RPL17

gene
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Also known as rpL23L17uL22

Summary

RPL17 (ribosomal protein L17, HGNC:10307) is a protein-coding gene on chromosome 18q21.1, encoding Large ribosomal subunit protein uL22 (P18621). Component of the large ribosomal subunit. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L22P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL23 because the encoded protein shares amino acid identity with ribosomal protein L23 from Halobacterium marismortui; however, its official symbol is RPL17. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream C18orf32 (chromosome 18 open reading frame 32) gene.

Source: NCBI Gene 6139 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 49 total — 1 likely-pathogenic
  • Phenotypes (HPO): 2
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_001035006

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10307
Approved symbolRPL17
Nameribosomal protein L17
Location18q21.1
Locus typegene with protein product
StatusApproved
AliasesrpL23, L17, uL22
Ensembl geneENSG00000265681
Ensembl biotypeprotein_coding
OMIM603661
Entrez6139

Gene structure

Transcript identifiers

Ensembl transcripts: 51 — 42 protein_coding, 8 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000578528, ENST00000578532, ENST00000578966, ENST00000579248, ENST00000579408, ENST00000579495, ENST00000580210, ENST00000580261, ENST00000580387, ENST00000581091, ENST00000581305, ENST00000581373, ENST00000581741, ENST00000582588, ENST00000582782, ENST00000582935, ENST00000583036, ENST00000583637, ENST00000584364, ENST00000615479, ENST00000615760, ENST00000617346, ENST00000618613, ENST00000618619, ENST00000851991, ENST00000851992, ENST00000851993, ENST00000851994, ENST00000851995, ENST00000851996, ENST00000851997, ENST00000914346, ENST00000914347, ENST00000914348, ENST00000914349, ENST00000914350, ENST00000914351, ENST00000914352, ENST00000914353, ENST00000914354, ENST00000914355, ENST00000914356, ENST00000914357, ENST00000914358, ENST00000914359, ENST00000914360, ENST00000914361, ENST00000914362, ENST00000914363, ENST00000914364, ENST00000962425

RefSeq mRNA: 16 — MANE Select: NM_001035006 NM_000985, NM_001035006, NM_001199340, NM_001199341, NM_001199342, NM_001199343, NM_001199344, NM_001199345, NM_001369555, NM_001369556, NM_001369557, NM_001369558, NM_001369560, NM_001369561, NM_001369562, NM_001369563

CCDS: CCDS45865, CCDS56070, CCDS92461

Canonical transcript exons

ENST00000580261 — 7 exons

ExonStartEnd
ENSE000017039144948848149488566
ENSE000026847904949245849492465
ENSE000034927174949153249491584
ENSE000036964514949140549491445
ENSE000036972384949045449490552
ENSE000036990274949079349490927
ENSE000037892474948935949489550

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.0838 / max 265.9175, expressed in 1735 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
171914100.96861826
1719159.89221666
1719167.19171497

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ovaryUBERON:000211999.93gold quality
ovaryUBERON:000099299.92gold quality
right ovaryUBERON:000211899.92gold quality
right uterine tubeUBERON:000130299.91gold quality
endometriumUBERON:000129599.90gold quality
adenohypophysisUBERON:000219699.90gold quality
pituitary glandUBERON:000000799.89gold quality
endocervixUBERON:000045899.89gold quality
left lobe of thyroid glandUBERON:000112099.89gold quality
body of pancreasUBERON:000115099.89gold quality
thyroid glandUBERON:000204699.89gold quality
calcaneal tendonUBERON:000370199.89gold quality
body of uterusUBERON:000985399.89gold quality
islet of LangerhansUBERON:000000699.88gold quality
cerebellumUBERON:000203799.88gold quality
cerebellar cortexUBERON:000212999.88gold quality
cerebellar hemisphereUBERON:000224599.88gold quality
metanephros cortexUBERON:001053399.88gold quality
muscle layer of sigmoid colonUBERON:003580599.88gold quality
right lobe of thyroid glandUBERON:000111999.87gold quality
fundus of stomachUBERON:000116099.87gold quality
left adrenal glandUBERON:000123499.87gold quality
pancreasUBERON:000126499.87gold quality
myometriumUBERON:000129699.87gold quality
fallopian tubeUBERON:000388999.87gold quality
thoracic mammary glandUBERON:000520099.87gold quality
lower esophagusUBERON:001347399.87gold quality
right hemisphere of cerebellumUBERON:001489099.87gold quality
left adrenal gland cortexUBERON:003582599.87gold quality
lower esophagus muscularis layerUBERON:003583399.87gold quality

Single-cell (SCXA)

Detected in 35 experiment(s), a significant marker in 17.

