RIOK2

gene
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Also known as FLJ11159

Summary

RIOK2 (RIO kinase 2, HGNC:18999) is a protein-coding gene on chromosome 5q15, encoding Serine/threonine-protein kinase RIO2 (Q9BVS4). Serine/threonine-protein kinase involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. It is a common-essential gene (DepMap: required in 95.6% of cancer cell lines).

Predicted to enable protein kinase activity. Involved in several processes, including positive regulation of rRNA processing; positive regulation of ribosomal small subunit export from nucleus; and regulation of mitotic metaphase/anaphase transition. Located in cytoplasm. Part of preribosome, small subunit precursor.

Source: NCBI Gene 55781 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 92 total
  • Druggable target: yes — 17 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 95.6% of screened cell lines (common-essential)
  • MANE Select transcript: NM_018343

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18999
Approved symbolRIOK2
NameRIO kinase 2
Location5q15
Locus typegene with protein product
StatusApproved
AliasesFLJ11159
Ensembl geneENSG00000058729
Ensembl biotypeprotein_coding
OMIM617754
Entrez55781

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000283109, ENST00000508447, ENST00000508991, ENST00000510384, ENST00000511012, ENST00000511293, ENST00000511920, ENST00000902084, ENST00000924329, ENST00000924330, ENST00000924331

RefSeq mRNA: 2 — MANE Select: NM_018343 NM_001159749, NM_018343

CCDS: CCDS4089, CCDS54884

Canonical transcript exons

ENST00000283109 — 10 exons

ExonStartEnd
ENSE000009082959717317597173263
ENSE000009082969717120697171397
ENSE000009082979716876097168852
ENSE000009082989716746797167991
ENSE000009082999716505197165147
ENSE000011598399718312697183247
ENSE000011750679717711697177291
ENSE000012291569716086797163225
ENSE000035099299717773297177848
ENSE000036569419717905597179193

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 94.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.9749 / max 598.3145, expressed in 1795 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
6271721.97491795

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002394.87gold quality
secondary oocyteCL:000065594.36gold quality
calcaneal tendonUBERON:000370192.43gold quality
ganglionic eminenceUBERON:000402392.14gold quality
stromal cell of endometriumCL:000225591.19gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.18gold quality
adrenal tissueUBERON:001830390.37gold quality
ventricular zoneUBERON:000305390.04gold quality
hindlimb stylopod muscleUBERON:000425289.53gold quality
cortical plateUBERON:000534389.40gold quality
body of pancreasUBERON:000115088.95gold quality
mucosa of transverse colonUBERON:000499188.27gold quality
islet of LangerhansUBERON:000000687.74gold quality
gastrocnemiusUBERON:000138887.68gold quality
pancreasUBERON:000126487.55gold quality
muscle of legUBERON:000138387.32gold quality
embryoUBERON:000092286.33gold quality
left ovaryUBERON:000211986.24gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.22gold quality
descending thoracic aortaUBERON:000234586.04gold quality
right lobe of liverUBERON:000111485.95gold quality
right ovaryUBERON:000211885.94gold quality
omental fat padUBERON:001041485.92gold quality
right adrenal glandUBERON:000123385.87gold quality
peritoneumUBERON:000235885.86gold quality
adipose tissue of abdominal regionUBERON:000780885.67gold quality
ovaryUBERON:000099285.63gold quality
body of stomachUBERON:000116185.57gold quality
left adrenal glandUBERON:000123485.54gold quality
rectumUBERON:000105285.46gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-124858no637.84
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting RIOK2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4776-3P100.0068.731340
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-450099.9972.722367
HSA-MIR-569699.9872.364487
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-570-3P99.9672.414910
HSA-MIR-144-3P99.9473.982698
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-22-3P99.9368.13917
HSA-MIR-130599.9171.433443
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-182-5P99.8774.032589
HSA-MIR-612499.8769.783551
HSA-MIR-450399.8571.451869
HSA-MIR-202-3P99.8471.411290
HSA-MIR-94499.8270.853042
HSA-MIR-430799.8270.453374
HSA-MIR-4760-5P99.8069.881619

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 11)

