RPL8

gene
On this page

Also known as L8uL2

Summary

RPL8 (ribosomal protein L8, HGNC:10368) is a protein-coding gene on chromosome 8q24.3, encoding Large ribosomal subunit protein uL2 (P62917). 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 L2P family of ribosomal proteins. It is located in the cytoplasm. In rat, the protein associates with the 5.8S rRNA, very likely participates in the binding of aminoacyl-tRNA, and is a constituent of the elongation factor 2-binding site at the ribosomal subunit interface. Alternatively spliced transcript variants encoding the same protein exist. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.

Source: NCBI Gene 6132 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Diamond-Blackfan anemia (Moderate, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 36 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_001317782

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10368
Approved symbolRPL8
Nameribosomal protein L8
Location8q24.3
Locus typegene with protein product
StatusApproved
AliasesL8, uL2
Ensembl geneENSG00000161016
Ensembl biotypeprotein_coding
OMIM604177
Entrez6132

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 7 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000262584, ENST00000394920, ENST00000525232, ENST00000526668, ENST00000527914, ENST00000528296, ENST00000528957, ENST00000529163, ENST00000529920, ENST00000531767, ENST00000531975, ENST00000532702, ENST00000533397, ENST00000534781, ENST00000913745

RefSeq mRNA: 4 — MANE Select: NM_001317782 NM_000973, NM_001317771, NM_001317782, NM_033301

CCDS: CCDS6433

Canonical transcript exons

ENST00000528957 — 5 exons

ExonStartEnd
ENSE00001131931144791773144791914
ENSE00002196410144791992144792390
ENSE00003575507144789769144789962
ENSE00003686489144791277144791495
ENSE00003789859144790355144790470

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 99.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 834.0082 / max 3723.8383, expressed in 1828 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
95719815.38781828
9571812.83721744
957173.55231442
957162.23091140

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endometrium epitheliumUBERON:000481199.92gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099199.88gold quality
ovaryUBERON:000099299.88gold quality
right ovaryUBERON:000211899.88gold quality
left ovaryUBERON:000211999.88gold quality
tracheaUBERON:000312699.88gold quality
thymusUBERON:000237099.87gold quality
mucosa of transverse colonUBERON:000499199.87gold quality
pituitary glandUBERON:000000799.86gold quality
zone of skinUBERON:000001499.86gold quality
skin of abdomenUBERON:000141699.86gold quality
skin of legUBERON:000151199.86gold quality
ventricular zoneUBERON:000305399.86gold quality
stromal cell of endometriumCL:000225599.85gold quality
endocervixUBERON:000045899.85gold quality
right uterine tubeUBERON:000130299.85gold quality
adenohypophysisUBERON:000219699.85gold quality
fallopian tubeUBERON:000388999.85gold quality
ganglionic eminenceUBERON:000402399.85gold quality
olfactory segment of nasal mucosaUBERON:000538699.85gold quality
body of uterusUBERON:000985399.85gold quality
lower esophagus mucosaUBERON:003583499.85gold quality
vermiform appendixUBERON:000115499.84gold quality
fundus of stomachUBERON:000116099.84gold quality
placentaUBERON:000198799.84gold quality
apex of heartUBERON:000209899.84gold quality
prostate glandUBERON:000236799.84gold quality
ectocervixUBERON:001224999.84gold quality
uterine cervixUBERON:000000299.83gold quality
right lobe of thyroid glandUBERON:000111999.83gold quality

Single-cell (SCXA)

Detected in 27 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-10042yes6226.18
E-CURD-122yes95.08
E-HCAD-9yes24.29
E-MTAB-9221yes21.45
E-MTAB-9543yes18.69
E-HCAD-35yes9.51
E-MTAB-9801yes7.67
E-MTAB-6653no8111.16
E-MTAB-8559no7271.47
E-MTAB-8410no7155.00
E-CURD-98no6928.13
E-CURD-55no6564.41
E-MTAB-8142no6519.31
E-MTAB-7606no5749.40
E-MTAB-11121no5129.16

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 5)

  • gain of RPL8 is associated with good response to chemotherapy in conventional osteosarcomas. (PMID:19449377)
  • Report dysregulated expression of RPL8 in disc degeneration. (PMID:25893343)
  • confirmed the hydroxylase activity of NO66 and showed that oligomerization is required for NO66 to efficiently catalyze the hydroxylation of Rpl8 (PMID:26327385)
  • Integrative Multi-Omics Analysis of Identified Ferroptosis-Marker RPL8 as a Candidate Oncogene Correlates with Poor Prognosis and Immune Infiltration in Liver Cancer. (PMID:36017842)
  • Silencing RPL8 inhibits the progression of hepatocellular carcinoma by down-regulating the mTORC1 signalling pathway. (PMID:36577883)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorpl8ENSDARG00000014867
mus_musculusRpl8ENSMUSG00000003970
rattus_norvegicusAC129049.1ENSRNOG00000031381
drosophila_melanogasterRpL8FBGN0261602
caenorhabditis_elegansWBGENE00004413

