RPS11

Summary

RPS11 (ribosomal protein S11, HGNC:10384) is a protein-coding gene on chromosome 19q13.3, encoding Small ribosomal subunit protein uS17 (P62280). Component of the small 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 member of the S17P family of ribosomal proteins that is a component of the 40S subunit. This gene is co-transcribed with the small nucleolar RNA gene U35B, which is located in the third intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed throughout the genome.

Source: NCBI Gene 6205 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 29 total
• 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_001015

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10384
Approved symbol	RPS11
Name	ribosomal protein S11
Location	19q13.3
Locus type	gene with protein product
Status	Approved
Aliases	S11, uS17
Ensembl gene	ENSG00000142534
Ensembl biotype	protein_coding
OMIM	180471
Entrez	6205

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000270625, ENST00000594493, ENST00000596873, ENST00000599167, ENST00000599561, ENST00000600027, ENST00000601216, ENST00000601306, ENST00000602252, ENST00000912774

RefSeq mRNA: 1 — MANE Select: NM_001015 NM_001015

CCDS: CCDS12769

Canonical transcript exons

ENST00000270625 — 5 exons

Exon	Start	End
ENSE00001116454	49496434	49496471
ENSE00003671356	49497520	49497595
ENSE00003681886	49497917	49498046
ENSE00003691005	49497194	49497325
ENSE00003851159	49499512	49499708

Expression profiles

Bgee: expression breadth ubiquitous, 309 present calls, max score 99.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 522.0137 / max 7963.9380, expressed in 1828 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177002	522.0137	1828

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	99.99	gold quality
upper leg skin	UBERON:0004262	99.99	gold quality
skin of hip	UBERON:0001554	99.98	gold quality
adult organism	UBERON:0007023	99.98	gold quality
urethra	UBERON:0000057	99.97	gold quality
embryo	UBERON:0000922	99.97	gold quality
penis	UBERON:0000989	99.97	gold quality
upper arm skin	UBERON:0004263	99.97	gold quality
type B pancreatic cell	CL:0000169	99.96	gold quality
superficial temporal artery	UBERON:0001614	99.96	gold quality
nipple	UBERON:0002030	99.96	gold quality
caput epididymis	UBERON:0004358	99.96	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.96	gold quality
lymph node	UBERON:0000029	99.95	gold quality
colonic mucosa	UBERON:0000317	99.95	gold quality
endocervix	UBERON:0000458	99.95	gold quality
ovary	UBERON:0000992	99.95	gold quality
germinal epithelium of ovary	UBERON:0001304	99.95	gold quality
right ovary	UBERON:0002118	99.95	gold quality
left ovary	UBERON:0002119	99.95	gold quality
ventricular zone	UBERON:0003053	99.95	gold quality
cauda epididymis	UBERON:0004360	99.95	gold quality
cortical plate	UBERON:0005343	99.95	gold quality
pituitary gland	UBERON:0000007	99.94	gold quality
mammalian vulva	UBERON:0000997	99.94	gold quality
pylorus	UBERON:0001166	99.94	gold quality
right uterine tube	UBERON:0001302	99.94	gold quality
left uterine tube	UBERON:0001303	99.94	gold quality
epithelium of nasopharynx	UBERON:0001951	99.94	gold quality
synovial joint	UBERON:0002217	99.94	gold quality

Single-cell (SCXA)

Detected in 28 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	175.93
E-CURD-122	yes	92.57
E-CURD-88	yes	70.96
E-MTAB-9221	yes	26.65
E-HCAD-9	yes	21.89
E-MTAB-10042	yes	11.61
E-CURD-112	yes	11.26
E-HCAD-35	yes	8.59
E-MTAB-6678	yes	8.19
E-HCAD-4	no	5377.29
E-MTAB-8530	no	4174.19
E-CURD-97	no	4118.41
E-MTAB-10596	no	3810.01
E-GEOD-124472	no	3381.55
E-CURD-79	no	3370.43

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 1)

• increased expression of RPS11 and RPS20 predicts shorter patient survival. treatment-resistant GSC clones are clinically relevant cells that represent resistant tumorigenic clones from patient tumors and that their properties (PMID:26506620)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	rps11	ENSDARG00000053058
danio_rerio	rps11l	ENSDARG00000093606
mus_musculus	Rps11	ENSMUSG00000003429
rattus_norvegicus	Rps11l1	ENSRNOG00000009583
drosophila_melanogaster	RpS11	FBGN0033699
caenorhabditis_elegans		WBGENE00004480

Protein

Protein identifiers

Small ribosomal subunit protein uS17 — P62280 (reviewed: P62280)

Alternative names: 40S ribosomal protein S11

All UniProt accessions (5): P62280, M0QZ90, M0QZC5, M0R1H5, M0R1H6

UniProt curated annotations — full annotation on UniProt →

Function. Component of the small ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome.

