RACK1

gene
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Also known as Gnb2-rs1H12.3

Summary

RACK1 (receptor for activated C kinase 1, HGNC:4399) is a protein-coding gene on chromosome 5q35.3, encoding Small ribosomal subunit protein RACK1 (P63244). Scaffolding protein involved in the recruitment, assembly and/or regulation of a variety of signaling molecules. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

Enables several functions, including cyclin binding activity; enzyme binding activity; and protein domain specific binding activity. Involved in several processes, including regulation of macromolecule metabolic process; regulation of signal transduction; and regulation of vesicle-mediated transport. Located in several cellular components, including midbody; perinuclear region of cytoplasm; and phagocytic cup. Part of IRE1-RACK1-PP2A complex.

Source: NCBI Gene 10399 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Limited, GenCC) — +1 more curated relationship
  • Clinical variants (ClinVar): 32 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_006098

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4399
Approved symbolRACK1
Namereceptor for activated C kinase 1
Location5q35.3
Locus typegene with protein product
StatusApproved
AliasesGnb2-rs1, H12.3
Ensembl geneENSG00000204628
Ensembl biotypeprotein_coding
OMIM176981
Entrez10399

Gene structure

Transcript identifiers

Ensembl transcripts: 49 — 32 protein_coding, 9 retained_intron, 5 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000376817, ENST00000502548, ENST00000502844, ENST00000502890, ENST00000502905, ENST00000503081, ENST00000503170, ENST00000503494, ENST00000504128, ENST00000504325, ENST00000504726, ENST00000505461, ENST00000506312, ENST00000507000, ENST00000507261, ENST00000507273, ENST00000507756, ENST00000508044, ENST00000508682, ENST00000508963, ENST00000509148, ENST00000509535, ENST00000510199, ENST00000511473, ENST00000511566, ENST00000511900, ENST00000512805, ENST00000512968, ENST00000513027, ENST00000513060, ENST00000514183, ENST00000514318, ENST00000514455, ENST00000515417, ENST00000626067, ENST00000889840, ENST00000889841, ENST00000923653, ENST00000923654, ENST00000923655, ENST00000923656, ENST00000923657, ENST00000923658, ENST00000923659, ENST00000923660, ENST00000923661, ENST00000923662, ENST00000923663, ENST00000923664

RefSeq mRNA: 1 — MANE Select: NM_006098 NM_006098

CCDS: CCDS34324

Canonical transcript exons

ENST00000512805 — 8 exons

ExonStartEnd
ENSE00001471776181243692181243906
ENSE00003459155181242174181242345
ENSE00003501952181239487181239582
ENSE00003542884181238099181238239
ENSE00003618867181237609181237719
ENSE00003646461181241492181241639
ENSE00003687752181239067181239177
ENSE00003894121181236897181237042

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 99.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2141.1977 / max 10164.8994, expressed in 1828 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter IDTPM avgSamples expressed
653732089.95301828
6537218.20001743
653605.90401510
653634.62941590
653643.85941484
653693.63781362
653672.80221233
653581.7477969
653681.59631031
653611.5087888

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
pericardiumUBERON:000240799.99gold quality
superior surface of tongueUBERON:000737199.99gold quality
endometrium epitheliumUBERON:000481199.98gold quality
body of tongueUBERON:001187699.98gold quality
pharyngeal mucosaUBERON:000035599.97gold quality
nippleUBERON:000203099.97gold quality
tracheaUBERON:000312699.97gold quality
vena cavaUBERON:000408799.97gold quality
saphenous veinUBERON:000731899.97gold quality
tongueUBERON:000172399.96gold quality
thymusUBERON:000237099.95gold quality
cerebellar vermisUBERON:000472099.95gold quality
lower lobe of lungUBERON:000894999.95gold quality
mammary ductUBERON:000176599.94gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099199.93gold quality
cardia of stomachUBERON:000116299.93gold quality
pylorusUBERON:000116699.93gold quality
caput epididymisUBERON:000435899.92gold quality
corpus epididymisUBERON:000435999.92gold quality
urethraUBERON:000005799.91gold quality
penisUBERON:000098999.91gold quality
trigeminal ganglionUBERON:000167599.91gold quality
cartilage tissueUBERON:000241899.88gold quality
renal medullaUBERON:000036299.86gold quality
ponsUBERON:000098899.86gold quality
embryoUBERON:000092299.85gold quality
mammalian vulvaUBERON:000099799.85gold quality
synovial jointUBERON:000221799.85gold quality
mucosa of sigmoid colonUBERON:000499399.85gold quality
paraflocculusUBERON:000535199.85gold quality

Single-cell (SCXA)

Detected in 27 experiment(s), a significant marker in 14.