ExperimentMarker?Max mean expression
E-MTAB-9543yes3117.44
E-HCAD-1yes106.03
E-MTAB-6701yes98.61
E-CURD-122yes84.68
E-MTAB-9221yes55.97
E-CURD-88yes55.94
E-CURD-46yes50.37
E-HCAD-11yes48.92
E-MTAB-8410yes43.79
E-MTAB-6678yes41.54
E-CURD-112yes28.36
E-GEOD-135922yes25.84
E-MTAB-9067yes25.55
E-HCAD-9yes25.42
E-ANND-3yes15.00

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

  • The present study combines an individual-based phenotypic profiling with a transdiagnostic approach and shows that several ribosomal genes including RPL17 is involved in stress vulnerability across nonclinical and clinical conditions. (PMID:30103068)
  • An atypical form of 60S ribosomal subunit in Diamond-Blackfan anemia linked to RPL17 variants. (PMID:39088281)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriorpl17ENSDARG00000057556
drosophila_melanogasterRpL17FBGN0029897
caenorhabditis_elegansrpl-17WBGENE00004429

Protein

Protein identifiers

Large ribosomal subunit protein uL22P18621 (reviewed: P18621)

Alternative names: 60S ribosomal protein L17, 60S ribosomal protein L23, PD-1

All UniProt accessions (10): A0A087WWH0, A0A087WXM6, A0A087WY81, P18621, J3KRB3, J3KRX5, J3KSJ0, J3QLC8, J3QQT2, J3QS96

UniProt curated annotations — full annotation on UniProt →

Function. Component of the large ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.

Subunit / interactions. Component of the large ribosomal subunit.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in pancreas, lung, colon, cystic duct, gall bladder, kidney and liver. Expressed at high levels in the well differentiated pancreatic tumor cell lines HPAF, COLO 357 and Capan-1, the moderately differentiated pancreatic tumor cell lines T3M-4, AsPc-1 and BxPc-3, the poorly differentiated pancreatic tumor cell line MIA PaCa-2, and the pancreatic tumor cell lines of undefined differentiation status such as SW979. Expressed at lower levels in the poorly differentiated pancreatic tumor cell lines HCG-25 and PANC-1.

Disease relevance. Diamond-Blackfan anemia 22 (DBA22) [MIM:621262] A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. DBA22 is an autosomal dominant form characterized by erythroid maturation failure and skeletal developmental defects. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the universal ribosomal protein uL22 family.

Isoforms (3)

UniProt IDNamesCanonical?
P18621-11yes
P18621-22
P18621-33

RefSeq proteins (16): NP_000976, NP_001030178, NP_001186269, NP_001186270, NP_001186271, NP_001186272, NP_001186273, NP_001186274, NP_001356484, NP_001356485, NP_001356486, NP_001356487, NP_001356489, NP_001356490, NP_001356491, NP_001356492 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001063Ribosomal_uL22Family
IPR005721Ribosomal_uL22_euk_arcFamily
IPR018260Ribosomal_uL22_CSConserved_site
IPR036394Ribosomal_uL22_sfHomologous_superfamily
IPR057265Ribosomal_uL22_arcFamily

Pfam: PF00237

UniProt features (7 total): splice variant 2, initiator methionine 1, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

195 structures, top 30 by resolution.