Paralogs (1): MRPL2 (ENSG00000112651)

Protein

Protein identifiers

Large ribosomal subunit protein uL2P62917 (reviewed: P62917)

Alternative names: 60S ribosomal protein L8

All UniProt accessions (6): P62917, E9PKU4, E9PKZ0, E9PP36, G3V1A1, H0YF23

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. Interacts with CRY1.

Subcellular location. Cytoplasm.

Post-translational modifications. Hydroxylated on His-216 by RIOX1. The modification is impaired by hypoxia.

Miscellaneous. This protein can be partially incorporated into E.coli polysomes in vivo, indicating it can replace the endogenous protein.

Similarity. Belongs to the universal ribosomal protein uL2 family.

RefSeq proteins (4): NP_000964, NP_001304700, NP_001304711, NP_150644 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002171Ribosomal_uL2Family
IPR008991Translation_prot_SH3-like_sfHomologous_superfamily
IPR012340NA-bd_OB-foldHomologous_superfamily
IPR014722Rib_uL2_dom2Homologous_superfamily
IPR014726Ribosomal_uL2_dom3Homologous_superfamily
IPR022666Ribosomal_uL2_RNA-bd_domDomain
IPR022669Ribosomal_uL2_CDomain
IPR022671Ribosomal_uL2_CSConserved_site
IPR023672Ribosomal_uL2_arc_eukFamily

Pfam: PF00181, PF03947

UniProt features (10 total): cross-link 4, initiator methionine 1, chain 1, region of interest 1, modified residue 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

181 structures, top 30 by resolution.

PDBMethodResolution (Å)
8A3DELECTRON MICROSCOPY1.67
8QYXELECTRON MICROSCOPY1.78
8QOIELECTRON MICROSCOPY1.9
9O3WELECTRON MICROSCOPY1.9
8YOOELECTRON MICROSCOPY2
9C3HELECTRON MICROSCOPY2
9I2DELECTRON MICROSCOPY2.19
9PBEELECTRON MICROSCOPY2.19
4Y3OX-RAY DIFFRACTION2.2
8QFDELECTRON MICROSCOPY2.2
8YOPELECTRON MICROSCOPY2.2
9GULELECTRON MICROSCOPY2.2
9O3VELECTRON MICROSCOPY2.2
9O3YELECTRON MICROSCOPY2.2
4CCNX-RAY DIFFRACTION2.23
8JDKELECTRON MICROSCOPY2.26
4CCOX-RAY DIFFRACTION2.3
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
9QLOELECTRON MICROSCOPY2.47
8FLEELECTRON MICROSCOPY2.48
9P8BELECTRON MICROSCOPY2.48

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P62917-F195.220.94

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 (5): 216, 42, 149, 234, 250

Mutagenesis-validated functional residues (1):

PositionPhenotype
209no incorporation into translating e.coli polysomes; ribosomes assembled normally. significantly reduced translational ac

Function

Pathways and Gene Ontology

Reactome pathways

17 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-9629569Protein hydroxylation
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: 360 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_CYTOPLASMIC_TRANSLATION, SWEET_KRAS_ONCOGENIC_SIGNATURE, XU_GH1_AUTOCRINE_TARGETS_UP, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, HSIAO_HOUSEKEEPING_GENES, GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION

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 (13): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), focal adhesion (GO:0005925), postsynaptic density (GO:0014069), membrane (GO:0016020), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), postsynapse (GO:0098794), ribosome (GO:0005840), large ribosomal subunit (GO:0015934), synapse (GO:0045202), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-12 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
Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation1
Cellular response to starvation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
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
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
cell-substrate junction1
asymmetric synapse1
postsynaptic specialization1
large ribosomal subunit1
cytosolic ribosome1
cytosol1
synapse1
intracellular membraneless organelle1
ribosomal subunit1
cell junction1
protein-containing complex1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

335 interactions, top by confidence:

ABTypeScore
MAP3K14CHUKpsi-mi:“MI:0914”(association)0.950
PPP1CCCCDC85Cpsi-mi:“MI:0914”(association)0.740
PPP1CCCCDC85Cpsi-mi:“MI:2364”(proximity)0.740
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
XPCCETN3psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
FAM90A1KPNA3psi-mi:“MI:0914”(association)0.670
RACK1RPS17psi-mi:“MI:0915”(physical association)0.610
NOM1RPLP0psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
RPL8RRP8psi-mi:“MI:0914”(association)0.530
DDX6MCRIP1psi-mi:“MI:0914”(association)0.510
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480

BioGRID (860): RPL8 (Affinity Capture-MS), RPL8 (Affinity Capture-MS), RPL8 (Affinity Capture-MS), RPL8 (Affinity Capture-MS), RPL8 (Affinity Capture-MS), RPL8 (Biochemical Activity), RPL8 (Affinity Capture-MS), RPL8 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), RPLP2 (Affinity Capture-MS), RPL4 (Affinity Capture-MS), CCDC137 (Affinity Capture-MS), RBM28 (Affinity Capture-MS), POP1 (Affinity Capture-MS), DDX24 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D8PF08, A0RZ09, A1RWQ7, A4YCW9, A8AC70, A8ME99, A9A141, B1L707, C3MQ62, C3MVI1, C3N5T0, C3NEE6, C3NHA6, C4KHF9, G1TT27, O15574, P0CT70, P0CT71, P0CT72, P0CX45, P0CX46, P0DJ52, P13023, P25998, P29766, P41116, P41569, P46286, P60408, P62917, P62918, P62919, Q3T0S6, Q42064, Q4JB43, Q4PSL7, Q5R7Y8, Q6FPN7, Q6L1C4, Q6P0V6

Diamond homologs: A0A1D8PF08, A0B9W7, A0RZ09, A1RTI4, A1RWQ7, A2BMB2, A2SPK6, A3CT00, A3DNA7, A3MS41, A4FVX9, A4WH02, A4YCW9, A5UL86, A6UQJ3, A6UV65, A6VHD5, A7I5P2, A8AC70, A8ME99, A9A141, A9A9B5, A9W4Q4, B0R659, B1L707, B1YA33, B1ZLK7, B6YSL6, B7L0R4, B8D5W9, B8GKD6, B9LSS4, C3MQ62, C3MVI1, C3N5T0, C3NEE6, C3NHA6, C4KHF9, C5A283, G1TT27

SIGNOR signaling

1 interactions.

AEffectBMechanism
RPL8“form complex”“60S cytosolic large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 219 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
SRP-dependent cotranslational protein targeting to membrane2315.3×2e-18
Eukaryotic Translation Termination1915.1×2e-15
Peptide chain elongation1815.1×8e-15
Viral mRNA Translation1815.1×8e-15
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1815.0×8e-15
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1914.8×2e-15
Selenocysteine synthesis1814.3×2e-14
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1814.0×2e-14

GO biological processes:

GO termPartnersFoldFDR
ribosomal large subunit biogenesis920.8×1e-07
cytoplasmic translation2120.2×7e-19
negative regulation of mRNA splicing, via spliceosome519.9×6e-04
stress granule assembly515.7×2e-03
ribosomal small subunit biogenesis1011.9×3e-06
translation2211.8×8e-15
rRNA processing1511.1×2e-09
mitophagy69.9×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

799 predictions. Top by Δscore:

VariantEffectΔscore
8:144789958:ACAGG:Aacceptor_gain1.0000
8:144789959:CAGG:Cacceptor_gain1.0000
8:144789959:CAGGC:Cacceptor_gain1.0000
8:144789960:AGG:Aacceptor_gain1.0000
8:144789961:GG:Gacceptor_gain1.0000
8:144789961:GGC:Gacceptor_loss1.0000
8:144789962:GCTGC:Gacceptor_loss1.0000
8:144789963:C:CAacceptor_loss1.0000
8:144789963:C:CCacceptor_gain1.0000
8:144789970:C:CTacceptor_gain1.0000
8:144790350:CT:Cdonor_loss1.0000
8:144790351:TT:Tdonor_loss1.0000
8:144790352:TACAT:Tdonor_loss1.0000
8:144790353:A:ACdonor_gain1.0000
8:144790353:ACATT:Adonor_gain1.0000
8:144790354:C:CTdonor_gain1.0000
8:144790354:CA:Cdonor_gain1.0000
8:144790354:CAT:Cdonor_gain1.0000
8:144790354:CATT:Cdonor_gain1.0000
8:144790354:CATTC:Cdonor_gain1.0000
8:144790468:CAC:Cacceptor_gain1.0000
8:144790470:CCTG:Cacceptor_loss1.0000
8:144790471:CTGT:Cacceptor_loss1.0000
8:144791274:CAC:Cdonor_loss1.0000
8:144791275:A:ACdonor_gain1.0000
8:144791275:AC:Adonor_gain1.0000
8:144791276:C:CTdonor_gain1.0000
8:144791276:C:Gdonor_loss1.0000
8:144791276:CC:Cdonor_gain1.0000
8:144791276:CCA:Cdonor_gain1.0000