  • Results show that the protein kinase human Rio2 (hRio2) is part of a late 40S preribosomal particle in human cells. (PMID:19564402)
  • Plk1-mediated phosphorylation of Rio2 regulates metaphase-anaphase transition during mitotic progression. (PMID:21880710)
  • reduced expression of RIOK1 or RIOK2 disrupted Akt signaling and caused cell cycle exit, apoptosis, and chemosensitivity in glioblastoma cells (PMID:23459592)
  • As RIO2 is involved in the biosynthesis of the ribosome and cell cycle regulation, our selective ligand may be useful for the delineation of the biological role of this kinase. (PMID:25891899)
  • These results suggested that RIOK2 and NOB1 may be potential targets in the treatment of Non-small cell lung cancer (NSCLC), and miR145 may be considered a therapeutic inhibitor of both genes. (PMID:29749434)
  • Results describe three atomic structures of RIO2 kinase showing that it forms homodimer in vitro. Upon self-association, each protomer ATP-binding pocket is partially remodeled. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This data reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. (PMID:31390939)
  • RIOK2 is negatively regulated by miR-4744 and promotes glioma cell migration/invasion through epithelial-mesenchymal transition. (PMID:32125767)
  • BYSL contributes to tumor growth by cooperating with the mTORC2 complex in gliomas. (PMID:33628587)
  • RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit. (PMID:34125833)
  • Identification of RIOK2 as a master regulator of human blood cell development. (PMID:34937919)
  • RIOK2 Contributes to Cell Growth and Protein Synthesis in Human Oral Squamous Cell Carcinoma. (PMID:36661680)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioriok2ENSDARG00000035264
mus_musculusRiok2ENSMUSG00000116564
rattus_norvegicusRiok2ENSRNOG00000012692
drosophila_melanogasterRIOK2FBGN0039306
caenorhabditis_elegansriok-2WBGENE00013688

Paralogs (3): RIOK3 (ENSG00000101782), RIOK1 (ENSG00000124784), ATMIN (ENSG00000166454)

Protein

Protein identifiers

Serine/threonine-protein kinase RIO2Q9BVS4 (reviewed: Q9BVS4)

Alternative names: RIO kinase 2

All UniProt accessions (4): Q9BVS4, D6RB96, H0Y8R4, H0Y919

UniProt curated annotations — full annotation on UniProt →

Function. Serine/threonine-protein kinase involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in export of the 40S pre-ribosome particles (pre-40S) from the nucleus to the cytoplasm. Its kinase activity is required for the release of NOB1, PNO1 and LTV1 from the late pre-40S and the processing of 18S-E pre-rRNA to the mature 18S rRNA. Regulates the timing of the metaphase-anaphase transition during mitotic progression, and its phosphorylation, most likely by PLK1, regulates this function.

Subunit / interactions. Associated with late 40S pre-ribosomal particles. Interacts with PLK1 (via its N-terminus).

Subcellular location. Cytoplasm.

Post-translational modifications. Autophosphorylated (in vitro). Phosphorylation at Ser-335, Ser-380, Ser-548 by PLK1 affects the timing of the metaphase-anaphase transition.

Similarity. Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BVS4-11yes
Q9BVS4-22

RefSeq proteins (2): NP_001153221, NP_060813* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000687RIO_kinaseDomain
IPR011009Kinase-like_dom_sfHomologous_superfamily
IPR015285RIO2_wHTH_NDomain
IPR018934RIO_domDomain
IPR018935RIO_kinase_CSConserved_site
IPR030484Rio2Domain
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily

Pfam: PF01163, PF09202

Catalyzed reactions (Rhea), 2 shown:

  • L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) (RHEA:17989)
  • L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+) (RHEA:46608)

UniProt features (72 total): helix 15, modified residue 14, strand 14, sequence variant 11, mutagenesis site 10, turn 2, chain 1, domain 1, splice variant 1, short sequence motif 1, active site 1, binding site 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
6FDMX-RAY DIFFRACTION2.1
5DHFX-RAY DIFFRACTION2.29
6HK6X-RAY DIFFRACTION2.35
7VBTX-RAY DIFFRACTION2.54
6FDOX-RAY DIFFRACTION2.6
6FDNX-RAY DIFFRACTION2.9
9F81X-RAY DIFFRACTION3.02
7WU0ELECTRON MICROSCOPY3.3
6G18ELECTRON MICROSCOPY3.6
6G51ELECTRON MICROSCOPY4.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BVS4-F167.800.32