PDBMethodResolution (Å)
8A3DELECTRON MICROSCOPY1.67
8GLPELECTRON MICROSCOPY1.67
8QYXELECTRON MICROSCOPY1.78
8QOIELECTRON MICROSCOPY1.9
9O3WELECTRON MICROSCOPY1.9
8YOOELECTRON MICROSCOPY2
9C3HELECTRON MICROSCOPY2
9I2DELECTRON MICROSCOPY2.19
9PBEELECTRON MICROSCOPY2.19
8QFDELECTRON MICROSCOPY2.2
8YOPELECTRON MICROSCOPY2.2
9GULELECTRON MICROSCOPY2.2
9O3VELECTRON MICROSCOPY2.2
9O3YELECTRON MICROSCOPY2.2
8JDKELECTRON MICROSCOPY2.26
8G5YELECTRON MICROSCOPY2.29
9S3DELECTRON MICROSCOPY2.32
9RPVELECTRON MICROSCOPY2.35
9S3BELECTRON MICROSCOPY2.38
7OW7ELECTRON MICROSCOPY2.4
8K2CELECTRON MICROSCOPY2.4
8XSXELECTRON MICROSCOPY2.4
9SPFELECTRON MICROSCOPY2.4
9SPIELECTRON MICROSCOPY2.4
8JDLELECTRON MICROSCOPY2.42
9S3CELECTRON MICROSCOPY2.42
8FKVELECTRON MICROSCOPY2.47
9QLOELECTRON MICROSCOPY2.47
8FLEELECTRON MICROSCOPY2.48
9P8BELECTRON MICROSCOPY2.48

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P18621-F191.850.81

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

IDPathway
R-HSA-156827L13a-mediated translational silencing of Ceruloplasmin expression
R-HSA-156902Peptide chain elongation
R-HSA-1799339SRP-dependent cotranslational protein targeting to membrane
R-HSA-192823Viral mRNA Translation
R-HSA-2408557Selenocysteine synthesis
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72689Formation of a pool of free 40S subunits
R-HSA-72706GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-72764Eukaryotic Translation Termination
R-HSA-9010553Regulation of expression of SLITs and ROBOs
R-HSA-9633012Response of EIF2AK4 (GCN2) to amino acid deficiency
R-HSA-975956Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-975957Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-9954709Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide
R-HSA-9954714PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA
R-HSA-9954716ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA

MSigDB gene sets: 436 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GRUETZMANN_PANCREATIC_CANCER_DN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GGGNRMNNYCAT_UNKNOWN, MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER, MODULE_151, GNF2_TPT1, GCM_NPM1, MORF_UBE2I, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, HSIAO_HOUSEKEEPING_GENES, GOBP_MALE_GAMETE_GENERATION

GO Biological Process (3): cytoplasmic translation (GO:0002181), translation (GO:0006412), RNA processing (GO:0006396)

GO Molecular Function (3): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (9): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), nucleolus (GO:0005730), ribosome (GO:0005840), large ribosomal subunit (GO:0015934), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

CategoryPathways
Ribosome-associated quality control3
Translation2
Cap-dependent Translation Initiation2
Nonsense-Mediated Decay (NMD)2
Eukaryotic Translation Initiation1
Eukaryotic Translation Elongation1
Influenza Viral RNA Transcription and Replication1
Selenoamino acid metabolism1
rRNA processing in the nucleus and cytosol1
Signaling by ROBO receptors1
Cellular response to starvation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ribosome2
cellular anatomical structure2
intracellular membraneless organelle2
translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
gene expression1
RNA biosynthetic process1
primary metabolic process1
nucleic acid binding1
structural molecule activity1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
large ribosomal subunit1
cytosolic ribosome1
cytosol1
nuclear lumen1
ribosomal subunit1
protein-containing complex1

Protein interactions and networks

STRING

4173 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPL17RPL23P23131971
RPL17RPL5P46777656
RPL17RPL11P25121629
RPL17MRPL22Q9NWU5571
RPL17E9PSI1E9PSI1507
RPL17RPS15P11174461
RPL17RPS17P08708450
RPL17RPS3AP33443446
RPL17RPS11P04643436
RPL17RPL6Q02878428
RPL17RPL26P61254428
RPL17RPL37P02403420
RPL17RPS9P46781411
RPL17FAUP35544404
RPL17MRPL12P52815402

IntAct

367 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
RACK1RPS17psi-mi:“MI:0915”(physical association)0.610
MAPTKIF2Apsi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
MAGEB10GTPBP10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF71NVLpsi-mi:“MI:0914”(association)0.530
NAP1L1RPL17psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
PPP2R2BDDX3Xpsi-mi:“MI:0914”(association)0.460
ESR1psi-mi:“MI:0914”(association)0.460
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
RPL17HSPA5psi-mi:“MI:0915”(physical association)0.400
RPL17SPTAN1psi-mi:“MI:0915”(physical association)0.400
RPL17OCIAD2psi-mi:“MI:0915”(physical association)0.400
CtcfRPL36Apsi-mi:“MI:0915”(physical association)0.400