ExperimentMarker?Max mean expression
E-MTAB-6308yes4409.42
E-MTAB-9221yes2882.97
E-HCAD-9yes2457.17
E-CURD-122yes88.76
E-CURD-46yes66.64
E-CURD-88yes57.24
E-HCAD-11yes49.48
E-MTAB-6678yes35.09
E-MTAB-9067yes32.95
E-HCAD-13yes27.81
E-CURD-112yes22.10
E-MTAB-10042yes16.35
E-MTAB-9543yes15.17
E-MTAB-9801yes6.47
E-MTAB-11121no4434.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR, FOXO1, REL, TP53

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • Aberrant expression of signaling-related proteins 14-3-3 gamma and RACK1 in fetal Down syndrome brain (trisomy 21).(RACK1 or PROTEIN KINASE C RECEPTOR) (PMID:11824616)
  • RACK1, an insulin-like growth factor I (IGF-I) receptor-interacting protein, modulates IGF-I-dependent integrin signaling and promotes cell spreading and contact with extracellular matrix (PMID:11884618)
  • The anchoring protein RACK1 links protein kinase Cepsilon to integrin beta chains. (PMID:11934885)
  • Protein kinase C epsilon-dependent regulation of cystic fibrosis transmembrane regulator involves binding to a receptor for activated C kinase (RACK1) and RACK1 binding to Na+/H+ exchange regulatory factor. (PMID:11956211)
  • RACK1 is an insulin-like growth factor 1 (IGF-1) receptor-interacting protein that can regulate IGF-1-mediated Akt activation and protection from cell death. (PMID:11964397)
  • As an interaction partner of factor associated with neutral sphingomyelinase (N-SMase) activation, RACK1 modulates activation of N-SMase by TNF. (PMID:12391233)
  • RACK-1 serves as a scaffold protein for a multiprotein complex that includes the IFN-alpha receptor 2/beta-chain of the receptor, STAT1, Janus kinase 1, and tyrosine kinase 2. (PMID:12960323)
  • eIF6 release regulates ribosome subunit joining and RACK1 provides a physical and functional link between PKC signalling and ribosome activation (PMID:14654845)
  • associate Ki-1/57 with the RACK1/PKC pathway and may be important for the regulation of its cellular functions (PMID:14699138)
  • RACK1 regulates specific functions of Gbetagamma (PMID:14963031)
  • propose a previously unrecognized function of plectin as cytoskeletal regulator of PKC signaling (dislocation of PKCdelta and elevated enzymatic activity), and possibly other signaling events, through sequestration of the scaffolding protein RACK1 (PMID:14966116)
  • interacts with the terminal region of the dopamine transporter (PMID:15202772)
  • RACK-I anchors activated PKC-beta on the melanosome membrane, allowing PKC-beta to phosphorylate tyrosinase (PMID:15252133)
  • RACK1 regulates G1/S progression by suppressing Src kinase activity (PMID:15254245)
  • RACK1 physically associated with the p63alpha C-terminal domain through its WD40 domain. However, stratifin binds with phosphorylated DeltaNp63alpha in response to cisplatin. (PMID:15467455)
  • The relevant consequence of RACK-1-reduced expression was the observation that release of tumor necrosis factor alpha following lipopolysaccharide challenge and mitogen-induced lymphocye proliferation. (PMID:15548575)
  • RACK1 is a structural component of the ribosomal small subunit (40S). (PMID:15577927)
  • RACK1 has a scaffolding function and regulates adhesion and insulin-like growth factor I signals that are necessary to regulate Akt activity and to promote turnover of focal adhesions and cell migration (PMID:15611085)
  • RACK1, the receptor for activated C kinase 1, serves as an adaptor for PKC-mediated JNK activation. (PMID:16061178)
  • RACK1 mRNA has a 5’ terminal oligopyrimidine sequence and that its translation is dependent on the availability of serum and amino acids in exactly the same way as any other vertebrate ribosomal protein mRNA. (PMID:16212959)
  • RACK1 mediates recruitment of STAT3 to IR and IGF-1R specifically for activation, suggesting a general paradigm for the need of an adaptor in mediating activation of STATs by receptor protein tyrosine kinases. (PMID:16382134)
  • RACK1 and beta-arrestin compete to sequester distinct ‘pools’ of PDE4D5. (PMID:16689683)
  • The dysregulation of cytokine production observed in Alzheimer’s disease patients may partially be explained by a significant reduction in the expression of RACK-1 (PMID:16702786)
  • RACK1 enhances IGF-I-mediated cell migration through its ability to exclusively associate with either beta1 integrin or PP2A in a complex at the IGF-IR. (PMID:16705158)
  • These results together suggested that RACK1 might act as a novel signal molecule to mediate or regulate the functions of PER1 through protein interaction. (PMID:16757810)
  • These results suggest that RACK1 modulates transcription of alpha2(I) collagen by TGF-beta1 through interference with Smad3 binding to the gene promoter. (PMID:16849317)
  • RACK1 activates NHE5 both by integrin-dependent and independent pathways, which may coordinate cellular ion homeostasis during cell-matrix adhesion. (PMID:16920332)
  • molecular complex most likely to obstruct RACK1 for functional attachment at syndecan-2, as revealed in cells transfected with oncogenic ras (PMID:16997272)
  • RACK1 regulates mitotic exit by suppressing Src-mediated Sam68 phosphorylation and maintaining the cyclin-dependent kinase (CDK) 1-cyclin B complex in an active state. (PMID:17072338)
  • RACK1 binds to the BK(Ca) channel and it may form part of a BK(Ca)-channel regulatory complex in vascular smooth muscle. (PMID:17166942)
  • Dpl interacts with RACK1 by means of its structured globular carboxyl-terminal region (PMID:17201176)
  • RACK1 amd Rac2 are components of complexes involved in NK cell homotypic adhesion. (PMID:17269730)
  • Review discusses how RACK1 promotes the ubiquitination and degradation of HIF-1 alpha through competition with HSP90 and recruitment of the elongin-C/B ubiquitin ligase complex. (PMID:17361105)
  • Model a RACK1 proteome consisting of PKCepsilon-RACK1-NHERF1-NHERF1-tubulin with a role in stable expression of CFTR in the apical plasma membrane of epithelial cells. (PMID:17409124)
  • primary pulmonary arterial smooth muscle cells demonstrated colocalization of BMPRII and RACK1 in vivo (PMID:17515463)
  • These findings support a novel role for RACK1 as a key regulator of cell migration and adhesion dynamics through the regulation of Src activity, and the modulation of paxillin phosphorylation at early adhesions. (PMID:17574549)
  • direct interaction between RACK1 and PER1 (PMID:17718421)
  • SSAT1, which shares 46% amino acid identity with SSAT2, also binds to HIF-1alpha and promotes its ubiquitination/degradation. However, in contrast to SSAT2, SSAT1 acts by stabilizing the interaction of HIF-1alpha with RACK1 (PMID:17875644)
  • These results suggest that PKCepsilon signaling in the basal airway cell may involve RACK1; however, PKCepsilon regulation in ciliated cells uses RACK1-independent pathways. (PMID:17875659)
  • Examine interactions between phosphodiesterase 4D5 (PDE4D5) and beta-arrestin and RACK1. (PMID:17900862)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorack1ENSDARG00000041619
mus_musculusRack1ENSMUSG00000020372
rattus_norvegicusRack1ENSRNOG00000052620
drosophila_melanogasterRack1FBGN0020618
caenorhabditis_elegansWBGENE00010556