Functional residue map

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

Catalytic / active sites (1): 228 (proton acceptor)

Ligand- & substrate-binding residues (1): 123

Post-translational modifications (14): 380, 382, 385, 390, 412, 417, 442, 445, 548, 332, 335, 337, 350, 362

Mutagenesis-validated functional residues (10):

PositionPhenotype
123abolishes autophosphorylation; impairs release of pre-40s trans-acting factors and rrna processing; when associated with
246abolishes autophosphorylation; impairs release of pre-40s trans-acting factors and rrna processing; when associated with
335does not affect autophosphorylation activity; when associated with a-380 and a-548. does not affect the timing of metaph
335increases time spent in metaphase; when associated with d-380 and d-548.
380does not affect autophosphorylation activity; when associated with a-335 and a-548. does not affect the timing of metaph
380increases time spent in metaphase; when associated with d-335 and d-548.
400nuclear relocalization; when associated with a-403.
403nuclear relocalization; when associated with a-400.
548does not affect autophosphorylation activity; when associated with a-335 and a-380. does not affect the timing of metaph
548increases time spent in metaphase; when associated with d-335 and d-380.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 165 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_TRANSPORT, GOBP_NUCLEAR_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, MARTINEZ_RB1_TARGETS_UP, GOBP_REGULATION_OF_CHROMOSOME_SEGREGATION, GOBP_REGULATION_OF_NUCLEOCYTOPLASMIC_TRANSPORT, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (8): regulation of mitotic metaphase/anaphase transition (GO:0030071), maturation of SSU-rRNA (GO:0030490), ribosomal small subunit biogenesis (GO:0042274), protein autophosphorylation (GO:0046777), positive regulation of ribosomal small subunit export from nucleus (GO:2000208), positive regulation of rRNA processing (GO:2000234), protein phosphorylation (GO:0006468), ribosome biogenesis (GO:0042254)

GO Molecular Function (10): protein kinase activity (GO:0004672), protein serine/threonine kinase activity (GO:0004674), ATP binding (GO:0005524), metal ion binding (GO:0046872), protein serine kinase activity (GO:0106310), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), preribosome, small subunit precursor (GO:0030688)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
rRNA processing in the nucleus and cytosol1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
rRNA processing2
ribonucleoprotein complex biogenesis2
protein kinase activity2
metaphase/anaphase transition of mitotic cell cycle1
regulation of mitotic cell cycle phase transition1
regulation of metaphase/anaphase transition of cell cycle1
ribosomal small subunit biogenesis1
ribosome biogenesis1
protein phosphorylation1
ribosomal small subunit export from nucleus1
positive regulation of ribosomal subunit export from nucleus1
regulation of ribosomal small subunit export from nucleus1
positive regulation of RNA metabolic process1
regulation of rRNA processing1
phosphorylation1
protein modification process1
kinase activity1
phosphotransferase activity, alcohol group as acceptor1
catalytic activity, acting on a protein1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
cation binding1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
binding1
transferase activity, transferring phosphorus-containing groups1
catalytic activity1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
preribosome1

Protein interactions and networks

STRING

2573 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RIOK2LTV1Q96GA3943
RIOK2BYSLQ13895942
RIOK2TSR1Q2NL82937
RIOK2PNO1Q9NRX1902
RIOK2NOB1Q9ULX3894
RIOK2RRP12Q5JTH9842
RIOK2RIOK3O14730775
RIOK2BMS1Q14692764
RIOK2RIOK1Q9BRS2725
RIOK2NMD3Q96D46723
RIOK2XPO1O14980699
RIOK2RPS10P46783675
RIOK2RPS3P23396667
RIOK2LSG1Q9H089658
RIOK2DHX15O43143647

IntAct

76 interactions, top by confidence:

ABTypeScore
NUP50KPNA3psi-mi:“MI:0914”(association)0.780
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
SRPK1SNRPCpsi-mi:“MI:0914”(association)0.640
BYSLPARNpsi-mi:“MI:0914”(association)0.640
RIOK2psi-mi:“MI:0915”(physical association)0.560
RIOK2BYSLpsi-mi:“MI:0914”(association)0.530
MINK1CNOT1psi-mi:“MI:0914”(association)0.530
TMEM63AAP3D1psi-mi:“MI:0914”(association)0.530
MYO1CTMOD1psi-mi:“MI:0914”(association)0.530
GHITMMFN2psi-mi:“MI:0914”(association)0.530
DDX21MED19psi-mi:“MI:2364”(proximity)0.480
CSNK2A1RIOK2psi-mi:“MI:0217”(phosphorylation reaction)0.440
RIOK2SMAD3psi-mi:“MI:0915”(physical association)0.370
RELARIOK2psi-mi:“MI:0915”(physical association)0.370
RIOK2GFUSpsi-mi:“MI:0915”(physical association)0.370
RIOK2RPRD1Apsi-mi:“MI:0915”(physical association)0.370
Rpl35RPS6psi-mi:“MI:0914”(association)0.350
Cep120TBC1D31psi-mi:“MI:0914”(association)0.350
VPS16TTC31psi-mi:“MI:0914”(association)0.350
HNRNPUpsi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
TAFA3FUOMpsi-mi:“MI:0914”(association)0.350
GRB7RIOK3psi-mi:“MI:0914”(association)0.350
Ppsi-mi:“MI:0914”(association)0.350
RYBPPIPSLpsi-mi:“MI:0914”(association)0.350
RIOK2MACROH2A1psi-mi:“MI:0914”(association)0.350
BYSLRPS3Apsi-mi:“MI:0914”(association)0.350
CAPZBENAHpsi-mi:“MI:0914”(association)0.350

BioGRID (145): TSR1 (Co-fractionation), RIOK2 (Proximity Label-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS), RIOK2 (Affinity Capture-MS)

ESM2 similar proteins: A1ZAJ2, A8WRG3, A8XQD5, E7F187, G5EEM9, G5EFD2, I2HAA0, O01583, O01991, O43166, O43314, O45818, O60333, O80528, O82486, O88658, P24583, P43125, P50526, P91309, P91682, Q06685, Q10003, Q11186, Q14149, Q17BU3, Q28WQ1, Q4R8E0, Q5R9Y9, Q5REW0, Q60575, Q60L58, Q61T02, Q640I9, Q6GQT0, Q6NSI8, Q6P158, Q7PHR1, Q7YZT6, Q8C0T5

Diamond homologs: A5UAM9, A5UG81, A6VQT5, B0RTE2, B0U358, B2FR65, B2I5R8, B2SLU1, B4SLP5, O86224, P58551, Q2P6W5, Q3BWM9, Q4QNS8, Q4URM8, Q5H410, Q65R39, Q6LVM6, Q7MPR5, Q87C81, Q87T74, Q8DDZ1, Q8PBX3, Q8PNH3, Q9BVS4, Q9CLD5, Q9CQS5, Q9KVB9, Q9PBJ1, Q9UYB9, P40160, Q54T05, Q58473, Q95Q34, Q9P7W5, O30245, Q57886, D4GYY1

SIGNOR signaling

3 interactions.

AEffectBMechanism
PLK1“up-regulates activity”RIOK2phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 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
Eukaryotic Translation Initiation624.7×4e-06
Cap-dependent Translation Initiation624.7×4e-06
SARS-CoV-1 modulates host translation machinery624.7×4e-06
Formation of the ternary complex, and subsequently, the 43S complex823.0×4e-07
Eukaryotic Translation Elongation622.3×7e-06
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S621.8×8e-06
Translation initiation complex formation820.3×6e-07
Ribosomal scanning and start codon recognition820.3×6e-07

GO biological processes:

GO termPartnersFoldFDR
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)534.8×7e-05
ribosomal small subunit biogenesis818.8×7e-06
cytoplasmic translation815.3×2e-05
translation88.5×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance72
Likely benign3
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1384 predictions. Top by Δscore:

VariantEffectΔscore
5:97163223:TTCC:Tacceptor_loss1.0000
5:97163226:C:CCacceptor_gain1.0000
5:97163226:C:CGacceptor_loss1.0000
5:97163227:T:Aacceptor_loss1.0000
5:97165044:TACTT:Tdonor_loss1.0000
5:97165045:ACTTA:Adonor_loss1.0000
5:97165046:CT:Cdonor_loss1.0000
5:97165047:TTACT:Tdonor_loss1.0000
5:97165048:TA:Tdonor_loss1.0000
5:97165049:A:ACdonor_gain1.0000
5:97165050:C:CTdonor_gain1.0000
5:97165050:CT:Cdonor_gain1.0000
5:97165050:CTG:Cdonor_gain1.0000
5:97165050:CTGG:Cdonor_gain1.0000
5:97165050:CTGGA:Cdonor_gain1.0000
5:97165143:CATCT:Cacceptor_gain1.0000
5:97165146:CT:Cacceptor_gain1.0000
5:97165148:C:CCacceptor_gain1.0000
5:97165148:CTAAA:Cacceptor_loss1.0000
5:97167989:CTC:Cacceptor_gain1.0000
5:97167990:TC:Tacceptor_gain1.0000
5:97167991:CC:Cacceptor_gain1.0000
5:97167992:C:CCacceptor_gain1.0000
5:97168755:CAAA:Cdonor_loss1.0000
5:97168756:AAACC:Adonor_loss1.0000
5:97168757:AAC:Adonor_loss1.0000
5:97168758:A:ATdonor_loss1.0000
5:97168759:C:CAdonor_loss1.0000
5:97171204:A:ACdonor_gain1.0000
5:97171205:C:CCdonor_gain1.0000

AlphaMissense

3671 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:97171289:A:CF232L1.000
5:97171289:A:TF232L1.000
5:97171291:A:GF232L1.000
5:97171302:T:AD228V1.000
5:97177166:A:GW150R1.000
5:97177166:A:TW150R1.000
5:97179162:A:TV33D1.000
5:97168839:C:GD265H0.999
5:97171238:C:AQ249H0.999
5:97171238:C:GQ249H0.999
5:97171247:A:CD246E0.999
5:97171247:A:TD246E0.999
5:97171248:T:AD246V0.999
5:97171248:T:CD246G0.999
5:97171248:T:GD246A0.999
5:97171249:C:GD246H0.999
5:97171284:A:GL234P0.999
5:97171286:A:CN233K0.999
5:97171286:A:TN233K0.999
5:97171288:T:CN233D0.999
5:97171301:A:CD228E0.999
5:97171301:A:TD228E0.999
5:97171302:T:CD228G0.999
5:97171302:T:GD228A0.999
5:97171303:C:GD228H0.999
5:97171314:A:GL224P0.999
5:97173214:C:GR183P0.999
5:97173215:G:TR183S0.999
5:97173238:A:TV175D0.999
5:97177141:G:TA158D0.999

dbSNP variants (sampled 300 via entrez): RS1000092017 (5:97185099 A>G), RS1000123404 (5:97184954 C>A,G), RS1000449841 (5:97174313 G>C), RS1000500450 (5:97174607 T>A,C,G), RS1000509148 (5:97160526 C>A,G,T), RS1000690652 (5:97166967 G>A,T), RS1000698878 (5:97167369 T>C,G), RS1000701141 (5:97174345 G>A), RS1001123959 (5:97166742 G>T), RS1001368713 (5:97172701 A>G), RS1001426337 (5:97179583 C>T), RS1001780151 (5:97165978 A>G), RS1001930198 (5:97168654 C>A,T), RS1001991177 (5:97161248 A>G), RS1002020244 (5:97160864 G>A)

Disease associations

OMIM: gene MIM:617754 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
male infertility with azoospermia or oligozoospermia due to single gene mutationLimitedAutosomal recessive

