RPL9

gene
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Also known as L9uL6

Summary

RPL9 (ribosomal protein L9, HGNC:10369) is a protein-coding gene on chromosome 4p14, encoding Large ribosomal subunit protein uL6 (P32969). 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 L6P family of ribosomal proteins. It is located in the cytoplasm. 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.

Source: NCBI Gene 6133 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Diamond-Blackfan anemia (Moderate, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 111 total
  • Phenotypes (HPO): 59
  • 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_000661

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10369
Approved symbolRPL9
Nameribosomal protein L9
Location4p14
Locus typegene with protein product
StatusApproved
AliasesL9, uL6
Ensembl geneENSG00000163682
Ensembl biotypeprotein_coding
OMIM603686
Entrez6133

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 26 protein_coding, 8 retained_intron

ENST00000295955, ENST00000437992, ENST00000449470, ENST00000503040, ENST00000503277, ENST00000506581, ENST00000508595, ENST00000511075, ENST00000511643, ENST00000514842, ENST00000642337, ENST00000644328, ENST00000645496, ENST00000645585, ENST00000645894, ENST00000894374, ENST00000894375, ENST00000894376, ENST00000894377, ENST00000894378, ENST00000894379, ENST00000894380, ENST00000928672, ENST00000928673, ENST00000928674, ENST00000928675, ENST00000928676, ENST00000928677, ENST00000928678, ENST00000928679, ENST00000928680, ENST00000928681, ENST00000928682, ENST00000961349

RefSeq mRNA: 2 — MANE Select: NM_000661 NM_000661, NM_001024921

CCDS: CCDS3452

Canonical transcript exons

ENST00000295955 — 8 exons

ExonStartEnd
ENSE000018636243945412439454225
ENSE000020213283945889139458922
ENSE000035950553945640639456538
ENSE000036117803945453339454649
ENSE000036327823945486439454944
ENSE000036359003945819439458309
ENSE000036710953945758639457681
ENSE000036744663945839439458440

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 99.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 60.3353 / max 731.2733, expressed in 1823 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
5184553.79611819
518443.17411442
518431.8753962
518421.4898992

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.86gold quality
left ovaryUBERON:000211999.85gold quality
right ovaryUBERON:000211899.84gold quality
embryoUBERON:000092299.83gold quality
ovaryUBERON:000099299.83gold quality
mucosa of stomachUBERON:000119999.83gold quality
right uterine tubeUBERON:000130299.83gold quality
calcaneal tendonUBERON:000370199.83gold quality
ganglionic eminenceUBERON:000402399.83gold quality
thoracic mammary glandUBERON:000520099.83gold quality
gall bladderUBERON:000211099.82gold quality
corpus callosumUBERON:000233699.82gold quality
olfactory segment of nasal mucosaUBERON:000538699.82gold quality
endometriumUBERON:000129599.81gold quality
adenohypophysisUBERON:000219699.81gold quality
body of uterusUBERON:000985399.81gold quality
islet of LangerhansUBERON:000000699.80gold quality
colonic epitheliumUBERON:000039799.80gold quality
uterusUBERON:000099599.80gold quality
granulocyteCL:000009499.79gold quality
body of pancreasUBERON:000115099.79gold quality
lower esophagus mucosaUBERON:003583499.79gold quality
uterine cervixUBERON:000000299.78gold quality
pituitary glandUBERON:000000799.78gold quality
endocervixUBERON:000045899.78gold quality
pancreasUBERON:000126499.78gold quality
myometriumUBERON:000129699.78gold quality
right lungUBERON:000216799.78gold quality
prostate glandUBERON:000236799.78gold quality
omental fat padUBERON:001041499.78gold quality

Single-cell (SCXA)

Detected in 43 experiment(s), a significant marker in 24.