Subunit / interactions. Component of the small ribosomal subunit. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3.

Subcellular location. Cytoplasm. Nucleus. Nucleolus.

Post-translational modifications. Citrullinated by PADI4.

Similarity. Belongs to the universal ribosomal protein uS17 family.

RefSeq proteins (1): NP_001006* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000266	Ribosomal_uS17	Family
IPR012340	NA-bd_OB-fold	Homologous_superfamily
IPR019979	Ribosomal_uS17_CS	Conserved_site
IPR028333	Ribosomal_uS17_arc/euk	Family
IPR032440	Ribosomal_uS17_N	Domain

Pfam: PF00366, PF16205

UniProt features (27 total): strand 10, modified residue 8, turn 3, helix 2, initiator methionine 1, chain 1, lipid moiety-binding region 1, mutagenesis site 1

Structure

Experimental structures (PDB)

212 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8GLP	ELECTRON MICROSCOPY	1.67
8QOI	ELECTRON MICROSCOPY	1.9
9O3W	ELECTRON MICROSCOPY	1.9
8YOO	ELECTRON MICROSCOPY	2
9C3H	ELECTRON MICROSCOPY	2
7R4X	ELECTRON MICROSCOPY	2.15
9I2D	ELECTRON MICROSCOPY	2.19
9PBE	ELECTRON MICROSCOPY	2.19
8YOP	ELECTRON MICROSCOPY	2.2
9O3V	ELECTRON MICROSCOPY	2.2
9O3Y	ELECTRON MICROSCOPY	2.2
8JDK	ELECTRON MICROSCOPY	2.26
8G5Y	ELECTRON MICROSCOPY	2.29
9S3D	ELECTRON MICROSCOPY	2.32
9RPV	ELECTRON MICROSCOPY	2.35
9S3B	ELECTRON MICROSCOPY	2.38
8K2C	ELECTRON MICROSCOPY	2.4
8XSX	ELECTRON MICROSCOPY	2.4
9SPF	ELECTRON MICROSCOPY	2.4
9SPI	ELECTRON MICROSCOPY	2.4
8JDL	ELECTRON MICROSCOPY	2.42
9S3C	ELECTRON MICROSCOPY	2.42
9QLO	ELECTRON MICROSCOPY	2.47
9P8B	ELECTRON MICROSCOPY	2.48
7XNY	ELECTRON MICROSCOPY	2.5
8JDJ	ELECTRON MICROSCOPY	2.5
9RUC	ELECTRON MICROSCOPY	2.5
8G60	ELECTRON MICROSCOPY	2.54
8IFE	ELECTRON MICROSCOPY	2.57
9P7D	ELECTRON MICROSCOPY	2.57

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62280-F1	88.33	0.67

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 (9): 60, 2, 22, 38, 45, 58, 67, 69, 110

Mutagenesis-validated functional residues (1):

Position	Phenotype
60	abolishes s-acylation.

Function

Pathways and Gene Ontology

Reactome pathways

50 pathways

ID	Pathway
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression
R-HSA-156902	Peptide chain elongation
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane
R-HSA-192823	Viral mRNA Translation
R-HSA-2408557	Selenocysteine synthesis
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72649	Translation initiation complex formation
R-HSA-72689	Formation of a pool of free 40S subunits
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex
R-HSA-72702	Ribosomal scanning and start codon recognition
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-72764	Eukaryotic Translation Termination
R-HSA-9010553	Regulation of expression of SLITs and ROBOs
R-HSA-9633012	Response of EIF2AK4 (GCN2) to amino acid deficiency
R-HSA-9735869	SARS-CoV-1 modulates host translation machinery
R-HSA-9754678	SARS-CoV-2 modulates host translation machinery
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-9954714	PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA
R-HSA-9954716	ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA
R-HSA-1266738	Developmental Biology
R-HSA-1430728	Metabolism
R-HSA-156842	Eukaryotic Translation Elongation
R-HSA-1643685	Disease
R-HSA-168255	Influenza Infection
R-HSA-168273	Influenza Viral RNA Transcription and Replication
R-HSA-2262752	Cellular responses to stress
R-HSA-2408522	Selenoamino acid metabolism
R-HSA-376176	Signaling by ROBO receptors
R-HSA-392499	Metabolism of proteins

