499158). {ECO:0000269|PubMed:11884618, ECO:0000269|PubMed:12589061, ECO:0000269|PubMed:12958311, ECO:0000269|PubMed:17108144, ECO:0000269|PubMed:17244529, ECO:0000269|PubMed:17956333, ECO:0000269|PubMed:18088317, ECO:0000269|PubMed:18258429, ECO:0000269|PubMed:18621736, ECO:0000269|PubMed:19423701, ECO:0000269|PubMed:19674157, ECO:0000269|PubMed:19785988, ECO:0000269|PubMed:20499158, ECO:0000269|PubMed:20541605, ECO:0000269|PubMed:20573744, ECO:0000269|PubMed:20976005, ECO:0000269|PubMed:21212275, ECO:0000269|PubMed:21347310, ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:28132843, ECO:0000269|PubMed:9584165}.; FUNCTION: (Microbial infection) Enhances phosphorylation of HIV-1 Nef by PKCs. {ECO:0000269|PubMed:11312657}.; FUNCTION: (Microbial infection) Contributes to the cap-independent internal ribosome entry site (IRES)-mediated translation by some RNA viruses. {ECO:0000269|PubMed:25416947}.;
- Pathway
- Measles - Homo sapiens (human);IGF-Ncore;JAK-STAT-Ncore;Androgen receptor signaling pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;VEGFA-VEGFR2 Signaling Pathway;Interferon type I signaling pathways;Signal Transduction;p73 transcription factor network;Hypoxic and oxygen homeostasis regulation of HIF-1-alpha;AndrogenReceptor;TNFR1-induced NFkappaB signaling pathway;TNFR1-mediated ceramide production;TNF signaling;CXCR4-mediated signaling events;Death Receptor Signalling;Regulation of TNFR1 signaling;IL3;IL5;TNFalpha;TNF receptor signaling pathway ;Validated transcriptional targets of deltaNp63 isoforms;IGF1 pathway;Regulation of Androgen receptor activity;Syndecan-2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.151
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Rack1
- Phenotype
- limbs/digits/tail phenotype; embryo phenotype; pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- rack1
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;cell cycle;gastrulation;negative regulation of gene expression;regulation of tumor necrosis factor-mediated signaling pathway;viral process;protein ubiquitination;negative regulation of translation;negative regulation of Wnt signaling pathway;negative regulation of cell growth;positive regulation of cell migration;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of protein homooligomerization;regulation of protein localization;negative regulation of peptidyl-serine phosphorylation;positive regulation of Golgi to plasma membrane protein transport;positive regulation of apoptotic process;pigmentation;positive regulation of GTPase activity;rhythmic process;negative regulation of phagocytosis;regulation of cell division;positive regulation of cyclic-nucleotide phosphodiesterase activity;regulation of cell cycle;negative regulation of protein kinase B signaling;positive regulation of mitochondrial depolarization;negative regulation of protein tyrosine kinase activity;cellular response to glucose stimulus;cellular response to growth factor stimulus;rescue of stalled ribosome;negative regulation of endoplasmic reticulum unfolded protein response;negative regulation of hydrogen peroxide-induced neuron death;regulation of establishment of cell polarity;positive regulation of ceramide biosynthetic process;positive regulation of gastrulation;positive regulation of intrinsic apoptotic signaling pathway
- Cellular component
- phagocytic cup;nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;small ribosomal subunit;cytosolic small ribosomal subunit;dendrite;midbody;neuronal cell body;perikaryon;perinuclear region of cytoplasm;extracellular exosome;IRE1-RACK1-PP2A complex
- Molecular function
- RNA binding;protein kinase C binding;signaling receptor binding;protein binding;ion channel inhibitor activity;cysteine-type endopeptidase activator activity involved in apoptotic process;enzyme binding;protein phosphatase binding;protein tyrosine kinase inhibitor activity;cyclin binding;receptor tyrosine kinase binding;protein-containing complex scaffold activity;signaling adaptor activity;SH2 domain binding;protein homodimerization activity;ribosome binding;cadherin binding