RPL31

gene
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Also known as L31eL31

Summary

RPL31 (ribosomal protein L31, HGNC:10334) is a protein-coding gene on chromosome 2q11.2, encoding Large ribosomal subunit protein eL31 (P62899). 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 L31E family of ribosomal proteins. It is located in the cytoplasm. Higher levels of expression of this gene in familial adenomatous polyps compared to matched normal tissues have been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

Source: NCBI Gene 6160 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Diamond-Blackfan anemia (Moderate, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 113 total — 1 likely-pathogenic
  • 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_000993

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10334
Approved symbolRPL31
Nameribosomal protein L31
Location2q11.2
Locus typegene with protein product
StatusApproved
AliasesL31, eL31
Ensembl geneENSG00000071082
Ensembl biotypeprotein_coding
OMIM617415
Entrez6160

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 21 protein_coding, 1 nonsense_mediated_decay

ENST00000264258, ENST00000409000, ENST00000409028, ENST00000409038, ENST00000409320, ENST00000409650, ENST00000409711, ENST00000409733, ENST00000419276, ENST00000441435, ENST00000456292, ENST00000870891, ENST00000870892, ENST00000938458, ENST00000938459, ENST00000938460, ENST00000938461, ENST00000938462, ENST00000938463, ENST00000938464, ENST00000938465, ENST00000938466

RefSeq mRNA: 3 — MANE Select: NM_000993 NM_000993, NM_001098577, NM_001099693

CCDS: CCDS2049, CCDS46373, CCDS46374

Canonical transcript exons

ENST00000264258 — 5 exons

ExonStartEnd
ENSE00000771963101004158101004283
ENSE00001383880101006350101007267
ENSE00001665150101002702101002808
ENSE00001876303101002289101002315
ENSE00003784733101005959101006071

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 247.8928 / max 3510.2488, expressed in 1824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
21605245.93571824
216061.8869846
2023230.070238

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skin of hipUBERON:000155499.98gold quality
upper leg skinUBERON:000426299.98gold quality
caput epididymisUBERON:000435899.97gold quality
trabecular bone tissueUBERON:000248399.96gold quality
cauda epididymisUBERON:000436099.96gold quality
mammalian vulvaUBERON:000099799.95gold quality
germinal epithelium of ovaryUBERON:000130499.95gold quality
mammary ductUBERON:000176599.95gold quality
left ovaryUBERON:000211999.95gold quality
corpus epididymisUBERON:000435999.95gold quality
mucosa of sigmoid colonUBERON:000499399.95gold quality
tendon of biceps brachiiUBERON:000818899.95gold quality
tendonUBERON:000004399.94gold quality
penisUBERON:000098999.94gold quality
ovaryUBERON:000099299.94gold quality
right ovaryUBERON:000211899.94gold quality
pericardiumUBERON:000240799.94gold quality
calcaneal tendonUBERON:000370199.94gold quality
pituitary glandUBERON:000000799.93gold quality
urethraUBERON:000005799.93gold quality
endocervixUBERON:000045899.93gold quality
superficial temporal arteryUBERON:000161499.93gold quality
synovial jointUBERON:000221799.93gold quality
choroid plexus epitheliumUBERON:000391199.93gold quality
ganglionic eminenceUBERON:000402399.93gold quality
vena cavaUBERON:000408799.93gold quality
embryoUBERON:000092299.92gold quality
epithelium of nasopharynxUBERON:000195199.92gold quality
cortical plateUBERON:000534399.92gold quality
Brodmann (1909) area 46UBERON:000648399.92gold quality

Single-cell (SCXA)

Detected in 47 experiment(s), a significant marker in 16.