Protein

Protein identifiers

Small ribosomal subunit protein RACK1P63244 (reviewed: P63244)

Alternative names: Cell proliferation-inducing gene 21 protein, Guanine nucleotide-binding protein subunit beta-2-like 1, Guanine nucleotide-binding protein subunit beta-like protein 12.3, Human lung cancer oncogene 7 protein, Receptor for activated C kinase, Receptor for activated C kinase 1, Receptor of activated protein C kinase 1

All UniProt accessions (23): D6R909, D6R9L0, D6R9Z1, D6RAC2, D6RAU2, D6RBD0, D6RDI0, D6REE5, D6RF23, D6RFX4, D6RFZ9, D6RGK8, D6RHH4, D6RHJ5, E9KL35, E9PD14, P63244, H0Y8R5, H0Y8W2, H0Y9P0, H0YAF8, H0YAM7, J3KPE3

UniProt curated annotations — full annotation on UniProt →

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. 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. 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. Promotes migration of breast carcinoma cells by binding to and activating RHOA. Acts as an adapter for the dephosphorylation and inactivation of AKT1 by promoting recruitment of PP2A phosphatase to AKT1. (Microbial infection) Binds to Y.pseudotuberculosis yopK which leads to inhibition of phagocytosis and survival of bacteria following infection of host cells. (Microbial infection) Enhances phosphorylation of HIV-1 Nef by PKCs. (Microbial infection) In case of poxvirus infection, remodels the ribosomes so that they become optimal for the viral mRNAs (containing poly-A leaders) translation but not for host mRNAs. (Microbial infection) Contributes to the cap-independent internal ribosome entry site (IRES)-mediated translation by some RNA viruses.