MSigDB gene sets: 229 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_CYTOPLASMIC_TRANSLATION, GOBP_RIBOSOME_BIOGENESIS, MODULE_151, GNF2_TPT1, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCM_NPM1, MORF_UBE2I, HSIAO_HOUSEKEEPING_GENES, GOBP_TRANSLATION, LU_TUMOR_VASCULATURE_UP, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, TIEN_INTESTINE_PROBIOTICS_2HR_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS

GO Biological Process (3): cytoplasmic translation (GO:0002181), translation (GO:0006412), ribosomal small subunit biogenesis (GO:0042274)

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 (14): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), ribosome (GO:0005840), focal adhesion (GO:0005925), membrane (GO:0016020), cytosolic ribosome (GO:0022626), cytosolic small ribosomal subunit (GO:0022627), small-subunit processome (GO:0032040), synapse (GO:0045202), extracellular exosome (GO:0070062), nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Cap-dependent Translation Initiation	4
Translation	2
Nonsense-Mediated Decay (NMD)	2
Ribosome-associated quality control	2
Eukaryotic Translation Initiation	1
Eukaryotic Translation Elongation	1
Influenza Viral RNA Transcription and Replication	1
Selenoamino acid metabolism	1
rRNA processing in the nucleus and cytosol	1
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	1
Signaling by ROBO receptors	1
Cellular response to starvation	1
SARS-CoV-1-host interactions	1
SARS-CoV-2-host interactions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
ribosome	2
nuclear lumen	2
intracellular membraneless organelle	2
translation	1
peptidyltransferase activity	1
translational initiation	1
translational elongation	1
translational termination	1
macromolecule biosynthetic process	1
protein metabolic process	1
protein biosynthetic process	1
ribonucleoprotein complex biogenesis	1
ribosome biogenesis	1
nucleic acid binding	1
structural molecule activity	1
RNA binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1
cell-substrate junction	1
cytosol	1
small ribosomal subunit	1
cytosolic ribosome	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
cell junction	1
extracellular vesicle	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

312 interactions, top by confidence:

A	B	Type	Score
PPP2R2A	PPP2R1A	psi-mi:“MI:2364”(proximity)	0.970
MAP3K14	CHUK	psi-mi:“MI:0914”(association)	0.950
FBL	NOP56	psi-mi:“MI:0914”(association)	0.800
YBX1	HNRNPR	psi-mi:“MI:0914”(association)	0.770
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
PPP1CC	CCDC85C	psi-mi:“MI:2364”(proximity)	0.740
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
INAVA	CYTH3	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
ESR1	TRIM24	psi-mi:“MI:0914”(association)	0.640
RACK1	RPS17	psi-mi:“MI:0915”(physical association)	0.610
RPS11	RPS8	psi-mi:“MI:0915”(physical association)	0.560
MAPT	KIF2A	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
DDX6	MCRIP1	psi-mi:“MI:0914”(association)	0.510
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
PPP2R2B	DDX3X	psi-mi:“MI:0914”(association)	0.460
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460

BioGRID (820): RPS11 (Affinity Capture-MS), RPS11 (Affinity Capture-MS), RPS11 (Affinity Capture-MS), EEF1A1 (Co-fractionation), KRR1 (Co-fractionation), MRPL18 (Co-fractionation), MRPL24 (Co-fractionation), NOC4L (Co-fractionation), RPL10 (Co-fractionation), RPL10A (Co-fractionation), RPL11 (Co-fractionation), RPL12 (Co-fractionation), RPL13 (Co-fractionation), RPL13A (Co-fractionation), RPL14 (Co-fractionation)

ESM2 similar proteins: A0A1D8PN83, A4IJI4, A5VLL0, A7GK15, A9NEN1, B1VAM4, B2G8Y2, B2GDX3, B2UUV8, B5Z8J2, G1TRM4, O65569, P09901, P0A0X4, P0A0X5, P0CT73, P0CT74, P0CX47, P0CX48, P14149, P16181, P17093, P17293, P25460, P41115, P42733, P42756, P47333, P52812, P61270, P61941, P62280, P62281, P62282, P75546, Q0E9B6, Q1CS69, Q1KVX0, Q292D0, Q3T0V4