ExperimentMarker?Max mean expression
E-GEOD-139324yes5311.94
E-MTAB-6653yes4306.82
E-HCAD-36yes3948.24
E-MTAB-9467yes3040.47
E-MTAB-8559yes2815.93
E-MTAB-8894yes2581.18
E-HCAD-5yes2378.74
E-MTAB-8221yes2324.96
E-MTAB-6701yes2310.81
E-CURD-88yes2266.36
E-CURD-7yes1003.89
E-MTAB-8142yes119.15
E-MTAB-8410yes40.93
E-HCAD-1yes38.87
E-MTAB-6678yes35.42

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

14 targeting RPL9, 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-513B-5P99.9969.962150
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-569699.9872.364487
HSA-MIR-137-3P99.8774.742401
HSA-MIR-445798.0967.121274
HSA-MIR-493-3P97.5066.44731
HSA-MIR-313797.2666.78761
HSA-MIR-125B-2-3P96.6968.381210
HSA-MIR-6826-5P93.8067.42514

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 7)

  • The authors propose that during rabies virus infection, viral phosphoprotein P binds to ribosomal protein L9 that translocates from the nucleus to the cytoplasm, inhibiting the initial stage of viral transcription. (PMID:26655239)
  • High RPL9 expression is associated with colorectal carcinoma. (PMID:27633352)
  • UNR could bind to the 3’UTR of PTEN and RPL9 in glioma cell lines, therefore promoting glioma cell migration and regulating the expression of RPL9. (PMID:30266104)
  • Here we report an individual diagnosed with DBA carrying a variant in the 5’UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant (PMID:31799629)
  • Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9. (PMID:33576138)
  • Genetic Variants of RPL5 and RPL9 Genes among Saudi Patients Diagnosed with Thrombosis. (PMID:34483448)
  • RPL9 acts as an oncogene by shuttling miRNAs through exosomes in human hepatocellular carcinoma cells. (PMID:38639179)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorpl9ENSDARG00000037350
rattus_norvegicusAABR07026048.1ENSRNOG00000031879
drosophila_melanogasterRpL9FBGN0015756
caenorhabditis_elegansWBGENE00004420

Protein

Protein identifiers

Large ribosomal subunit protein uL6P32969 (reviewed: P32969)

Alternative names: 60S ribosomal protein L9

All UniProt accessions (6): A0A2R8Y5Y7, D6RAN4, P32969, H0Y9R4, H0Y9V9, Q53Z07

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 uL6 family.

RefSeq proteins (2): NP_000652, NP_001020092 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000702Ribosomal_uL6-likeFamily
IPR002359Ribosomal_uL6_CS2Conserved_site
IPR020040Ribosomal_uL6_a/b-domDomain
IPR036789Ribosomal_uL6-like_a/b-dom_sfHomologous_superfamily

Pfam: PF00347

UniProt features (12 total): strand 8, chain 1, modified residue 1, helix 1, sequence conflict 1

Structure

Experimental structures (PDB)

193 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-P32969-F194.110.93

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 (1): 121

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: 367 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, MODULE_151, GNF2_TPT1, GCM_NPM1, MORF_UBE2I, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_MUSCLE_CONTRACTION, GOBP_REGULATION_OF_SYNCYTIUM_FORMATION_BY_PLASMA_MEMBRANE_FUSION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GNF2_FBL, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS

GO Biological Process (2): cytoplasmic translation (GO:0002181), translation (GO:0006412)

GO Molecular Function (4): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), rRNA binding (GO:0019843), protein binding (GO:0005515)

GO Cellular Component (9): nucleus (GO:0005634), 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), 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 structure3
ribosome2
translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
nucleic acid binding1
structural molecule activity1
RNA binding1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
intracellular membraneless organelle1
cell-substrate junction1
large ribosomal subunit1
cytosolic ribosome1
cytosol1
protein-containing complex1

Protein interactions and networks

STRING

4813 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPL9RPS25P25111818
RPL9RPL21P46778803
RPL9RPL4P36578797
RPL9RPS5P46782787
RPL9RPL14P50914784
RPL9RPL19P14118771
RPL9RPL7P18124771
RPL9RPS3P23396770
RPL9RPS20P17075767
RPL9ACADMP11310763
RPL9RPL30P04645763
RPL9RPL5P46777758
RPL9RPL8P25120754
RPL9RPL11P25121743
RPL9RPS23P39028740

IntAct

280 interactions, top by confidence:

ABTypeScore
MAP3K14CHUKpsi-mi:“MI:0914”(association)0.950
RPL9DHPSpsi-mi:“MI:0915”(physical association)0.870
DHPSRPL9psi-mi:“MI:0915”(physical association)0.870
RPL9DHPSpsi-mi:“MI:0914”(association)0.870
CEP76RPL9psi-mi:“MI:0915”(physical association)0.830
RPL9CEP76psi-mi:“MI:0915”(physical association)0.830
RPL9VCPpsi-mi:“MI:0915”(physical association)0.780
CCDC184RPL9psi-mi:“MI:0915”(physical association)0.720
HMBOX1RPL9psi-mi:“MI:0915”(physical association)0.720
RPL9ZBTB8Apsi-mi:“MI:0915”(physical association)0.720
RPL9TIFApsi-mi:“MI:0915”(physical association)0.720
RPL9PNMA2psi-mi:“MI:0915”(physical association)0.720
ZBTB8ARPL9psi-mi:“MI:0915”(physical association)0.720
TIFARPL9psi-mi:“MI:0915”(physical association)0.720
PNMA2RPL9psi-mi:“MI:0915”(physical association)0.720

BioGRID (691): RPL9 (Affinity Capture-MS), RPL9 (Two-hybrid), RPL9 (Two-hybrid), VCP (Two-hybrid), ZBTB14 (Two-hybrid), CALCOCO2 (Two-hybrid), PNMA2 (Two-hybrid), MTUS2 (Two-hybrid), ZBTB7B (Two-hybrid), HOMEZ (Two-hybrid), KXD1 (Two-hybrid), HMBOX1 (Two-hybrid), CEP76 (Two-hybrid), TIFA (Two-hybrid), FAM9B (Two-hybrid)

ESM2 similar proteins: A5IHP9, A6KYI0, A7ZFZ7, A8EZK1, A8F4S6, B0B888, B0BCF3, B2RLX7, B3EUK8, B8HMR8, G1SWI6, O74905, P05738, P0CE01, P17077, P30707, P32969, P49209, P49210, P50882, P51401, P51410, Q09865, Q10232, Q11QC7, Q1CRV6, Q1D760, Q1MPQ0, Q22AX5, Q3KLI3, Q3SYR7, Q54XI5, Q5AEN2, Q5IFJ7, Q5L8C4, Q5R9Q7, Q5WZJ7, Q5X844, Q64NM3, Q7MTM8

Diamond homologs: A0B9V4, A2BMD5, A3DNC3, A4FWA5, A4XLR5, A5IM98, A5UL72, A5WCK5, A6UQ60, A6UWV4, A6VH01, A7Z0Q3, A8AC04, A9A9P8, B0K5Q8, B1LBM5, B2A4F4, B5ELZ4, B6YSN0, B7J482, B8D0D9, B8D5V4, B8DB23, B8GV43, B9K8A1, B9MKG6, C5A269, C5CC48, G1SWI6, O02376, O05637, O26127, O28370, O59433, O74905, P05738, P14030, P14135, P17077, P30707

SIGNOR signaling

1 interactions.

AEffectBMechanism
RPL9“form complex”“60S cytosolic large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 116 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
SARS-CoV-2 modulates host translation machinery515.6×4e-04
Formation of a pool of free 40S subunits812.4×5e-05
Peptide chain elongation712.3×1e-04
Viral mRNA Translation712.3×1e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA712.2×1e-04
Selenocysteine synthesis711.7×1e-04
Eukaryotic Translation Termination711.7×1e-04
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)711.4×1e-04

GO biological processes:

GO termPartnersFoldFDR
mRNA stabilization518.7×2e-03
cytoplasmic translation917.0×2e-06
translation1010.5×1e-05
rRNA processing68.7×6e-03
RNA splicing76.3×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance48
Likely benign46
Benign11

Top pathogenic / likely-pathogenic (0)

SpliceAI

688 predictions. Top by Δscore:

VariantEffectΔscore
4:39454221:GGTAA:Gacceptor_gain1.0000
4:39454222:GTAA:Gacceptor_gain1.0000
4:39454223:TAA:Tacceptor_gain1.0000
4:39454224:AA:Aacceptor_gain1.0000
4:39454224:AACT:Aacceptor_loss1.0000
4:39454225:AC:Aacceptor_loss1.0000
4:39454226:C:CCacceptor_gain1.0000
4:39454226:CT:Cacceptor_loss1.0000
4:39454528:CTTA:Cdonor_loss1.0000
4:39454529:TTAC:Tdonor_loss1.0000
4:39454530:TACC:Tdonor_loss1.0000
4:39454531:A:ACdonor_gain1.0000
4:39454531:AC:Adonor_gain1.0000
4:39454531:ACCT:Adonor_gain1.0000
4:39454532:C:CAdonor_gain1.0000
4:39454532:CC:Cdonor_gain1.0000
4:39454532:CCT:Cdonor_gain1.0000
4:39454532:CCTC:Cdonor_gain1.0000
4:39454532:CCTCT:Cdonor_gain1.0000
4:39454645:AGCCG:Aacceptor_gain1.0000
4:39454646:GCCG:Gacceptor_gain1.0000
4:39454647:CCG:Cacceptor_gain1.0000
4:39454647:CCGC:Cacceptor_gain1.0000
4:39454647:CCGCT:Cacceptor_gain1.0000
4:39454648:CG:Cacceptor_gain1.0000
4:39454648:CGCTA:Cacceptor_gain1.0000
4:39454650:C:CAacceptor_loss1.0000
4:39454650:C:CCacceptor_gain1.0000
4:39454652:A:ACacceptor_gain1.0000
4:39454652:A:Cacceptor_gain1.0000

AlphaMissense

1259 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:39454589:C:TG178D1.000
4:39454590:C:GG178R1.000
4:39454591:A:CD177E1.000
4:39454591:A:TD177E1.000
4:39454592:T:AD177V1.000
4:39454593:C:GD177H1.000
4:39454597:A:CF175L1.000
4:39454597:A:TF175L1.000
4:39454598:A:CF175C1.000
4:39454598:A:GF175S1.000
4:39454599:A:GF175L1.000
4:39454603:C:AR173S1.000
4:39454603:C:GR173S1.000
4:39454604:C:AR173M1.000
4:39454604:C:GR173T1.000
4:39454610:T:AD171V1.000
4:39454611:C:GD171H1.000
4:39454612:C:AK170N1.000
4:39454612:C:GK170N1.000
4:39456441:C:AG119V1.000
4:39456441:C:TG119D1.000
4:39456446:G:CF117L1.000
4:39456446:G:TF117L1.000
4:39456448:A:GF117L1.000
4:39456500:G:CF99L1.000
4:39456500:G:TF99L1.000
4:39456501:A:CF99C1.000
4:39456501:A:GF99S1.000
4:39456502:A:CF99V1.000
4:39456502:A:GF99L1.000

dbSNP variants (sampled 300 via entrez): RS1000123042 (4:39460427 A>G,T), RS1000173649 (4:39460587 A>G), RS1000334101 (4:39455710 C>T), RS1000669423 (4:39456838 A>G), RS1001021701 (4:39456707 T>A,C), RS1001058677 (4:39457117 T>A,C), RS1001112046 (4:39457330 A>AAG), RS1001670616 (4:39454853 A>C), RS1001966949 (4:39459625 G>C), RS1002114507 (4:39456009 G>A), RS10025155 (4:39455015 T>C), RS1002902444 (4:39459209 A>C,G), RS1004772202 (4:39459458 A>G), RS1004864084 (4:39459779 G>A), RS1005864202 (4:39458893 C>A,G,T)

Disease associations

OMIM: gene MIM:603686 | disease phenotypes: MIM:105650

GenCC curated gene-disease

DiseaseClassificationInheritance
Diamond-Blackfan anemiaModerateAutosomal dominant

Mondo (1): Diamond-Blackfan anemia (MONDO:0015253)

Orphanet (1): Diamond-Blackfan anemia (Orphanet:124)

HPO phenotypes

59 total (30 of 59 shown, HPO-id order):

HPOTerm
HP:0000047Hypospadias
HP:0000085Horseshoe kidney
HP:0000104Renal agenesis
HP:0000119Abnormality of the genitourinary system
HP:0000185Cleft soft palate
HP:0000218High palate
HP:0000234Abnormality of the head
HP:0000252Microcephaly
HP:0000286Epicanthus
HP:0000294Low anterior hairline
HP:0000316Hypertelorism
HP:0000347Micrognathia
HP:0000369Low-set ears
HP:0000431Wide nasal bridge
HP:0000465Webbed neck
HP:0000470Short neck
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000519Developmental cataract
HP:0000912Sprengel anomaly
HP:0000980Pallor
HP:0001087Developmental glaucoma
HP:0001199Triphalangeal thumb
HP:0001227Abnormality of the thenar eminence
HP:0001254Lethargy
HP:0001510Growth delay
HP:0001518Small for gestational age
HP:0001627Abnormal heart morphology
HP:0001629Ventricular septal defect
HP:0001631Atrial septal defect