Subunit / interactions. Monomer; also forms homodimers and homooligomers. Interacts with CPNE3. May interact with ABCB4. Component of the small (40S) ribosomal subunit. Interacts with the 80S ribosome. Binds NHERF1. Forms a ternary complex with TRIM63 and PRKCE. Interacts with HABP4, KRT1 and OTUB1. Interacts with SRC (via SH2 domain); the interaction is enhanced by tyrosine phosphorylation of RACK1. Recruited in a circadian manner into a nuclear complex which also includes BMAL1 and PRKCA. Interacts with AR. Interacts with IGF1R but not with INSR. Interacts with ADAM12. Interacts with CLEC1B (via N-terminal region) and with HIF1A; the interaction promotes their degradation. Interacts with RHOA; this enhances RHOA activation and promotes cell migration. Interacts with CHRM2; the interaction regulates CHRM2 internalization. Interacts with TRPM6 (via kinase domain). Interacts with PTK2/FAK1; required for PTK2/FAK1 phosphorylation and dephosphorylation. Interacts with FLT1. Interacts with TBXA2R isoform 2. Interacts with HRAS. Interacts with LARP4B. Interacts with LARP4. Interacts with PKD2L1. Interacts with isoform 2 of SLC4A7. Interacts with SLC9A5; this interaction regulates SLC9A5 cell-surface targeting and SLC9A5 activity. Interacts with SLC9A6; this interaction regulates the distribution of SLC9A6 between endosomes and the plasma membrane. Interacts with LACC1; this interaction may regulate macrophage autophagic flux. (Microbial infection) Interacts with Y.pseudotuberculosis yopK. (Microbial infection) Interacts with Y.pseudotuberculosis yopK. Interacts with a number of viral proteins including Epstein-Barr virus BZLF1 and HIV-1 Nef; interaction with Nef increases Nef phosphorylation by PKC. (Microbial infection) Interacts with human respiratory syncytial virus matrix protein M; this interaction suppresses interferon signaling. (Microbial infection) Interacts with Influenza protein PA-X. (Microbial infection) Interacts with Toxoplasma gondii SAG1; the interaction promotes viability of host cells.

Subcellular location. Cell membrane. Cytoplasm. Perinuclear region. Nucleus. Perikaryon. Cell projection. Dendrite. Phagocytic cup.

Tissue specificity. In the liver, expressed at higher levels in activated hepatic stellate cells than in hepatocytes or Kupffer cells. Up-regulated in hepatocellular carcinomas and in the adjacent non-tumor liver tissue.

Post-translational modifications. Phosphorylated on Tyr-228 and/or Tyr-246 by SRC. This is required for binding to SRC. (Microbial infection) Phosphorylated by vaccinia virus B1 kinase on serine and threonine residues; this phosphorylation remodels the ribosome properties, favoring the viral mRNA translation.

Domain organisation. The 7 WD repeats mediate protein-protein interactions with binding partners.

Similarity. Belongs to the WD repeat G protein beta family. Ribosomal protein RACK1 subfamily.

RefSeq proteins (1): NP_006089* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR020472WD40_PAC1Repeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR045223RACK1-likeFamily

Pfam: PF00400

UniProt features (83 total): strand 39, modified residue 14, mutagenesis site 13, repeat 7, turn 4, sequence conflict 3, chain 2, initiator methionine 1

Structure

Experimental structures (PDB)

204 structures, top 30 by resolution.

PDBMethodResolution (Å)
8GLPELECTRON MICROSCOPY1.67
8QOIELECTRON MICROSCOPY1.9
9O3WELECTRON MICROSCOPY1.9
8YOOELECTRON MICROSCOPY2
9C3HELECTRON MICROSCOPY2
7R4XELECTRON MICROSCOPY2.15
9I2DELECTRON MICROSCOPY2.19
9PBEELECTRON MICROSCOPY2.19
8YOPELECTRON MICROSCOPY2.2
9O3VELECTRON MICROSCOPY2.2
9O3YELECTRON MICROSCOPY2.2
8JDKELECTRON MICROSCOPY2.26
8G5YELECTRON MICROSCOPY2.29
9S3DELECTRON MICROSCOPY2.32
9RPVELECTRON MICROSCOPY2.35
9S3BELECTRON MICROSCOPY2.38
8K2CELECTRON MICROSCOPY2.4
8XSXELECTRON MICROSCOPY2.4
9SPFELECTRON MICROSCOPY2.4
9SPIELECTRON MICROSCOPY2.4
8JDLELECTRON MICROSCOPY2.42
9S3CELECTRON MICROSCOPY2.42
4AOWX-RAY DIFFRACTION2.45
9QLOELECTRON MICROSCOPY2.47
9P8BELECTRON MICROSCOPY2.48
7XNYELECTRON MICROSCOPY2.5
8JDJELECTRON MICROSCOPY2.5
9RUCELECTRON MICROSCOPY2.5
8G60ELECTRON MICROSCOPY2.54
8IFEELECTRON MICROSCOPY2.57