Diamond homologs: A0A0N0BLS5, A0A1D8PN83, A0KRN3, A1ALV0, A1S227, A2SPL1, A3CT06, A5IM92, A5USI0, A7I5P8, A7NR54, A8G1D9, A9A5I6, A9KD22, A9NAX9, B0B893, B0BCF8, B0R665, B1LBN1, B3E7U4, B5YG38, B6IRR5, B8GKE2, B9K895, C0Q9W4, C5BQ70, C5CGQ5, G1TRM4, O24786, O26120, O28363, O59426, O65569, P0CE05, P0CT73, P0CT74, P0CX47, P0CX48, P0DOY7, P12741

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RPS11	“form complex”	“40S cytosolic small ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 204 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:

Pathway	Partners	Fold	FDR
Nonsense-Mediated Decay (NMD)	10	15.5×	3e-08
TRAF6 mediated NF-kB activation	5	15.2×	5e-04
Formation of the ternary complex, and subsequently, the 43S complex	9	12.9×	1e-06
Ribosomal scanning and start codon recognition	10	12.7×	2e-07
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	16	12.6×	2e-11
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	19	12.4×	5e-13
Eukaryotic Translation Initiation	6	12.3×	3e-04
Cap-dependent Translation Initiation	6	12.3×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
non-canonical NF-kappaB signal transduction	5	23.0×	4e-04
cytoplasmic translation	17	17.2×	1e-13
stress granule assembly	5	16.4×	1e-03
regulation of translational initiation	6	15.3×	4e-04
mRNA stabilization	7	14.0×	2e-04
translational initiation	7	13.7×	2e-04
ribosomal small subunit biogenesis	8	10.0×	3e-04
translation	16	9.0×	2e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

532 predictions. Top by Δscore:

Variant	Effect	Δscore
19:49496468:TCAG:T	donor_loss	1.0000
19:49496469:CAGGT:C	donor_loss	1.0000
19:49496470:AGGT:A	donor_loss	1.0000
19:49496471:GGTGC:G	donor_loss	1.0000
19:49496473:T:G	donor_loss	1.0000
19:49497185:A:AG	acceptor_gain	1.0000
19:49497186:A:G	acceptor_gain	1.0000
19:49497189:T:TA	acceptor_gain	1.0000
19:49497192:A:AG	acceptor_gain	1.0000
19:49497192:AGACT:A	acceptor_gain	1.0000
19:49497193:G:GC	acceptor_gain	1.0000
19:49497193:GA:G	acceptor_gain	1.0000
19:49497193:GAC:G	acceptor_gain	1.0000
19:49497193:GACT:G	acceptor_gain	1.0000
19:49497193:GACTG:G	acceptor_gain	1.0000
19:49497323:G:GT	donor_gain	1.0000
19:49497400:GCATC:G	donor_gain	1.0000
19:49497404:C:CG	donor_gain	1.0000
19:49497514:TTTCA:T	acceptor_loss	1.0000
19:49497515:TTCA:T	acceptor_loss	1.0000
19:49497516:TCAG:T	acceptor_loss	1.0000
19:49497518:A:AG	acceptor_gain	1.0000
19:49497518:AG:A	acceptor_gain	1.0000
19:49497518:AGGCT:A	acceptor_loss	1.0000
19:49497519:G:GA	acceptor_gain	1.0000
19:49497519:GG:G	acceptor_gain	1.0000
19:49497519:GGCT:G	acceptor_gain	1.0000
19:49497594:TGGTA:T	donor_loss	1.0000
19:49497596:G:GG	donor_gain	1.0000
19:49497597:TAAG:T	donor_loss	1.0000