Mondo (1): (MONDO:0018393)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008708_1Chronic mountain sickness7.000000e-06
GCST009391_2148Metabolite levels7.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0010143chronic mountain sickness
EFO:0010551xanthurenate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL6000 (SINGLE PROTEIN), CHEMBL6195604 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

17 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 139,815 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1287853FEDRATINIB43,554
CHEMBL1789941RUXOLITINIB411,547
CHEMBL477772PAZOPANIB415,540
CHEMBL535SUNITINIB479,020
CHEMBL608533MIDOSTAURIN47,259
CHEMBL1908391MASITINIB32,808
CHEMBL522892DOVITINIB34,944
CHEMBL603469LESTAURTINIB3
CHEMBL1721885SU-0148132363
CHEMBL230011TG100-11521,504
CHEMBL475251R-4062762
CHEMBL521851PICTILISIB26,071
CHEMBL572878TOZASERTIB22,998
CHEMBL1908397KW-24491622
CHEMBL296468BMS-38703212,075
CHEMBL4647810ELIMUSERTIB1297
CHEMBL574738AST-4871451

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — RIO2 subfamily

ChEMBL bioactivities

83 potent at pChembl≥5 of 88 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.21Kd6.1nMCHEMBL5172767
8.14Kd7.3nMCHEMBL5174723
8.14Kd7.3nMCHEMBL5172767
8.08Kd8.4nMCHEMBL5199096
7.75Kd18nMCHEMBL5190698
7.72Kd19nMCHEMBL5399070
7.32Kd47.5nMCHEMBL5184015
7.32Kd48nMCHEMBL5417058
7.31Kd49nMCHEMBL5192566
7.31Kd49nMSUNITINIB
7.28Kd53nMCHEMBL5417476
7.25Kd56nMCHEMBL5439857
7.25IC5056nMCHEMBL5172767
7.21Kd62nMCHEMBL5406944
7.20Kd63nMCHEMBL5190197
7.20Kd63nMCHEMBL5194039
7.01Kd97nMMIDOSTAURIN
7.01IC5098nMCHEMBL6145816
6.92Kd120nMCHEMBL5190993
6.89Kd130nMCHEMBL2348353
6.89IC50130nMCHEMBL4858983
6.86IC50139nMCHEMBL5172767
6.85Kd140nMCHEMBL4781866
6.85Kd140nMCHEMBL5527885
6.85Kd140nMSU-014813
6.82Kd150nMCHEMBL4781866
6.80Kd160nMCHEMBL4781866
6.78Kd165nMCHEMBL5416400
6.70Kd200nMCHEMBL5174394
6.70Kd200nMCHEMBL2094383
6.63Kd235nMCHEMBL5187692
6.62Kd240nMCHEMBL2348350
6.60Kd250nMTOZASERTIB
6.58Kd260nMDOVITINIB
6.42Kd385nMCHEMBL5184335
6.41Kd390nMSTAUROSPORINE
6.34Kd455nMCHEMBL5189953
6.28Kd520nMCHEMBL4754518
6.26Kd550nMAST-487
6.24Kd575nMCHEMBL5177849
6.21Kd610nMPAZOPANIB
6.18Kd660nMELIMUSERTIB
6.17Kd670nMPICTILISIB
6.11Kd770nMPI-103
6.11Kd770nMPLX-4720
6.09Kd810nMCHEMBL5205288
6.08Kd840nMCHEMBL5188981
6.00IC501000nMTP-030-1
6.00IC501000nMTP-030-2
6.00IC501000nMTP-030n