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P63244-F192.540.82

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (14): 1, 2, 6, 10, 52, 96, 130, 183, 228, 276, 277, 278, 279, 316

Mutagenesis-validated functional residues (13):

PositionPhenotype
36–38in demut; abolishes association with the ribosome and ability to initiate the ribosome quality control (rqc).
52no effect on binding to src. abolishes binding to ptk2/fak1 and reduces cell adhesion and foci formation.
57decreased binding to ptk2/fak1; when associated with a-60.
60decreased binding to ptk2/fak1; when associated with a-57.
127decreased binding to ptk2/fak1; when associated with a-130.
130decreased binding to ptk2/fak1; when associated with a-127.
140no effect on binding to src.
194no effect on binding to src.
228no effect on binding to src. does not abolish phosphorylation by src. abolishes phosphorylation by src; when associated
246abolishes binding to src. does not abolish phosphorylation by src. abolishes phosphorylation by src; when associated wit
276–279enhanced translation of mrnas containing poly-a leaders.
278enhanced translation of mrnas containing poly-a leaders.
302no effect on binding to src. abolishes phosphorylation by src; when associated with f-228 and f-246.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-5357905Regulation of TNFR1 signaling
R-HSA-5357956TNFR1-induced NF-kappa-B signaling pathway
R-HSA-5626978TNFR1-mediated ceramide production
R-HSA-9766229Degradation of CDH1

MSigDB gene sets: 533 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_CYTOPLASMIC_TRANSLATION, GOBP_MEMBRANE_DEPOLARIZATION, HONMA_DOCETAXEL_RESISTANCE, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, GOBP_REGULATION_OF_PROTEIN_BINDING, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_REGULATION_OF_PHOSPHORYLATION, SWEET_KRAS_ONCOGENIC_SIGNATURE, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GCM_NPM1, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH

GO Biological Process (38): positive regulation of protein phosphorylation (GO:0001934), cytoplasmic translation (GO:0002181), gastrulation (GO:0007369), negative regulation of gene expression (GO:0010629), protein ubiquitination (GO:0016567), negative regulation of translation (GO:0017148), negative regulation of Wnt signaling pathway (GO:0030178), negative regulation of cell growth (GO:0030308), positive regulation of cell migration (GO:0030335), positive regulation of protein-containing complex assembly (GO:0031334), negative regulation of protein binding (GO:0032091), positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436), regulation of protein localization (GO:0032880), positive regulation of Golgi to plasma membrane protein transport (GO:0042998), positive regulation of apoptotic process (GO:0043065), pigmentation (GO:0043473), positive regulation of GTPase activity (GO:0043547), negative regulation of smoothened signaling pathway (GO:0045879), rhythmic process (GO:0048511), negative regulation of phagocytosis (GO:0050765), regulation of cell division (GO:0051302), regulation of cell cycle (GO:0051726), negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051898), positive regulation of mitochondrial depolarization (GO:0051901), cellular response to glucose stimulus (GO:0071333), cellular response to growth factor stimulus (GO:0071363), rescue of stalled cytosolic ribosome (GO:0072344), regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway (GO:0106070), negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102), negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide (GO:1903751), regulation of establishment of cell polarity (GO:2000114), positive regulation of gastrulation (GO:2000543), negative regulation of translational frameshifting (GO:2001125), positive regulation of intrinsic apoptotic signaling pathway (GO:2001244), RNA processing (GO:0006396), translation (GO:0006412), regulation of translation (GO:0006417), apoptotic process (GO:0006915)

GO Molecular Function (22): RNA binding (GO:0003723), protein kinase C binding (GO:0005080), signaling receptor binding (GO:0005102), enzyme activator activity (GO:0008047), ion channel inhibitor activity (GO:0008200), cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656), enzyme binding (GO:0019899), protein phosphatase binding (GO:0019903), protein serine/threonine kinase inhibitor activity (GO:0030291), protein tyrosine kinase inhibitor activity (GO:0030292), cyclin binding (GO:0030332), receptor tyrosine kinase binding (GO:0030971), signaling adaptor activity (GO:0035591), SH2 domain binding (GO:0042169), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), ribosome binding (GO:0043022), translation regulator activity (GO:0045182), cadherin binding (GO:0045296), BH3 domain binding (GO:0051434), molecular adaptor activity (GO:0060090), protein binding (GO:0005515)