AlphaMissense

1037 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:49497300:G:A	G41D	1.000
19:49497521:C:A	A50D	1.000
19:49497541:G:C	D57H	1.000
19:49497542:A:T	D57V	1.000
19:49497550:T:C	C60R	1.000
19:49497551:G:A	C60Y	1.000
19:49497552:C:G	C60W	1.000
19:49497556:T:C	F62L	1.000
19:49497557:T:C	F62S	1.000
19:49497558:C:A	F62L	1.000
19:49497558:C:G	F62L	1.000
19:49497562:G:C	G64R	1.000
19:49497563:G:T	G64V	1.000
19:49497580:G:A	G70R	1.000
19:49497580:G:C	G70R	1.000
19:49497580:G:T	G70W	1.000
19:49497581:G:A	G70E	1.000
19:49497581:G:T	G70V	1.000
19:49497590:T:C	L73P	1.000
19:49497595:G:C	G75R	1.000
19:49497917:G:A	G75D	1.000
19:49497917:G:T	G75V	1.000
19:49497923:T:A	V77E	1.000
19:49497938:T:C	M82T	1.000
19:49497939:G:A	M82I	1.000
19:49497939:G:C	M82I	1.000
19:49497939:G:T	M82I	1.000
19:49497947:C:T	T85I	1.000
19:49497953:T:A	V87D	1.000
19:49497958:C:A	R89S	1.000

dbSNP variants (sampled 300 via entrez): RS1000106134 (19:49499294 C>A,T), RS1000428049 (19:49498401 A>C,G), RS1000878761 (19:49498269 C>A,G,T), RS1001270349 (19:49497009 A>G), RS1002649887 (19:49496802 C>T), RS1002715265 (19:49496404 A>G,T), RS1002960613 (19:49496653 C>A,T), RS1003275195 (19:49495285 A>C), RS1003431573 (19:49499348 A>G), RS1003569188 (19:49496198 C>G,T), RS1003723776 (19:49495484 G>A), RS1004394342 (19:49498759 C>G), RS1004732611 (19:49494530 A>G), RS1004946872 (19:49497654 C>T), RS1006227790 (19:49496510 C>T)

Disease associations

OMIM: gene MIM:180471 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000583_10	Hematological and biochemical traits	3.000000e-08
GCST001233_10	Metabolite levels	9.000000e-13
GCST001698_11	Serum total protein levels	3.000000e-06
GCST001698_4	Serum total protein levels	7.000000e-08
GCST001699_1	Serum albumin levels	8.000000e-07
GCST001699_11	Serum albumin levels	6.000000e-09
GCST005989_35	Serum total protein levels	1.000000e-62
GCST005990_25	Non-albumin protein levels	4.000000e-16
GCST011346_41	Total cholesterol levels	4.000000e-10
GCST011351_24	Aspartate aminotransferase levels	2.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004747	protein measurement
EFO:0004536	total blood protein measurement
EFO:0004574	total cholesterol measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3987582 (PROTEIN NUCLEIC-ACID COMPLEX), CHEMBL6067557 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

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

Molecule	Name	Phase	Patents
CHEMBL6067484	GENTAMICIN SULFATE	4

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).

pChembl	Type	Value	Unit	Molecule
7.72	Kd	18.95	nM	CHEMBL5653589
7.72	ED50	18.95	nM	CHEMBL5653589
7.60	Kd	25.09	nM	CHEMBL3752910
7.60	ED50	25.09	nM	CHEMBL3752910
6.52	IC50	300	nM	CHEMBL4109308
6.42	IC50	380	nM	CHEMBL4109308
6.42	IC50	380	nM	CHEMBL4574496
6.41	IC50	390	nM	CHEMBL4126894
6.39	IC50	410	nM	CHEMBL4114159
6.35	IC50	450	nM	CHEMBL4126496
6.30	IC50	500	nM	CHEMBL4574496
6.30	IC50	500	nM	CHEMBL4560206
6.16	IC50	690	nM	CHEMBL4130157
6.15	IC50	710	nM	CHEMBL4108338
6.11	IC50	780	nM	CHEMBL4114159
6.09	IC50	820	nM	CHEMBL4109308
6.07	IC50	850	nM	CHEMBL4107559
6.07	IC50	850	nM	CHEMBL4533299
6.05	IC50	900	nM	CHEMBL4126894
6.05	IC50	900	nM	CHEMBL4126496
6.04	IC50	920	nM	CHEMBL4554909
5.97	IC50	1060	nM	CHEMBL4128388
5.89	IC50	1290	nM	CHEMBL4130157
5.86	IC50	1370	nM	CHEMBL4107559
5.84	IC50	1440	nM	CHEMBL4108338
5.81	IC50	1540	nM	CHEMBL4534859
5.76	IC50	1730	nM	CHEMBL4534859
5.69	IC50	2050	nM	CHEMBL4566239
5.68	IC50	2080	nM	CHEMBL4446635
5.66	IC50	2210	nM	CHEMBL4446635
5.66	EC50	2200	nM	CHEMBL4464929
5.64	IC50	2270	nM	CHEMBL4533299
5.63	IC50	2330	nM	CHEMBL4566239
5.62	IC50	2380	nM	CHEMBL4128388
5.58	IC50	2630	nM	CHEMBL4128250
5.55	IC50	2820	nM	CHEMBL4127458
5.53	IC50	2970	nM	CHEMBL4127311
5.51	IC50	3080	nM	CHEMBL4126072
5.46	IC50	3500	nM	CHEMBL4525277
5.44	IC50	3630	nM	CHEMBL4469712
5.39	IC50	4100	nM	CHEMBL4128560
5.37	IC50	4300	nM	CHEMBL4127016
5.36	IC50	4380	nM	CHEMBL4527910
5.16	IC50	7000	nM	CHEMBL4109308
5.13	IC50	7400	nM	CHLORAMPHENICOL SULFATE SALT
5.09	IC50	8040	nM	CHEMBL4128250
5.08	IC50	8370	nM	CHEMBL4128250
5.03	IC50	9320	nM	CHEMBL4127016
5.03	IC50	9240	nM	CHEMBL4128560

