RPL23

gene
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Also known as rpL17L23uL14

Summary

RPL23 (ribosomal protein L23, HGNC:10316) is a protein-coding gene on chromosome 17q12, encoding Large ribosomal subunit protein uL14 (P62829). 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 L14P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL17 because the encoded protein shares amino acid identity with ribosomal protein L17 from Saccharomyces cerevisiae; however, its official symbol is RPL23. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.

Source: NCBI Gene 9349 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 49 total — 1 likely-pathogenic
  • Phenotypes (HPO): 54
  • 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_000978

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10316
Approved symbolRPL23
Nameribosomal protein L23
Location17q12
Locus typegene with protein product
StatusApproved
AliasesrpL17, L23, uL14
Ensembl geneENSG00000125691
Ensembl biotypeprotein_coding
OMIM603662
Entrez9349

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 15 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000245857, ENST00000378096, ENST00000394332, ENST00000394333, ENST00000470646, ENST00000479035, ENST00000577407, ENST00000577760, ENST00000584056, ENST00000584583, ENST00000584912, ENST00000716859, ENST00000716860, ENST00000716861, ENST00000716862, ENST00000716863, ENST00000716864, ENST00000716865, ENST00000716866, ENST00000929683

RefSeq mRNA: 1 — MANE Select: NM_000978 NM_000978

CCDS: CCDS11330

Canonical transcript exons

ENST00000479035 — 5 exons

ExonStartEnd
ENSE000013159893885369838853721
ENSE000019006223884786038850214
ENSE000035777303885260438852732
ENSE000035824483885302238853105
ENSE000040309153885036238850475

Expression profiles

Bgee: expression breadth ubiquitous, 210 present calls, max score 99.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2681 / max 162.8225, expressed in 1705 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
165567673.52681828
1655665.49861597
1655631.2618660
1655640.9357575
1655650.5721331

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402399.92gold quality
left ovaryUBERON:000211999.91gold quality
right ovaryUBERON:000211899.90gold quality
ventricular zoneUBERON:000305399.89gold quality
cortical plateUBERON:000534399.89gold quality
monocyteCL:000057699.86gold quality
right uterine tubeUBERON:000130299.86gold quality
endocervixUBERON:000045899.85gold quality
right lungUBERON:000216799.85gold quality
body of uterusUBERON:000985399.85gold quality
colonic epitheliumUBERON:000039799.84gold quality
left uterine tubeUBERON:000130399.84gold quality
left adrenal gland cortexUBERON:003582599.84gold quality
right adrenal gland cortexUBERON:003582799.84gold quality
right lobe of thyroid glandUBERON:000111999.83gold quality
left lobe of thyroid glandUBERON:000112099.83gold quality
right adrenal glandUBERON:000123399.83gold quality
left adrenal glandUBERON:000123499.83gold quality
skin of abdomenUBERON:000141699.83gold quality
metanephros cortexUBERON:001053399.83gold quality
ectocervixUBERON:001224999.83gold quality
granulocyteCL:000009499.82gold quality
mucosa of stomachUBERON:000119999.82gold quality
rectumUBERON:000105299.81gold quality
left coronary arteryUBERON:000162699.81gold quality
calcaneal tendonUBERON:000370199.81gold quality
olfactory segment of nasal mucosaUBERON:000538699.81gold quality
muscle layer of sigmoid colonUBERON:003580599.81gold quality
esophagogastric junction muscularis propriaUBERON:003584199.81gold quality
stromal cell of endometriumCL:000225599.80gold quality

Single-cell (SCXA)

Detected in 29 experiment(s), a significant marker in 12.

ExperimentMarker?Max mean expression
E-MTAB-8142yes173.24
E-CURD-88yes56.22
E-CURD-46yes53.09
E-GEOD-125970yes48.26
E-CURD-112yes31.68
E-HCAD-31yes25.48
E-HCAD-9yes23.39
E-MTAB-9221yes17.51
E-MTAB-10042yes14.80
E-CURD-122yes11.09
E-MTAB-9801yes5.98
E-MTAB-10596no5809.52
E-MTAB-8559no4271.59
E-MTAB-10283no4087.09
E-MTAB-11121no3882.20

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 10)