ExperimentMarker?Max mean expression
E-MTAB-9067yes4759.35
E-MTAB-8142yes4505.98
E-MTAB-10283yes4016.01
E-HCAD-36yes3827.06
E-HCAD-25yes1230.29
E-CURD-122yes78.90
E-CURD-88yes58.80
E-MTAB-9221yes53.47
E-MTAB-8410yes50.80
E-HCAD-9yes30.13
E-MTAB-10042yes15.48
E-MTAB-7316yes14.98
E-CURD-112yes10.68
E-HCAD-35yes8.41
E-MTAB-9801yes6.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting RPL31, 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-569699.9872.364487
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-335-3P99.9373.364958
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-427699.5667.662514
HSA-MIR-1212399.5271.792990
HSA-MIR-317199.4969.06776
HSA-MIR-122B-5P99.4670.811457
HSA-MIR-442799.3470.331854
HSA-MIR-6828-5P99.3169.211433
HSA-MIR-126499.2566.811317
HSA-MIR-470599.1069.101091
HSA-MIR-806699.0568.661532
HSA-MIR-6871-5P98.9066.67671
HSA-MIR-4680-3P98.6468.602093
HSA-MIR-6837-3P98.4266.711149
HSA-MIR-3689A-5P98.3570.121049
HSA-MIR-3689B-5P98.3570.121049
HSA-MIR-3689E98.3570.121049
HSA-MIR-3689F98.3570.081052
HSA-MIR-316698.2466.631223
HSA-MIR-466097.7967.441328
HSA-MIR-477197.4367.69596
HSA-MIR-214-5P97.3466.50617
HSA-MIR-3200-5P97.3465.97826

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 3)

  • gene discovery in DBA, resulting in the identification of RPL31 as a novel DBA gene. (PMID:25042156)
  • protein levels of the tumor suppressor p53 and its targets, p21 and MDM2, were increased in LNCaP and bicalutamide-resistant LNCaP cells treated with RPL31 siRNA. (PMID:25285958)
  • Silencing eL31 suppresses the progression of colorectal cancer via targeting DEPDC1. (PMID:36309731)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorpl31ENSDARG00000053365
rattus_norvegicusRpl31ENSRNOG00000013508
drosophila_melanogasterRpL31FBGN0285949
caenorhabditis_elegansrpl-31WBGENE00004445

Protein

Protein identifiers

Large ribosomal subunit protein eL31P62899 (reviewed: P62899)

Alternative names: 60S ribosomal protein L31

All UniProt accessions (6): P62899, B7Z4C8, B7Z4E3, B8ZZK4, C9JU56, H7C2W9

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 eukaryotic ribosomal protein eL31 family.

Isoforms (3)

UniProt IDNamesCanonical?
P62899-11yes
P62899-22
P62899-33

RefSeq proteins (3): NP_000984, NP_001092047, NP_001093163 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000054Ribosomal_eL31Family
IPR020052Ribosomal_eL31_CSConserved_site
IPR023621Ribosomal_eL31_dom_sfHomologous_superfamily

Pfam: PF01198

UniProt features (10 total): modified residue 7, splice variant 2, chain 1

Structure

Experimental structures (PDB)

186 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-P62899-F188.620.73

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 (7): 1, 15, 55, 70, 75, 75, 98

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: 441 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, RRAGTTGT_UNKNOWN, YAGI_AML_WITH_INV_16_TRANSLOCATION, MODULE_151, GNF2_TPT1, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GCM_NPM1, MORF_UBE2I, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, HSIAO_HOUSEKEEPING_GENES, GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION, HAHTOLA_MYCOSIS_FUNGOIDES_DN, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT

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

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

GO Cellular Component (12): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), focal adhesion (GO:0005925), membrane (GO:0016020), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), synapse (GO:0045202), extracellular exosome (GO:0070062), ribosome (GO:0005840), large ribosomal subunit (GO:0015934), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
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
binding1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
cell-substrate junction1
large ribosomal subunit1
cytosolic ribosome1
cytosol1
cell junction1
extracellular vesicle1
intracellular membraneless organelle1
ribosomal subunit1
protein-containing complex1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

323 interactions, top by confidence:

ABTypeScore
IFIT2IFIT3psi-mi:“MI:0914”(association)0.780
NHNRNPRpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
NRPL31psi-mi:“MI:0915”(physical association)0.700
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
RACK1RPS17psi-mi:“MI:0915”(physical association)0.610
CHATRPL31psi-mi:“MI:0915”(physical association)0.560
RPL31FGFR3psi-mi:“MI:0915”(physical association)0.560
RPL31GSNpsi-mi:“MI:0915”(physical association)0.560
RPL31psi-mi:“MI:0915”(physical association)0.560
UBQLN1RPL31psi-mi:“MI:0915”(physical association)0.560
HTTRPL31psi-mi:“MI:0915”(physical association)0.560
NNOP56psi-mi:“MI:0914”(association)0.530