BioGRID (832): RPL17 (Affinity Capture-MS), RPL17 (Affinity Capture-MS), RPL17 (Affinity Capture-MS), AHCYL2 (Co-fractionation), GFM2 (Co-fractionation), MRPS7 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation), RPL17 (Co-fractionation)

ESM2 similar proteins: A0NGY0, A2I3Y6, A4FWB7, A6VGY9, A8CAG3, A9A9R0, G1SCJ6, O14339, O48557, O59794, P05740, P06389, P0DJ16, P18621, P24049, P35266, P35267, P37380, P46990, P51413, P62649, Q06R92, Q09JW2, Q0PXV9, Q1HR65, Q29IM3, Q33BZ2, Q3T025, Q4GXH5, Q4GXH6, Q4GXH7, Q4KTG9, Q4N4B9, Q4PM54, Q4UF75, Q54NG2, Q59TE0, Q5I5J1, Q5MGD1, Q5MIR6

Diamond homologs: A0B9W5, A0NGY0, A0RVX8, A1RVA1, A1RXG7, A1SNL3, A2BMC4, A2I3Y6, A2SPK8, A3CT02, A3DNB2, A3MTL6, A4FWB7, A4WIY9, A4YCX1, A5UL84, A6UQ48, A6UWU2, A6VGY9, A7I5P4, A8AA19, A8CAG3, A8MBL4, A9A5J0, A9A9R0, B1YD24, B4U505, B4U749, C0M7R4, G1SCJ6, O14339, O26115, O28359, O48557, O59423, O59794, P05740, P0C0D4, P0DE22, P0DJ16

SIGNOR signaling

1 interactions.

AEffectBMechanism
RPL17“form complex”“60S cytosolic large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 189 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) independent of the Exon Junction Complex (EJC)1917.9×1e-16
SRP-dependent cotranslational protein targeting to membrane2217.6×4e-19
Eukaryotic Translation Termination1817.3×9e-16
Peptide chain elongation1717.3×3e-15
Viral mRNA Translation1717.3×3e-15
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1717.1×3e-15
Selenocysteine synthesis1716.4×7e-15
Formation of a pool of free 40S subunits1816.1×2e-15

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation2023.0×4e-19
ribosomal large subunit biogenesis822.0×5e-07
stress granule assembly518.7×7e-04
translation2415.3×4e-19
rRNA processing1614.1×8e-12
translational initiation613.4×7e-04
negative regulation of translation1012.2×2e-06
regulation of signal transduction by p53 class mediator511.9×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance22
Likely benign16
Benign2

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3233357NM_001035006.5(RPL17):c.452del (p.Thr151fs)Likely pathogenic

SpliceAI

1845 predictions. Top by Δscore:

VariantEffectΔscore
17:38850356:TCCTA:Tdonor_loss1.0000
17:38850357:CCTA:Cdonor_loss1.0000
17:38850358:CTA:Cdonor_loss1.0000
17:38850359:TA:Tdonor_loss1.0000
17:38850360:A:ATdonor_loss1.0000
17:38850361:C:Tdonor_loss1.0000
17:38850471:ATGTA:Aacceptor_gain1.0000
17:38850472:TGTA:Tacceptor_gain1.0000
17:38850473:GTA:Gacceptor_gain1.0000
17:38850474:TA:Tacceptor_gain1.0000
17:38850476:C:CCacceptor_gain1.0000
17:38850476:C:Tacceptor_loss1.0000
17:38852601:CAC:Cdonor_loss1.0000
17:38852602:A:ACdonor_gain1.0000
17:38852602:AC:Adonor_gain1.0000
17:38852602:ACC:Adonor_gain1.0000
17:38852603:C:Adonor_gain1.0000
17:38852603:C:CCdonor_gain1.0000
17:38852603:CCC:Cdonor_gain1.0000
17:38852603:CCCT:Cdonor_gain1.0000
17:38852603:CCCTT:Cdonor_gain1.0000
17:38852728:GGCTC:Gacceptor_gain1.0000
17:38852729:GCTC:Gacceptor_gain1.0000
17:38852730:CTC:Cacceptor_gain1.0000
17:38852730:CTCC:Cacceptor_gain1.0000
17:38852731:TC:Tacceptor_gain1.0000
17:38852731:TCCT:Tacceptor_gain1.0000
17:38852732:CC:Cacceptor_gain1.0000
17:38852732:CCTAC:Cacceptor_loss1.0000
17:38852733:C:CCacceptor_gain1.0000