  • either RPS13 or RPL23 can promote MDR in gastric cancer cells by suppressing drug-induced apoptosis, and RPL23 may also promote MDR in gastric cancer cells through regulation of glutathione S-transferase-mediated drug-detoxifying system (PMID:15149863)
  • the MDM2-L5-L11-L23 complex functions to inhibit MDM2-mediated p53 ubiquitination and thus activates p53 (PMID:15308643)
  • These results reveal that ribosomal protein L23 is another regulator of the p53-MDM2 feedback regulation involved in cell growth. (PMID:15314173)
  • Data show that, when overexpressed, ribosomal protein L23 inhibits HDM2-induced p53 polyubiquitination and degradation and causes a p53-dependent cell cycle arrest. (PMID:15314174)
  • The ribosomal protein L23 is a negative regulator of Miz1-dependent transactivation. (PMID:19160485)
  • Increased RPL23 expression is found in patients with higher-risk myelodysplastic syndrome (MDS) than in patients with lower-risk disease. (PMID:22580751)
  • L23 is a novel oncogene in the squamous cell carcinoma of the head and neck (PMID:23160375)
  • the data presented here demonstrate that co-transduction of RPL23 enhances the therapeutic efficacy of adenoviral-mediated p53 gene transfer in models of human gastric cancer and support the use of this strategy for cancer treatment. (PMID:23933826)
  • the data presented here suggest that CEA promoter-targeted exogenous RPL23 expression could be of therapeutic value against human colorectal carcinoma that retains wt-p53. (PMID:26044651)
  • Because RPL23 is encoded by a target gene of c-Myc, the RPL23/Miz-1/c-Myc regulatory circuit provides a feedback loop that links efficient RPL23 expression with c-Myc’s function to suppress Miz-1-induced Cdk inhibitors and thereby leads to apoptotic resistance in higher-risk myelodysplastic syndrome patients (PMID:28539603)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorpl23ENSDARG00000053457
mus_musculusRpl23ENSMUSG00000071415
rattus_norvegicusLOC134480573ENSRNOG00000004107
drosophila_melanogasterRpL23FBGN0010078
caenorhabditis_elegansWBGENE00004435

Protein

Protein identifiers

Large ribosomal subunit protein uL14P62829 (reviewed: P62829)

Alternative names: 60S ribosomal protein L17, 60S ribosomal protein L23

All UniProt accessions (6): B9ZVP7, C9JD32, P62829, J3KT29, J3KTJ3, J3QQT9

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.

Similarity. Belongs to the universal ribosomal protein uL14 family.

RefSeq proteins (1): NP_000969* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000218Ribosomal_uL14Family
IPR019972Ribosomal_uL14_CSConserved_site
IPR036853Ribosomal_uL14_sfHomologous_superfamily

Pfam: PF00238

UniProt features (4 total): modified residue 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

190 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-P62829-F192.800.88

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 (2): 17, 38

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 (15): negative regulation of transcription by RNA polymerase II (GO:0000122), cytoplasmic translation (GO:0002181), translation (GO:0006412), ribosomal protein import into nucleus (GO:0006610), positive regulation of cell population proliferation (GO:0008284), protein-DNA complex disassembly (GO:0032986), protein stabilization (GO:0050821), G1 to G0 transition (GO:0070314), positive regulation of signal transduction by p53 class mediator (GO:1901798), regulation of G1 to G0 transition (GO:1903450), negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059), RNA processing (GO:0006396), positive regulation of gene expression (GO:0010628), cellular response to actinomycin D (GO:0072717), negative regulation of ubiquitin protein ligase activity (GO:1904667)

GO Molecular Function (7): transcription coactivator binding (GO:0001223), RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), ubiquitin protein ligase binding (GO:0031625), large ribosomal subunit rRNA binding (GO:0070180), ubiquitin ligase inhibitor activity (GO:1990948), protein binding (GO:0005515)

GO Cellular Component (14): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), ribosome (GO:0005840), focal adhesion (GO:0005925), membrane (GO:0016020), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), protein-containing complex (GO:0032991), synapse (GO:0045202), extracellular exosome (GO:0070062), 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
cellular anatomical structure4
gene expression2
ribosome2
nuclear lumen2
intracellular membraneless organelle2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
protein import into nucleus1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
protein-containing complex disassembly1
protein-DNA complex organization1
regulation of protein stability1
cell cycle process1
signal transduction by p53 class mediator1
regulation of signal transduction by p53 class mediator1
positive regulation of intracellular signal transduction1
regulation of cell cycle process1
G1 to G0 transition1
ubiquitin-dependent protein catabolic process1
negative regulation of protein catabolic process1
regulation of ubiquitin-dependent protein catabolic process1
RNA biosynthetic process1
primary metabolic process1
regulation of gene expression1
positive regulation of macromolecule biosynthetic process1
cellular response to antibiotic1
response to actinomycin D1
cellular response to nitrogen compound1
cellular response to oxygen-containing compound1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