GO Cellular Component (23): phagocytic cup (GO:0001891), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), small ribosomal subunit (GO:0015935), cytosolic small ribosomal subunit (GO:0022627), dendrite (GO:0030425), midbody (GO:0030496), neuronal cell body (GO:0043025), perikaryon (GO:0043204), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), IRE1-RACK1-PP2A complex (GO:1990630), nucleolus (GO:0005730), ribosome (GO:0005840), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995), neuron projection (GO:0043005), cell body (GO:0044297), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
TNF signaling3
Regulation of CDH1 Function1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure9
protein binding5
cytoplasm3
translation2
regulation of translation2
negative regulation of signal transduction2
biological_process2
protein kinase inhibitor activity2
intracellular membrane-bounded organelle2
nuclear lumen2
intracellular membraneless organelle2
regulation of protein phosphorylation1
protein phosphorylation1
positive regulation of protein modification process1
positive regulation of phosphorylation1
ectoderm formation1
endoderm formation1
mesoderm formation1
embryonic morphogenesis1
gene expression1
regulation of gene expression1
negative regulation of macromolecule biosynthetic process1
protein modification by small protein conjugation1
negative regulation of gene expression1
negative regulation of protein metabolic process1
Wnt signaling pathway1
regulation of Wnt signaling pathway1
regulation of cell growth1
cell growth1
negative regulation of growth1
negative regulation of cellular process1
cell migration1
regulation of cell migration1
positive regulation of cell motility1
regulation of protein-containing complex assembly1
positive regulation of cellular component biogenesis1
positive regulation of cellular component organization1
protein-containing complex assembly1
regulation of protein binding1
negative regulation of binding1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

403 interactions, top by confidence:

ABTypeScore
RACK1LARP4Bpsi-mi:“MI:0915”(physical association)0.880
MAPK14OBSL1psi-mi:“MI:0914”(association)0.790
RACK1HELZpsi-mi:“MI:0914”(association)0.770
CFTRESYT2psi-mi:“MI:0914”(association)0.710
FBXW2RACK1psi-mi:“MI:0915”(physical association)0.680
FBXW2RACK1psi-mi:“MI:0403”(colocalization)0.680
FBXW2RACK1psi-mi:“MI:0914”(association)0.680
RACK1USP10psi-mi:“MI:0915”(physical association)0.670
RACK1BYSLpsi-mi:“MI:0915”(physical association)0.670
NCBP1KPNA3psi-mi:“MI:0914”(association)0.640
NCBP2KPNA3psi-mi:“MI:0914”(association)0.640
RACK1DYNLL1psi-mi:“MI:0915”(physical association)0.630
RACK1DYNLL1psi-mi:“MI:0407”(direct interaction)0.630
DYNLL1RACK1psi-mi:“MI:0915”(physical association)0.630
RACK1RPS17psi-mi:“MI:0915”(physical association)0.610
ACTN2RACK1psi-mi:“MI:0915”(physical association)0.560
RACK1USP54psi-mi:“MI:0915”(physical association)0.560

BioGRID (1074): GNB2L1 (Affinity Capture-MS), LARP4B (Two-hybrid), MKRN2 (Two-hybrid), GNB2L1 (Affinity Capture-MS), SYN2 (Affinity Capture-Western), JAK1 (Affinity Capture-Western), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Affinity Capture-MS), GNB2L1 (Reconstituted Complex), LARP4 (Affinity Capture-MS)

ESM2 similar proteins: A0A223GEB2, G1SJB4, G4MQX3, O18640, O24076, O24456, O35353, O42248, O42249, P16520, P17343, P23232, P25387, P26308, P29387, P38011, P46800, P49026, P49027, P52287, P54311, P62871, P63243, P63244, P63245, P63246, P63247, P68040, P69103, P69104, P79147, P83774, P93340, Q01369, Q08706, Q10281, Q20636, Q21215, Q25189, Q39336

Diamond homologs: A0A223GEB2, A1L271, A2QPZ4, A4R3M4, A6H603, A6RRD4, B2VWG7, B3MHX6, B3MJV8, B4GT01, B4JPT9, B5DG67, B8N9H4, C0S902, C1GB49, C4R6H3, C4YPI7, C5GVJ9, C5JD40, E3LB80, G0S8H7, G1SJB4, G4MQX3, O14775, O18640, O24076, O24456, O42248, O42249, O94527, P0CS34, P0CS35, P25382, P25387, P38011, P40968, P46800, P49026, P49027, P52287

SIGNOR signaling

12 interactions.