AlphaMissense

1209 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:49489434:G:CC144W1.000
18:49489435:C:TC144Y1.000
18:49489436:A:GC144R1.000
18:49489465:C:AG134V1.000
18:49489465:C:TG134D1.000
18:49489466:C:AG134C1.000
18:49489466:C:GG134R1.000
18:49489469:G:CH133D1.000
18:49489471:G:TA132D1.000
18:49489473:T:AR131S1.000
18:49489473:T:GR131S1.000
18:49489474:C:AR131I1.000
18:49489474:C:GR131T1.000
18:49489487:G:TR127S1.000
18:49489531:A:GL112P1.000
18:49490464:G:TA102D1.000
18:49490465:C:GA102P1.000
18:49490522:A:GW83R1.000
18:49490522:A:TW83R1.000
18:49490527:C:TG81D1.000
18:49490528:C:GG81R1.000
18:49490803:C:AR69M1.000
18:49490866:A:GL48P1.000
18:49490911:G:TA33D1.000
18:49490918:C:TE31K1.000
18:49489417:A:GL150P0.999
18:49489417:A:TL150H0.999
18:49489426:T:AE147V0.999
18:49489427:C:TE147K0.999
18:49489431:G:CH145Q0.999

dbSNP variants (sampled 300 via entrez): RS1000261753 (18:49488623 G>A), RS1000314483 (18:49488255 A>T), RS1000701955 (18:49492482 A>G), RS1000813008 (18:49492437 C>A,T), RS1001163459 (18:49492530 A>T), RS1001237844 (18:49492188 C>G,T), RS1001704327 (18:49492884 A>G), RS1003263502 (18:49488658 G>A,C,T), RS1003504134 (18:49492507 A>G), RS1003669680 (18:49491177 A>G), RS1004231534 (18:49492179 A>C), RS1004393866 (18:49491018 T>C,G), RS1004461199 (18:49492014 G>A), RS1004731249 (18:49492201 C>G), RS1004788738 (18:49490658 A>G)

Disease associations

OMIM: gene MIM:603661 | disease phenotypes: MIM:209850

GenCC curated gene-disease

Mondo (5): pancytopenia (MONDO:0001529), macrocytic anemia (MONDO:0002281), fetal growth restriction (MONDO:0005030), autism (MONDO:0005260), attention deficit-hyperactivity disorder (MONDO:0007743)

Orphanet (0):

HPO phenotypes

2 total (2 of 2 shown, HPO-id order):

HPOTerm
HP:0001972Macrocytic anemia
HP:0000717Autism

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007692_2Chronic obstructive pulmonary disease1.000000e-08

MeSH disease descriptors (4)

DescriptorNameTree numbers
D000748Anemia, MacrocyticC15.378.050.252
D001321Autistic DisorderF03.625.164.113.500
D005317Fetal Growth RetardationC12.050.703.277.370; C16.300.390; C23.550.393.450
D010198PancytopeniaC15.378.243.875

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3987582 (PROTEIN NUCLEIC-ACID COMPLEX), CHEMBL6066947 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds).