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007328_35Alcohol consumption (drinks per week)2.000000e-10

MeSH disease descriptors (1)

DescriptorNameTree numbers
D029503Anemia, Diamond-BlackfanC15.378.050.085.080.090; C15.378.050.750.500; C15.378.190.223.500.500.090; C16.320.077.090

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3987582 (PROTEIN NUCLEIC-ACID COMPLEX), CHEMBL6066916 (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

50 potent at pChembl≥5 of 54 total, top 49 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
5.89Kd1273nMCHEMBL3752910
5.89ED501273nMCHEMBL3752910
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
5.28Kd5231nMCHEMBL5653589
5.28ED505231nMCHEMBL5653589
5.16IC507000nMCHEMBL4109308
5.13IC507400nMCHLORAMPHENICOL SULFATE SALT
5.09IC508040nMCHEMBL4128250
5.08IC508370nMCHEMBL4128250
5.03IC509320nMCHEMBL4127016
5.03IC509240nMCHEMBL4128560

PubChem BioAssay actives

48 with measured affinity, of 209 total; 28 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
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149276: Binding affinity to human RPL9 incubated for 45 mins by Kinobead based pull down assaykd1.2731uM
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-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149276: Binding affinity to human RPL9 incubated for 45 mins by Kinobead based pull down assaykd5.2306uM
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

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression3
sodium arseniteincreases abundance, increases expression, decreases expression3
Air Pollutantsincreases abundance, increases expression, decreases expression, affects cotreatment3
Smokedecreases expression, increases abundance2
Particulate Matterincreases abundance, increases expression, decreases expression2
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
titanium dioxideincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, decreases reaction1
methylparabenincreases expression1
ochratoxin Aincreases expression1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
beta-methylcholineaffects expression1
azoxystrobinincreases expression1
CGP 52608affects binding, increases reaction1
chloropicrinaffects expression1
deguelinincreases expression1
fenpyroximateincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
pyrimidifenincreases expression1
abrinedecreases expression1
pyrachlostrobinincreases expression1
LDN 193189affects cotreatment, decreases expression1
picoxystrobinincreases expression1
nabiximolsincreases expression1
Sunitinibincreases expression1
Arsenic Trioxidedecreases 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)