AEffectBMechanism
RACK1up-regulatesPTK7binding
ABL1up-regulatesRACK1phosphorylation
RACK1“down-regulates activity”TRPM6binding
RACK1“up-regulates activity”LARP4Bbinding
RACK1“up-regulates activity”PPP2CAbinding
RACK1“down-regulates quantity by destabilization”CLEC1Bbinding
RACK1“up-regulates activity”“Elongin E3-Cul-5”binding
GNAS“down-regulates activity”RACK1binding
JUN“up-regulates quantity by expression”RACK1
SRCup-regulatesRACK1phosphorylation
RACK1“up-regulates activity”PKCbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 164 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Nonsense-Mediated Decay (NMD)512.4×6e-03
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)78.8×3e-03
Signaling by ROBO receptors67.9×7e-03
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)77.3×6e-03
Regulation of expression of SLITs and ROBOs96.6×2e-03
Infectious disease174.5×1e-04
Metabolism of RNA104.4×6e-03

GO biological processes:

GO termPartnersFoldFDR
mRNA stabilization514.4×9e-03
translation97.3×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

32 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1187 predictions. Top by Δscore:

VariantEffectΔscore
5:181237604:CTTA:Cdonor_loss1.0000
5:181237605:TTA:Tdonor_loss1.0000
5:181237606:TACCT:Tdonor_loss1.0000
5:181237607:ACC:Adonor_loss1.0000
5:181237608:CCTGG:Cdonor_gain1.0000
5:181238093:ACTC:Adonor_loss1.0000
5:181238094:CTCA:Cdonor_loss1.0000
5:181238095:T:TAdonor_loss1.0000
5:181238096:CACC:Cdonor_loss1.0000
5:181238097:A:ACdonor_gain1.0000
5:181238097:A:Tdonor_loss1.0000
5:181238097:AC:Adonor_gain1.0000
5:181238098:C:Adonor_loss1.0000
5:181238098:C:CCdonor_gain1.0000
5:181238098:CC:Cdonor_gain1.0000
5:181238235:CCATC:Cacceptor_gain1.0000
5:181238236:CATCC:Cacceptor_gain1.0000
5:181239481:GCTCA:Gdonor_loss1.0000
5:181239482:CTCA:Cdonor_loss1.0000
5:181239483:TCA:Tdonor_loss1.0000
5:181239484:CACC:Cdonor_loss1.0000
5:181239485:A:Cdonor_loss1.0000
5:181239486:C:Tdonor_loss1.0000
5:181239578:TCATC:Tacceptor_gain1.0000
5:181239579:CATC:Cacceptor_gain1.0000
5:181239579:CATCC:Cacceptor_gain1.0000
5:181239580:ATC:Aacceptor_gain1.0000
5:181239581:TC:Tacceptor_gain1.0000
5:181239582:CC:Cacceptor_gain1.0000
5:181239582:CCTAC:Cacceptor_loss1.0000

AlphaMissense

2068 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:181237003:A:GW310R1.000
5:181237003:A:TW310R1.000
5:181237008:C:GR308P1.000
5:181237029:C:TG301D1.000
5:181237030:C:GG301R1.000
5:181237032:G:TA300D1.000
5:181237035:A:GF299S1.000
5:181237038:A:GL298P1.000
5:181237038:A:TL298Q1.000
5:181237613:C:AG295V1.000
5:181237613:C:TG295D1.000
5:181237614:C:AG295C1.000
5:181237614:C:GG295R1.000
5:181237623:A:GS292P1.000
5:181237624:C:AW291C1.000
5:181237624:C:GW291C1.000
5:181237625:C:GW291S1.000
5:181237626:A:GW291R1.000
5:181237626:A:TW291R1.000
5:181237629:C:GA290P1.000
5:181237631:A:GL289P1.000
5:181237639:G:CC286W1.000
5:181237640:C:TC286Y1.000
5:181237641:A:GC286R1.000
5:181237712:T:AE262V1.000
5:181237714:T:AL261F1.000
5:181237714:T:GL261F1.000
5:181237715:A:GL261S1.000
5:181237718:T:AD260V1.000
5:181237718:T:CD260G1.000

dbSNP variants (sampled 300 via entrez): RS1000466305 (5:181236534 T>C), RS1000509016 (5:181245802 G>A), RS1000515879 (5:181245022 C>A), RS1000522892 (5:181240033 G>A,C), RS1000755576 (5:181244778 G>A), RS1001023217 (5:181240915 G>A,C), RS1001141054 (5:181236465 A>C), RS1001146823 (5:181244576 C>G), RS1001718850 (5:181241395 A>C), RS1001803648 (5:181243972 T>C), RS1002026664 (5:181237214 G>C,T), RS1002028942 (5:181242282 G>C), RS1002096335 (5:181238537 G>A), RS1002131846 (5:181241728 T>C), RS1002573161 (5:181237993 G>A)