AlphaMissense

1644 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:144789943:C:TG212E1.000
8:144789847:C:TG244E0.999
8:144789859:G:TA240D0.999
8:144789871:C:TG236D0.999
8:144789872:C:GG236R0.999
8:144789919:C:TG220D0.999
8:144789932:G:CH216D0.999
8:144789937:C:AG214V0.999
8:144789937:C:TG214D0.999
8:144789943:C:AG212V0.999
8:144789944:C:GG212R0.999
8:144789944:C:TG212R0.999
8:144789945:A:CF211L0.999
8:144789945:A:TF211L0.999
8:144789947:A:GF211L0.999
8:144789951:A:CH209Q0.999
8:144789951:A:TH209Q0.999
8:144789952:T:CH209R0.999
8:144790355:A:CN205K0.999
8:144790355:A:TN205K0.999
8:144790384:A:GW196R0.999
8:144790384:A:TW196R0.999
8:144790458:C:TG171E0.999
8:144790461:G:TA170D0.999
8:144791277:C:GG167R0.999
8:144791327:A:GL150P0.999
8:144791369:A:TV136D0.999
8:144791384:C:AG131V0.999
8:144791384:C:TG131E0.999
8:144791385:C:AG131W0.999

dbSNP variants (sampled 300 via entrez): RS1000119275 (8:144790231 C>A,G), RS1002056004 (8:144792813 G>T), RS1002820317 (8:144790714 A>G), RS1002823533 (8:144793907 C>T), RS1002893912 (8:144790858 T>C), RS1003032910 (8:144790038 A>G), RS1003653628 (8:144793579 A>T), RS1004132367 (8:144793850 C>G,T), RS1004369356 (8:144791953 G>C), RS1004494023 (8:144791620 G>A,C,T), RS1004569162 (8:144791808 A>G), RS1005645837 (8:144793459 G>A), RS1006209661 (8:144793714 C>G,T), RS1006234631 (8:144792560 C>T), RS1006240819 (8:144793874 A>C,G)

Disease associations

OMIM: gene MIM:604177 | 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

5 associations (top):

StudyTraitp-value
GCST006879_12Blood metabolite levels4.000000e-10
GCST006879_13Blood metabolite levels2.000000e-09
GCST006879_14Blood metabolite levels2.000000e-11
GCST006879_5Blood metabolite levels2.000000e-12
GCST007005_4Logical memory (immediate recall) in normal cognition2.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004874memory performance

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), CHEMBL6067550 (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
7.30Kd50.25nMCHEMBL3752910
7.30ED5050.25nMCHEMBL3752910
6.92Kd120.7nMCHEMBL5653589
6.92ED50120.7nMCHEMBL5653589
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
5.09IC508040nMCHEMBL4128250
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
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149275: Binding affinity to human RPL8 incubated for 45 mins by Kinobead based pull down assaykd0.0503uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149275: Binding affinity to human RPL8 incubated for 45 mins by Kinobead based pull down assaykd0.1207uM
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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, affects cotreatment, increases methylation, decreases expression4
arseniteaffects binding, increases reaction, increases methylation2
sodium arsenitedecreases expression2
perfluorooctanoic acidincreases expression, decreases expression2
perfluorooctane sulfonic aciddecreases expression, increases expression2
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
beauvericinaffects cotreatment, decreases expression1
deoxynivalenolincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression1
ochratoxin Aincreases expression1
azoxystrobinincreases expression1
CD 437decreases expression1
chloropicrinincreases expression1
enniatinsaffects cotreatment, decreases expression1
perfluoro-n-nonanoic aciddecreases expression1
deguelinincreases expression1
poly(propyleneimine)decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
perfluorohexanesulfonic aciddecreases expression1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic aciddecreases expression1
pyrimidifenincreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
pyrachlostrobinincreases expression1
bisphenol Sincreases expression1
LDN 193189affects cotreatment, decreases expression1
picoxystrobinincreases expression1
bisphenol AFincreases expression1
Sunitinibincreases 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)