PubChem BioAssay actives

74 with measured affinity, of 375 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0061uM
1-(3-chloro-4-piperazin-1-ylphenyl)-8-(6-methoxy-3-pyridinyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0073uM
8-(6-methoxy-3-pyridinyl)-1-(3-methyl-4-piperazin-1-ylphenyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0084uM
1-(3-fluoro-4-piperazin-1-ylphenyl)-8-(6-methoxy-3-pyridinyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0180uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-pyrazolo[4,5-c]quinolin-4-one1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.0190uM
1-(3-methoxy-4-piperazin-1-ylphenyl)-8-(6-methoxy-3-pyridinyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0475uM
8-(6-methoxy-3-pyridinyl)-3-methyl-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-imidazo[4,5-c]quinoline-2,4-dione1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.0480uM
8-(6-methoxy-3-pyridinyl)-5-methyl-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0490uM
Sunitinib508063: Binding affinity to RIOK2kd0.0490uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-imidazo[1,2-a]quinoxalin-4-one1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.0530uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-imidazo[1,5-a]quinoxalin-4-one1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.0560uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-imidazo[4,5-c]quinolin-4-one1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.0620uM
8-(6-methoxy-3-pyridinyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0630uM
8-(6-methoxy-3-pyridinyl)-1-(4-piperazin-1-ylphenyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.0630uM
Midostaurin508063: Binding affinity to RIOK2kd0.0970uM
1-(4-methoxyphenyl)-8-(6-methoxy-3-pyridinyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.1200uM
5-(dimethylamino)-2-(pyridin-2-yldiazenyl)phenol;methanesulfonic acid1766474: Inhibition of RIOK2 in human VCaP cells after 48 hrs by Western blotting analysisic500.1300uM
5-[(Z)-(5-fluoro-2-oxo-1H-indol-3-ylidene)methyl]-N-[(2S)-2-hydroxy-3-morpholin-4-ylpropyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide625111: Binding constant for RIOK2 kinase domainkd0.1400uM
N-(4-methyl-2-pyridinyl)-2-naphthalen-2-ylacetamide1685593: Binding affinity to RIOK2 (unknown origin)kd0.1400uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-pyrrolo[1,2-a]quinoxalin-4-one1977525: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constant by KINOMEscan assaykd0.1650uM
N-(3-methoxy-2-methyl-16-oxo-29-oxa-1,7,17-triazaoctacyclo[12.12.2.12,6.07,28.08,13.015,19.020,27.021,26]nonacosa-8,10,12,14,19,21,23,25,27-nonaen-4-yl)-N-methylbenzamide1910805: Binding affinity to RIOK2 (unknown origin) assessed as dissociation constantkd0.2000uM
1-[(E)-2-(1,3-thiazol-2-yl)ethenyl]naphthalen-2-ol1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.2000uM
1-(1,3-thiazol-2-yldiazenyl)naphthalen-2-ol1977520: Binding affinity to human RIOK2 assessed as dissociation constant by KINOMEscan assaykd0.2000uM
8-(6-methoxy-3-pyridinyl)-1-(4-phenylphenyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.2350uM
N-[4-[4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl]sulfanylphenyl]cyclopropanecarboxamide625111: Binding constant for RIOK2 kinase domainkd0.2500uM
4-amino-5-fluoro-3-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-quinolin-2-one625111: Binding constant for RIOK2 kinase domainkd0.2600uM
8-(6-ethoxy-3-pyridinyl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.3850uM
(2S,3R,4R,6R)-3-methoxy-2-methyl-4-(methylamino)-29-oxa-1,7,17-triazaoctacyclo[12.12.2.12,6.07,28.08,13.015,19.020,27.021,26]nonacosa-8,10,12,14,19,21,23,25,27-nonaen-16-one625111: Binding constant for RIOK2 kinase domainkd0.3900uM
1-(4-chlorophenyl)-8-(6-methoxy-3-pyridinyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.4550uM
1-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]-3-[4-[6-(methylamino)pyrimidin-4-yl]oxyphenyl]urea625111: Binding constant for RIOK2 kinase domainkd0.5500uM
8-(6-methoxy-3-pyridinyl)-1-[4-piperazin-1-yl-2-(trifluoromethyl)phenyl]-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.5750uM