MoleculeNamePhasePatents
CHEMBL6067484GENTAMICIN SULFATE4

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

ChEMBL bioactivities

48 potent at pChembl≥5 of 54 total, top 47 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.52IC50300nMCHEMBL4109308
6.42IC50380nMCHEMBL4109308
6.42IC50380nMCHEMBL4574496
6.41IC50390nMCHEMBL4126894
6.39IC50410nMCHEMBL4114159
6.35IC50450nMCHEMBL4126496
6.30IC50500nMCHEMBL4574496
6.30IC50500nMCHEMBL4560206
6.16IC50690nMCHEMBL4130157
6.15IC50710nMCHEMBL4108338
6.11IC50780nMCHEMBL4114159
6.09IC50820nMCHEMBL4109308
6.07IC50850nMCHEMBL4107559
6.07IC50850nMCHEMBL4533299
6.05IC50900nMCHEMBL4126894
6.05IC50900nMCHEMBL4126496
6.04IC50920nMCHEMBL4554909
5.97IC501060nMCHEMBL4128388
5.89IC501290nMCHEMBL4130157
5.86IC501370nMCHEMBL4107559
5.84IC501440nMCHEMBL4108338
5.81IC501540nMCHEMBL4534859
5.76IC501730nMCHEMBL4534859
5.69IC502050nMCHEMBL4566239
5.68IC502080nMCHEMBL4446635
5.66IC502210nMCHEMBL4446635
5.66EC502200nMCHEMBL4464929
5.64IC502270nMCHEMBL4533299
5.63IC502330nMCHEMBL4566239
5.62IC502380nMCHEMBL4128388
5.58IC502630nMCHEMBL4128250
5.55IC502820nMCHEMBL4127458
5.53IC502970nMCHEMBL4127311
5.51IC503080nMCHEMBL4126072
5.46IC503500nMCHEMBL4525277
5.44IC503630nMCHEMBL4469712
5.39IC504100nMCHEMBL4128560
5.37IC504300nMCHEMBL4127016
5.36IC504380nMCHEMBL4527910
5.18Kd6615nMCHEMBL3752910
5.18ED506615nMCHEMBL3752910
5.16IC507000nMCHEMBL4109308
5.13IC507400nMCHLORAMPHENICOL SULFATE SALT
5.09IC508040nMCHEMBL4128250
5.08IC508370nMCHEMBL4128250
5.03IC509320nMCHEMBL4127016
5.03IC509240nMCHEMBL4128560

PubChem BioAssay actives

47 with measured affinity, of 209 total; 27 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide1585498: Binding affinity to 80S ribosome in human HuH7 cells expressing human C-terminal V5/6-His-tagged PCSK9 assessed as inhibition of PCSK9 secretion after 16 to 24 hrs by AlphaLISA methodic500.3000uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-3-[4-(triazolo[4,5-b]pyridin-3-yl)phenyl]propanamide1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.3800uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.3900uM
N-(3-chloro-2-pyridinyl)-4-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.4100uM
N-(3-chloro-2-pyridinyl)-4-(5-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.4500uM
N-(1-methylpyrrolo[2,3-c]pyridin-7-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic500.5000uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylbenzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.6900uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-5-(triazolo[4,5-b]pyridin-3-yl)pyridine-2-carboxamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.7100uM
N-(3-chloro-2-pyridinyl)-3-[5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-2-pyridinyl]-N-[(3R)-piperidin-3-yl]propanamide1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.8500uM
N-(3-chloro-2-pyridinyl)-5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]pyridine-2-carboxamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic500.8500uM
N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylpiperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic500.9200uM
N-isoquinolin-1-yl-4-(1-methylpyrazol-4-yl)-N-[(3R)-piperidin-3-yl]benzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic501.0600uM
N-isoquinolin-1-yl-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic501.5400uM
N-(3-methyl-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic502.0500uM
N-(3-chloro-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic502.0800uM
N-(5,8-dihydroisoquinolin-1-yl)-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide1584424: Inhibition of human 80S ribosome-mediated PCSK9 translation expressed in CHO-K1 cells assessed as reduction in PCSK9 secretionec502.2000uM
N-isoquinolin-1-yl-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic502.6300uM
N-(3-chloro-2-pyridinyl)-4-(6-methylpyrazin-2-yl)-N-[(3R)-piperidin-3-yl]benzamide1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISAic502.8200uM
N-(3-chloro-2-pyridinyl)-4-[6-(dimethylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISAic502.9700uM
N-(3-chloro-2-pyridinyl)-4-[6-(methylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISAic503.0800uM
N-isoquinolin-1-yl-4-(6-methyl-1,2-benzoxazol-3-yl)-N-[(3R)-piperidin-3-yl]piperazine-1-carboxamide1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic503.5000uM
N-(3-methylpyrazin-2-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic503.6300uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-6-(triazolo[4,5-b]pyridin-3-yl)pyridine-3-carboxamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic504.1000uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazin-2-ylbenzamide1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assayic504.3000uM
4-(2-fluorophenyl)-N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assayic504.3800uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149247: Binding affinity to human RPL17 incubated for 45 mins by Kinobead based pull down assaykd6.6146uM
2,2-dichloro-N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]acetamide;sulfuric acid717551: Inhibition of mitochondrial ribosome-mediated protein synthesis in human HeLa cells assessed as {35S]methionine incorporation by autoradiographyic507.4000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases methylation, decreases expression, affects expression5
sodium arseniteincreases activity, decreases expression3
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, decreases expression3
bisphenol Fincreases expression, affects cotreatment, decreases expression2
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance2
bisphenol Sdecreases methylation, increases expression2
Arsenic Trioxidedecreases expression, increases expression2
Acroleinaffects cotreatment, increases oxidation, increases abundance2
Caffeinedecreases phosphorylation, increases expression2
Doxorubicinaffects expression, decreases expression2
Ozoneaffects cotreatment, increases oxidation, increases abundance2
Smokedecreases expression, increases abundance2
FR900359decreases phosphorylation1
TAK-243increases sumoylation1
methylmercuric chlorideincreases expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
arseniteaffects binding, increases reaction1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
perfluorooctanoic acidincreases expression1
epigallocatechin gallateincreases expression1
arsenic disulfidedecreases expression1
di-n-butylphosphoric acidaffects expression1
azoxystrobinincreases expression1
chloropicrindecreases expression1
deguelinincreases expression1
calfactantaffects cotreatment, increases expression1
fenpyroximateincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1