Disease associations

OMIM: gene MIM:176981 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorderLimitedAutosomal dominant
Tourette syndromeLimitedUnknown

Mondo (2): neurodevelopmental disorder (MONDO:0700092), Tourette syndrome (MONDO:0007661)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625
D005879Tourette SyndromeC10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725031 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.54Kd2871nMCHEMBL3752910
5.54ED502871nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 8 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148445: Binding affinity to human GNB2L1 incubated for 45 mins by Kinobead based pull down assaykd2.8712uM

CTD chemical–gene interactions

85 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression3
Flutamideincreases expression, decreases reaction3
Valproic Aciddecreases expression, increases methylation3
bisphenol Fdecreases expression, increases expression, affects cotreatment2
arseniteaffects binding, increases reaction, increases methylation2
sodium arsenitedecreases expression, increases activity2
perfluorooctane sulfonic aciddecreases expression, increases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression2
Dehydroepiandrosteroneaffects reaction, increases expression, decreases reaction2
Leadaffects expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Quercetindecreases expression, increases expression2
Zinc Sulfateaffects expression, decreases expression2
Particulate Matterincreases methylation, decreases expression, increases abundance2
FR900359decreases phosphorylation1
moringinincreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
diethyl phthalatedecreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression1
salinomycindecreases expression1
ferric ammonium citratedecreases reaction, increases expression1
beta-lapachoneincreases expression1
cobaltous chlorideincreases expression1
perfluorooctanoic aciddecreases expression1
estradiol-bovine serum albuminincreases expression1
testosterone-3-carboxymethyloxime-bovine serum albumin conjugateincreases expression1
chloropicrinaffects expression1
U 0126affects expression, affects reaction1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651487BindingBinding affinity to human GNB2L1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

299 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00152750PHASE4UNKNOWNStudy of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824PHASE4TERMINATEDSafety Study of Galantamine in Tic Disorders
NCT00241176PHASE4COMPLETEDOpen Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838PHASE4COMPLETEDComparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056PHASE4COMPLETEDDeveloping New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000PHASE4COMPLETEDGuanfacine in Children With Tic Disorders
NCT03239210PHASE4COMPLETEDEffects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT00004376PHASE3COMPLETEDPhase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323PHASE3COMPLETEDA Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336PHASE3COMPLETEDAn Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842PHASE3COMPLETEDPallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863PHASE3TERMINATEDOpen-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695PHASE3COMPLETEDPhase III Study of 5LGr to Treat Tic Disorder
NCT03087201PHASE3COMPLETEDCANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783PHASE3COMPLETEDAripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291PHASE3TERMINATEDEvaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256PHASE3COMPLETEDA Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00004393PHASE2COMPLETEDPhase II Double Blind Placebo Controlled Trial of Risperidone in Tourette Syndrome
NCT00004652PHASE2COMPLETEDPhase II Pilot Controlled Study of Short Vs Longer Term Pimozide (Orap) Therapy in Tourette Syndrome
NCT00231985PHASE2COMPLETEDEffectiveness of Behavior Therapy and Psychosocial Therapy for the Treatment of Tourette Syndrome and Chronic Tic Disorder
NCT00311909PHASE2COMPLETEDThalamic Deep Brain Stimulation for Tourette Syndrome
NCT00529308PHASE2COMPLETEDTranscranial Magnetic Stimulation (TMS) for Individuals With Tourette’s Syndrome
NCT00558467PHASE2COMPLETEDPramipexole Pilot Phase II Study in Children and Adolescents With Tourette Disorder According to DSM-IV Criteria
NCT01043549PHASE2TERMINATEDRepetitive Transcranial Magnetic Stimulation of the Posterior Parietal Cortex in Patients Suffering From Gilles de la Tourette Syndrome
NCT01133353PHASE2WITHDRAWNA Study of the Effectiveness and Safety of Tetrabenazine MR in Pediatric Subjects With Tourette’s Syndrome
NCT01475383PHASE2WITHDRAWNStudy Evaluating The Safety And Efficacy Of PF-03654746 In Adult Subjects With Tourette’s Syndrome
NCT01647269PHASE2COMPLETEDA Trial of Bilateral Deep Brain Stimulation to the Globus Pallidus Internum in Tourette Syndrome
NCT01904773PHASE2COMPLETEDSafety, Tolerability, Pharmacokinetic, and Efficacy Study of AZD5213 in Adolescents With Tourette’s Disorder
NCT02102698PHASE2COMPLETEDEcopipam Treatment of Tourette’s Syndrome in Subjects 7-17 Years
NCT02217007PHASE2WITHDRAWNA Trial Evaluating the Efficacy, Safety, and Pharmacokinetics of SNC-102 in Subjects With Tourette Syndrome