BioGRID (970): RPL31 (Affinity Capture-MS), RPL31 (Affinity Capture-MS), RPL31 (Two-hybrid), DDX27 (Co-fractionation), EIF6 (Co-fractionation), LYAR (Co-fractionation), NIFK (Co-fractionation), PES1 (Co-fractionation), RPL10A (Co-fractionation), RPL12 (Co-fractionation), RPL13 (Co-fractionation), RPL13A (Co-fractionation), RPL14 (Co-fractionation), RPL15 (Co-fractionation), RPL21 (Co-fractionation)

ESM2 similar proteins: A0A1D8PHF5, A3CWZ5, A7I9I7, B8GEU5, G1SHG0, J9PAS6, O18602, O61749, O65071, P09132, P0C2H8, P0C2H9, P0CX31, P0CX32, P45841, P46290, P51420, P62899, P62900, P62901, P62902, Q1KSC7, Q22DH9, Q2FS98, Q3ZBG7, Q54XB5, Q56JX3, Q5RBR1, Q5RBR9, Q6FWF4, Q6NUH0, Q757D7, Q75K27, Q7KF90, Q8LC83, Q8PYQ4, Q8SSC8, Q8TIN3, Q90YT7, Q9D7A6

Diamond homologs: A0A1D8PHF5, A2STI8, A4G0C8, A6UR55, A6VI49, A7I9I7, A9A8N0, B8GEU5, C5A7H3, G1SHG0, O18602, O27649, O28213, O65071, P0C2H8, P0C2H9, P45841, P46290, P51420, P54009, P58189, P62899, P62900, P62901, P62902, Q1KSC7, Q22DH9, Q2FS98, Q54XB5, Q56JX3, Q5RBR9, Q6FWF4, Q6M155, Q6NUH0, Q757D7, Q7KF90, Q8TUY4, Q8U3S7, Q90YT7, Q9GN74

SIGNOR signaling

1 interactions.

AEffectBMechanism
RPL31“form complex”“60S cytosolic large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 191 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 membrane1812.8×2e-12
GTP hydrolysis and joining of the 60S ribosomal subunit1712.1×1e-11
Eukaryotic Translation Termination1411.9×1e-09
Formation of a pool of free 40S subunits1511.9×2e-10
Peptide chain elongation1311.7×4e-09
Viral mRNA Translation1311.7×4e-09
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1411.7×1e-09
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1311.6×4e-09

GO biological processes:

GO termPartnersFoldFDR
stress granule assembly620.9×7e-05
cytoplasmic translation1617.1×1e-12
negative regulation of innate immune response514.8×2e-03
translational initiation714.5×9e-05
ribosomal large subunit biogenesis512.8×3e-03
negative regulation of translation1112.5×4e-07
positive regulation of interferon-beta production511.3×5e-03
mitophagy611.0×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance59
Likely benign30
Benign12

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4531762NM_000993.5(RPL31):c.*23_*24delLikely pathogenic

SpliceAI

1308 predictions. Top by Δscore:

VariantEffectΔscore
2:101002311:GCAGA:Gdonor_gain1.0000
2:101002314:GA:Gdonor_gain1.0000
2:101002697:TTTA:Tacceptor_loss1.0000
2:101002698:TTAG:Tacceptor_loss1.0000
2:101002699:TA:Tacceptor_loss1.0000
2:101002700:AG:Aacceptor_loss1.0000
2:101002700:AGAT:Aacceptor_gain1.0000
2:101002700:AGATG:Aacceptor_gain1.0000
2:101002701:GAT:Gacceptor_gain1.0000
2:101002701:GATG:Gacceptor_gain1.0000
2:101002701:GATGG:Gacceptor_gain1.0000
2:101002804:GGAGT:Gdonor_gain1.0000
2:101002805:GAGT:Gdonor_gain1.0000
2:101002805:GAGTG:Gdonor_gain1.0000
2:101002807:GT:Gdonor_gain1.0000
2:101002807:GTGTG:Gdonor_loss1.0000
2:101002809:G:Cdonor_loss1.0000
2:101002809:G:GGdonor_gain1.0000
2:101002811:GAGTA:Gdonor_loss1.0000
2:101004153:CGTA:Cacceptor_loss1.0000
2:101004154:GTA:Gacceptor_loss1.0000
2:101004155:TA:Tacceptor_loss1.0000
2:101004156:A:AGacceptor_gain1.0000
2:101004156:AG:Aacceptor_gain1.0000
2:101004156:AGG:Aacceptor_gain1.0000
2:101004156:AGGG:Aacceptor_gain1.0000
2:101004157:G:GAacceptor_gain1.0000
2:101004157:GG:Gacceptor_gain1.0000
2:101004157:GGG:Gacceptor_gain1.0000
2:101004157:GGGG:Gacceptor_gain1.0000