Pazopanib625111: Binding constant for RIOK2 kinase domainkd0.6100uM
(3R)-3-methyl-4-[4-(2-methylpyrazol-3-yl)-8-(1H-pyrazol-5-yl)-1,7-naphthyridin-2-yl]morpholine1652484: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system by Kinomescan methodkd0.6600uM
4-[2-(1H-indazol-4-yl)-6-[(4-methylsulfonylpiperazin-1-yl)methyl]thieno[3,2-d]pyrimidin-4-yl]morpholine625111: Binding constant for RIOK2 kinase domainkd0.6700uM
N-[3-(5-chloro-1H-pyrrolo[2,3-b]pyridine-3-carbonyl)-2,4-difluorophenyl]propane-1-sulfonamide625111: Binding constant for RIOK2 kinase domainkd0.7700uM
3-(6-morpholin-4-yl-8-oxa-3,5,10-triazatricyclo[7.4.0.02,7]trideca-1(9),2(7),3,5,10,12-hexaen-4-yl)phenol625111: Binding constant for RIOK2 kinase domainkd0.7700uM
8-(6-methoxy-3-pyridinyl)-1-(4-methylphenyl)-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.8100uM
1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-8-pyridin-3-yl-5H-triazolo[4,5-c]quinolin-4-one1910807: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system assessed as dissociation constant by KINOMEscan assaykd0.8400uM
2-[4-[(1E)-1-hydroxyimino-2,3-dihydroinden-5-yl]-3-pyridin-4-ylpyrazol-1-yl]ethanol625111: Binding constant for RIOK2 kinase domainkd1.2000uM
Ruxolitinib625111: Binding constant for RIOK2 kinase domainkd1.2000uM
3-[2,4-diamino-7-(3-hydroxyphenyl)pteridin-6-yl]phenol625111: Binding constant for RIOK2 kinase domainkd1.5000uM
N-[5-[(5-tert-butyl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]piperidine-4-carboxamide625111: Binding constant for RIOK2 kinase domainkd1.5000uM
4-[(4-methylpiperazin-1-yl)methyl]-N-[4-methyl-3-[(4-pyridin-3-yl-1,3-thiazol-2-yl)amino]phenyl]benzamide625111: Binding constant for RIOK2 kinase domainkd1.7000uM
2-[[2-[[1-[2-(dimethylamino)acetyl]-5-methoxy-2,3-dihydroindol-6-yl]amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl]amino]-6-fluoro-N-methylbenzamide625111: Binding constant for RIOK2 kinase domainkd2.0000uM
N-[[2-methyl-4-[2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]phenyl]methyl]-3-propan-2-yloxyazetidine-1-carboxamide1696278: Binding affinity to wild-type human partial length RIOK2 (M1 to D313 residues) expressed in mammalian expression system by Kinomescan methodkd2.4000uM
Fedratinib625111: Binding constant for RIOK2 kinase domainkd2.6000uM
6-[[5-fluoro-2-(3,4,5-trimethoxyanilino)pyrimidin-4-yl]amino]-2,2-dimethyl-4H-pyrido[3,2-b][1,4]oxazin-3-one625111: Binding constant for RIOK2 kinase domainkd3.4000uM
[4-[(E)-2-(1H-indazol-3-yl)ethenyl]phenyl]-piperazin-1-ylmethanone625111: Binding constant for RIOK2 kinase domainkd5.0000uM
N-(4-chloro-2-pyridinyl)-2-naphthalen-2-ylacetamide1685587: Displacement of tracer K5 from N-terminal nanoluciferase-tagged RIOK2 (unknown origin) expressed in HEK293 cells measured after 2 hrs by NanoBRET assayic505.0000uM
N-(4-methoxy-2-pyridinyl)-2-naphthalen-2-ylacetamide1685587: Displacement of tracer K5 from N-terminal nanoluciferase-tagged RIOK2 (unknown origin) expressed in HEK293 cells measured after 2 hrs by NanoBRET assayic505.2000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionincreases expression2
Cadmium Chloridedecreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
methylparabendecreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
zinc chromateincreases abundance, increases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
hydroquinonedecreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
perfluorooctane sulfonic acidincreases expression1
abrineincreases expression1
jinfukangdecreases expression1
MT19c compoundincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Caffeinedecreases phosphorylation1
Dexamethasoneaffects cotreatment, increases expression1
Dimethyl Sulfoxideincreases expression1
Formaldehydedecreases expression1

ChEMBL screening assays

156 unique, capped per target: 156 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1052945BindingInhibition of RIOK2 assessed as enzyme activity at 1 uM relative to untreated controlSelective inhibitors of the mutant B-Raf pathway: discovery of a potent and orally bioavailable aminoisoquinoline. — J Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.