421 interactions, top by confidence:

ABTypeScore
MAP3K14CHUKpsi-mi:“MI:0914”(association)0.950
BCCIPRPL23psi-mi:“MI:0915”(physical association)0.830
RPL23BCCIPpsi-mi:“MI:0915”(physical association)0.830
ARL3UNC119Bpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
DCCNTN1psi-mi:“MI:0914”(association)0.700
TUBBPLD2psi-mi:“MI:0914”(association)0.640
NCBP2KPNA3psi-mi:“MI:0914”(association)0.640
RACK1RPS17psi-mi:“MI:0915”(physical association)0.610
RPL23MDM2psi-mi:“MI:0915”(physical association)0.570
RPL5RPL23psi-mi:“MI:0915”(physical association)0.560
RPL23MEOX2psi-mi:“MI:0915”(physical association)0.560
MAPTKIF2Apsi-mi:“MI:0914”(association)0.530
TOR1AIP2TMEM223psi-mi:“MI:0914”(association)0.530
ANTXR1POTEFpsi-mi:“MI:0914”(association)0.530
CD79AMETTL15psi-mi:“MI:0914”(association)0.530
EMILIN1METTL15psi-mi:“MI:0914”(association)0.530
PCDHB16UPK3BL1psi-mi:“MI:0914”(association)0.530
LRP1NME4psi-mi:“MI:0914”(association)0.530
CDH13INSIG1psi-mi:“MI:0914”(association)0.530
ASGR2MT-CO1psi-mi:“MI:0914”(association)0.530
EIPR1LDHCpsi-mi:“MI:0914”(association)0.530

BioGRID (882): RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-Western), BCCIP (Two-hybrid), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS), RPL23 (Affinity Capture-MS)

ESM2 similar proteins: A0RM16, A1W1V5, A4IJL3, A5D5E6, A6Q1I3, A6QCQ3, A6U882, A7H107, A7H651, A7HWT4, A7HZL1, A7Z0R4, A7ZG07, A8ESU8, A8F9B1, A8FP16, B1HMV6, B1YGX6, B2UV77, B5Z8W2, B6JNF2, B7GJ93, B8F760, B9KEE5, B9L6M8, C3MB02, C5D3U3, G1T6D1, O50633, P04969, P56047, P62829, P62830, P62831, P62832, Q17ZD3, Q1CRU6, Q2RQY3, Q2W2L2, Q30TV9

Diamond homologs: A0A1D8PPT5, A0B9W0, A0RVY3, A1RRV9, A1RXG2, A2BMC9, A2SPL2, A3CT07, A3DNB7, A3MX34, A4FPL5, A4FWB1, A4WLG6, A4YCX6, A5FRY5, A5UL78, A6UQ54, A6UWU8, A6VGZ5, A7I5P9, A8ACD2, A8M8T7, A9A5I5, A9A9Q4, B0R666, B1GZ93, B1L776, B1XJS9, B3EP51, B3QR72, B7K238, B7KHZ7, B8HMR4, B9KZX7, B9LSR7, G1T6D1, O24787, O26121, O28364, O59427

SIGNOR signaling

1 interactions.

AEffectBMechanism
RPL23“form complex”“60S cytosolic large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 236 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
RIP-mediated NFkB activation via ZBP1626.5×2e-05
TRAF6 mediated NF-kB activation618.0×9e-05
TNFR1-induced NF-kappa-B signaling pathway715.5×7e-05
TNF signaling513.9×8e-04
TAK1-dependent IKK and NF-kappa-B activation611.9×4e-04
Fc epsilon receptor (FCERI) signaling58.9×4e-03
Interleukin-1 family signaling58.9×4e-03
Toll Like Receptor 3 (TLR3) Cascade78.9×5e-04

GO biological processes:

GO termPartnersFoldFDR
non-canonical NF-kappaB signal transduction730.4×2e-06
amyloid fibril formation515.5×2e-03
canonical NF-kappaB signal transduction713.2×3e-04
mRNA stabilization713.2×3e-04
tumor necrosis factor-mediated signaling pathway711.9×5e-04
intrinsic apoptotic signaling pathway611.1×2e-03
cytoplasmic translation1110.5×6e-06
obsolete positive regulation of NF-kappaB transcription factor activity77.4×6e-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

0 predictions. Top by Δscore:

AlphaMissense

892 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:38850180:A:CC125W1.000
17:38850199:C:TG119E1.000
17:38850200:C:GG119R1.000
17:38850200:C:TG119R1.000
17:38850214:C:AG114V1.000
17:38850362:C:GG114R1.000
17:38850394:C:TG103E1.000
17:38850395:C:GG103R1.000
17:38850395:C:TG103R1.000
17:38850399:A:CN101K1.000
17:38850399:A:TN101K1.000
17:38852628:C:GG68R1.000
17:38852636:A:TV65D1.000
17:38852732:C:TG33E1.000
17:38853030:T:AD30V1.000
17:38853031:C:GD30H1.000
17:38853035:A:CC28W1.000
17:38853036:C:TC28Y1.000
17:38853037:A:GC28R1.000
17:38850148:G:TA136D0.999
17:38850157:G:TA133E0.999
17:38850170:A:GW129R0.999
17:38850170:A:TW129R0.999
17:38850181:C:TC125Y0.999
17:38850182:A:GC125R0.999
17:38850185:C:TE124K0.999
17:38850193:A:TV121E0.999
17:38850205:A:TI117N0.999
17:38850214:C:TG114D0.999
17:38850362:C:AG114C0.999

dbSNP variants (sampled 300 via entrez): RS1000125424 (17:38854507 G>C), RS1000500603 (17:38854655 G>C,T), RS1001082164 (17:38855351 C>G,T), RS1001492971 (17:38855641 G>C), RS1001954447 (17:38851486 T>C), RS1001985685 (17:38851875 G>A,C), RS1002800004 (17:38851562 C>CA), RS1003108377 (17:38847552 G>GC), RS1003884779 (17:38851542 T>C), RS1003941809 (17:38851051 A>C), RS1004377081 (17:38850726 A>G), RS1004881934 (17:38852736 C>A), RS1004963868 (17:38852461 T>A,C), RS1005967110 (17:38853540 T>C), RS1006128134 (17:38848533 G>A,C)

Disease associations

OMIM: gene MIM:603662 | 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

54 total (30 of 54 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000023Inguinal hernia
HP:0000162Glossoptosis
HP:0000175Cleft palate
HP:0000201Pierre-Robin sequence
HP:0000218High palate
HP:0000272Malar flattening
HP:0000278Retrognathia
HP:0000286Epicanthus
HP:0000325Triangular face
HP:0000331Short chin
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000365Hearing impairment
HP:0000369Low-set ears
HP:0000407Sensorineural hearing impairment
HP:0000413Atresia of the external auditory canal
HP:0000717Autism
HP:0000767Pectus excavatum
HP:0001508Failure to thrive
HP:0001864Clinodactyly of the 5th toe
HP:0001873Thrombocytopenia
HP:0001875Decreased total neutrophil count
HP:0001876Pancytopenia
HP:0001882Decreased total leukocyte count
HP:0001903Anemia
HP:0001909Leukemia
HP:0001943Hypoglycemia
HP:0001945Fever
HP:0001972Macrocytic anemia

GWAS associations

2 associations (top):

StudyTraitp-value
GCST009391_2139Metabolite levels2.000000e-06
GCST90020028_1635Hip circumference adjusted for BMI2.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0010384phosphatidylcholine 38:2 measurement
EFO:0008039BMI-adjusted hip circumference

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), CHEMBL6067560 (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
5.16IC507000nMCHEMBL4109308
5.13IC507400nMCHLORAMPHENICOL SULFATE SALT
5.12Kd7501nMCHEMBL5653589
5.12ED507501nMCHEMBL5653589
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
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
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149253: Binding affinity to human RPL23 incubated for 45 mins by Kinobead based pull down assaykd7.5006uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression4
sodium arseniteaffects cotreatment, increases expression, decreases expression, increases activity3
Arsenic Trioxideincreases expression2
Tretinoinaffects cotreatment, increases expression, decreases expression2
Cadmium Chlorideincreases abundance, increases expression2
aristolochic acid Idecreases expression1
bisphenol Fincreases expression1
dicrotophosdecreases expression1
2,4,6-tribromophenoldecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
pyrogallol 1,3-dimethyl etherincreases expression, affects localization, affects cotreatment1
decabromobiphenyl etherdecreases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
tetrabromobisphenol Adecreases expression1
nickel sulfatedecreases expression1
chloropicrinaffects expression1
perfluoro-n-nonanoic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
2-amino-14,16-dimethyloctadecan-3-oldecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol Sincreases expression1

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