AlphaMissense

809 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:101004204:T:CF52L1.000
2:101004206:T:AF52L1.000
2:101004206:T:GF52L1.000
2:101004208:C:AA53D1.000
2:101004253:T:AL68H1.000
2:101004265:T:AV72D1.000
2:101004267:T:AW73R1.000
2:101004267:T:CW73R1.000
2:101004276:G:AG76R1.000
2:101004276:G:CG76R1.000
2:101004277:G:AG76E1.000
2:101004277:G:TG76V1.000
2:101005994:G:CR90T1.000
2:101005994:G:TR90I1.000
2:101005995:A:CR90S1.000
2:101005995:A:TR90S1.000
2:101002769:G:CR23P0.999
2:101004162:T:CF38L0.999
2:101004164:C:AF38L0.999
2:101004164:C:GF38L0.999
2:101004167:G:CK39N0.999
2:101004167:G:TK39N0.999
2:101004171:C:AR41S0.999
2:101004184:C:AA45E0.999
2:101004205:T:CF52S0.999
2:101004221:G:AM57I0.999
2:101004221:G:CM57I0.999
2:101004221:G:TM57I0.999
2:101004237:C:AR63S0.999
2:101004238:G:CR63P0.999

dbSNP variants (sampled 300 via entrez): RS1000073466 (2:101002603 C>T), RS1000242396 (2:101005949 T>C), RS1000395132 (2:101011366 C>T), RS1000405701 (2:101017268 T>C), RS1000408316 (2:101005644 A>G), RS1000494114 (2:101017505 C>T), RS1000833193 (2:101009415 A>C), RS1000861630 (2:101015330 A>G), RS1000893819 (2:101009685 A>G), RS1001069323 (2:101015029 A>G), RS1001125783 (2:101001256 A>G), RS1001344887 (2:101011278 C>G,T), RS1001541847 (2:101015266 T>C), RS1001564777 (2:101011046 A>G), RS1001671078 (2:101006329 T>G)

Disease associations

OMIM: gene MIM:617415 | 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
GCST90013407_115Liver enzyme levels (gamma-glutamyl transferase)3.000000e-13

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004532serum gamma-glutamyl transferase measurement

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), CHEMBL6067546 (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
8.35Kd4.489nMCHEMBL5653589
8.35ED504.489nMCHEMBL5653589
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

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
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149262: Binding affinity to human RPL31 incubated for 45 mins by Kinobead based pull down assaykd0.0045uM
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

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression, affects expression8
bisphenol Adecreases expression4
trichostatin Aaffects cotreatment, decreases expression3
sodium arsenitedecreases expression3
methylmercuric chloridedecreases expression2
deoxynivalenoldecreases expression, increases expression2
entinostataffects cotreatment, decreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression2
Panobinostataffects cotreatment, decreases expression2
Formaldehydedecreases expression, increases expression2
Nickeldecreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cadmium Chlorideincreases abundance, increases palmitoylation, increases expression, decreases reaction2
Particulate Matterdecreases expression, increases abundance2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamideaffects splicing1
FR900359decreases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
2,4,6-tribromophenoldecreases expression1
triphenyl phosphateaffects expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression1
decabromobiphenyl etherdecreases expression1
terbufosdecreases methylation1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
sodium bichromateincreases expression1
3,3’-diindolylmethanedecreases reaction, increases expression1
tetrabromobisphenol Adecreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
cyclic 3’,5’-uridine monophosphateaffects binding1

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)