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

TrialPhaseStatusTitle
NCT00673608PHASE4COMPLETEDMagnetic Resonance Imaging (MRI) Assessments of the Heart and Liver Iron Load in Patients With Transfusion Induced Iron Overload
NCT00235391PHASE3COMPLETEDExpanded Access of Deferasirox to Patients With Congenital Disorders of Red Blood Cells and Chronic Iron Overload
NCT00001962PHASE2TERMINATEDA Study to Determine Whether Therapy With Daclizumab Will Benefit Patients With Bone Marrow Failure
NCT00011505PHASE2COMPLETEDMobilization of Stem Cells With G-CSF for Collection From Patients With Diamond-Blackfan Anemia
NCT00301834PHASE2COMPLETEDAlemtuzumab, Fludarabine, and Busulfan Followed By Donor Stem Cell Transplant in Treating Young Patients With Hematologic Disorders
NCT00957931PHASE2COMPLETEDAllo-HCT MUD for Non-malignant Red Blood Cell (RBC) Disorders: Sickle Cell, Thal, and DBA: Reduced Intensity Conditioning, Co-tx MSCs
NCT01529827PHASE2COMPLETEDFludarabine Phosphate, Melphalan, and Low-Dose Total-Body Irradiation Followed by Donor Peripheral Blood Stem Cell Transplant in Treating Patients With Hematologic Malignancies
NCT02386267PHASE2UNKNOWNL-leucine in Diamond Blackfan Anemia Patients
NCT02512679PHASE2TERMINATEDRelated Hematopoietic Stem Cell Transplantation (HSCT) for Genetic Diseases of Blood Cells
NCT03333486PHASE2TERMINATEDFludarabine Phosphate, Cyclophosphamide, Total Body Irradiation, and Donor Stem Cell Transplant in Treating Patients With Blood Cancer
NCT04099966PHASE2RECRUITINGAlloSCT for Malignant and Non-malignant Hematologic Diseases Utilizing Alpha/Beta T Cell and CD19+ B Cell Depletion
NCT04965597PHASE2COMPLETEDTreosulfan-Based Conditioning Regimen Before a Blood or Bone Marrow Transplant for the Treatment of Bone Marrow Failure Diseases (BMT CTN 1904)
NCT01586455PHASE1COMPLETEDHuman Placental-Derived Stem Cell Transplantation
NCT01917708PHASE1COMPLETEDBone Marrow Transplant With Abatacept for Non-Malignant Diseases
NCT00176852PHASE2/PHASE3COMPLETEDStem Cell Transplant for Hemoglobinopathy
NCT00176878PHASE2/PHASE3COMPLETEDStem Cell Transplant for Bone Marrow Failure Syndromes
NCT00305708PHASE1/PHASE2COMPLETEDBusulfan, Antithymocyte Globulin, and Fludarabine Followed By a Donor Stem Cell Transplant in Treating Young Patients With Blood Disorders, Bone Marrow Disorders, Chronic Myelogenous Leukemia in First Chronic Phase, or Acute Myeloid Leukemia in First Remission
NCT01362595PHASE1/PHASE2COMPLETEDPilot Phase I/II Study of Amino Acid Leucine in Treatment of Patients With Transfusion-Dependent Diamond Blackfan Anemia
NCT01419704PHASE1/PHASE2WITHDRAWNPhase I/II Pilot Study of Mixed Chimerism to Treat Hemoglobinopathies
NCT01464164PHASE1/PHASE2TERMINATEDSafety and Efficacy Study of Sotatercept in Adults With Transfusion Dependent Diamond Blackfan Anemia
NCT01966367PHASE1/PHASE2ACTIVE_NOT_RECRUITINGCD34+ (Non-Malignant) Stem Cell Selection for Patients Receiving Allogeneic Stem Cell Transplantation
NCT02065869PHASE1/PHASE2TERMINATEDSafety Study of Gene Modified Donor T-cells Following TCRαβ+ Depleted Stem Cell Transplant
NCT03513328PHASE1/PHASE2COMPLETEDConditioning Regimen for Allogeneic Hematopoietic Stem-Cell Transplantation
NCT03653338PHASE1/PHASE2RECRUITINGT-Cell Depleted Alternative Donor Bone Marrow Transplant for Sickle Cell Disease (SCD) and Other Anemias
NCT03733249PHASE1/PHASE2TERMINATEDLong Term Follow-up Study for Patients Enrolled on the BP-004 Clinical Study
NCT03966053PHASE1/PHASE2TERMINATEDThe Use of Trifluoperazine in Transfusion Dependent DBA
NCT00027274Not specifiedRECRUITINGCancer in Inherited Bone Marrow Failure Syndromes
NCT00244010Not specifiedCOMPLETEDPartially Matched Stem Cell Transplantation for Patients With Refractory Severe Aplastic Anemia or Refractory Cytopenias
NCT00290628Not specifiedTERMINATEDDonor Umbilical Cord Blood Transplant in Treating Patients With Hematologic Cancer
NCT01114776Not specifiedCOMPLETEDMulti-Center Study of Iron Overload: Pilot Study
NCT01319851Not specifiedTERMINATEDAlefacept and Allogeneic Hematopoietic Stem Cell Transplantation
NCT01758042Not specifiedCOMPLETEDBone Marrow and Kidney Transplant for Patients With Chronic Kidney Disease and Blood Disorders
NCT01913548Not specifiedCOMPLETEDMulti-Center Study of Iron Overload: Survey Study (MCSIO)
NCT02179359Not specifiedTERMINATEDHematopoietic Stem Cell Transplant for High Risk Hemoglobinopathies
NCT02720679Not specifiedRECRUITINGInvestigation of the Genetics of Hematologic Diseases
NCT03050268Not specifiedRECRUITINGFamilial Investigations of Childhood Cancer Predisposition
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT07186179Not specifiedRECRUITINGMobilization of CD34+ Peripheral Blood Stem Cells in Patients With Diamond Blackfan Anemia Syndrome (DBAS)