ChEMBL screening assays

90 unique, capped per target: 90 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1920845BindingInduction of ribosome to readthrough in human A-T lymphoblastoid cells assessed as ATM ser1981 autophosphorylation at 30 uM after 4 days by PTT-ELISA assaySynthesis and evaluation of compounds that induce readthrough of premature termination codons. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00347867PHASE4UNKNOWNViagra for the Treatment of IUGR
NCT00909974PHASE4COMPLETEDEffect of Prenatal Nutritional Supplementation on Birth Outcome in Hounde District, Burkina Faso
NCT01352234PHASE4COMPLETEDComparison of Doses of Acetylsalicylic Acid in Women With Previous History of Preeclampsia
NCT01390051PHASE4COMPLETEDCan Low Molecular Weight Heparin During Pregnancy With Intrauterine Growth Restriction Increase Birth Weight?
NCT01695070PHASE4COMPLETEDMelatonin to Prevent Brain Injury in Unborn Growth Restricted Babies
NCT03674606PHASE4COMPLETEDTrial of Early Screening Test for Pre-eclampsia and Growth Restriction
NCT04051567PHASE4UNKNOWNLow-dose Aspirin for Prevention of Adverse Pregnancy Outcomes in Twin Pregnancies
NCT05029778PHASE4UNKNOWNArginine + Citrulline as a Supplement for Weight Gain in Fetus With a Decrease in Their Growth Curve
NCT05800938PHASE4COMPLETEDThe Effect of Oral Isosorbide Mononitrate Therapy on Umbilical Artery Doppler Resistance Index in Pregnancies With Intrauterine Growth Restriction: Prospective Randomized Control Trial
NCT07171086PHASE4NOT_YET_RECRUITINGAI-POCUS for Maternal and Neonatal Health in Ethiopia
NCT00211796PHASE4COMPLETEDDivalproex Sodium ER in Adult Autism
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747PHASE4COMPLETEDMinocycline to Treat Childhood Regressive Autism
NCT00576732PHASE4COMPLETEDA Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753PHASE4COMPLETEDAtomoxetine, Placebo and Parent Management Training in Autism
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383PHASE4UNKNOWNTreatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977PHASE4UNKNOWNStudy to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925PHASE4UNKNOWNAn Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565PHASE4COMPLETEDDose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT00000597PHASE3COMPLETEDMulti-Center Trial of Anti-Thymocyte Globulin in Treatment of Aplastic Anemia and Other Hematologic Disorders