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.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149283: Binding affinity to human RPS11 incubated for 45 mins by Kinobead based pull down assay	kd	0.0190	uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149283: Binding affinity to human RPS11 incubated for 45 mins by Kinobead based pull down assay	kd	0.0251	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide	1585498: 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 method	ic50	0.3000	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-3-[4-(triazolo[4,5-b]pyridin-3-yl)phenyl]propanamide	1532845: 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 assay	ic50	0.3800	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide	1497947: 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 assay	ic50	0.3900	uM
N-(3-chloro-2-pyridinyl)-4-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: 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 assay	ic50	0.4100	uM
N-(3-chloro-2-pyridinyl)-4-(5-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: 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 assay	ic50	0.4500	uM
N-(1-methylpyrrolo[2,3-c]pyridin-7-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: 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 assay	ic50	0.5000	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylbenzamide	1497947: 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 assay	ic50	0.6900	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-5-(triazolo[4,5-b]pyridin-3-yl)pyridine-2-carboxamide	1497947: 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 assay	ic50	0.7100	uM
N-(3-chloro-2-pyridinyl)-3-[5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-2-pyridinyl]-N-[(3R)-piperidin-3-yl]propanamide	1532845: 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 assay	ic50	0.8500	uM
N-(3-chloro-2-pyridinyl)-5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]pyridine-2-carboxamide	1497947: 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 assay	ic50	0.8500	uM
N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylpiperidine-1-carboxamide	1532846: 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 assay	ic50	0.9200	uM
N-isoquinolin-1-yl-4-(1-methylpyrazol-4-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: 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 assay	ic50	1.0600	uM
N-isoquinolin-1-yl-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: 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 assay	ic50	1.5400	uM
N-(3-methyl-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532845: 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 assay	ic50	2.0500	uM
N-(3-chloro-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: 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 assay	ic50	2.0800	uM
N-(5,8-dihydroisoquinolin-1-yl)-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide	1584424: Inhibition of human 80S ribosome-mediated PCSK9 translation expressed in CHO-K1 cells assessed as reduction in PCSK9 secretion	ec50	2.2000	uM
N-isoquinolin-1-yl-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide	1497947: 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 assay	ic50	2.6300	uM
N-(3-chloro-2-pyridinyl)-4-(6-methylpyrazin-2-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	2.8200	uM
N-(3-chloro-2-pyridinyl)-4-[6-(dimethylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	2.9700	uM
N-(3-chloro-2-pyridinyl)-4-[6-(methylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	3.0800	uM
N-isoquinolin-1-yl-4-(6-methyl-1,2-benzoxazol-3-yl)-N-[(3R)-piperidin-3-yl]piperazine-1-carboxamide	1532845: 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 assay	ic50	3.5000	uM
N-(3-methylpyrazin-2-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: 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 assay	ic50	3.6300	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-6-(triazolo[4,5-b]pyridin-3-yl)pyridine-3-carboxamide	1497947: 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 assay	ic50	4.1000	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazin-2-ylbenzamide	1497947: 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 assay	ic50	4.3000	uM
4-(2-fluorophenyl)-N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: 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 assay	ic50	4.3800	uM
2,2-dichloro-N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]acetamide;sulfuric acid	717551: Inhibition of mitochondrial ribosome-mediated protein synthesis in human HeLa cells assessed as {35S]methionine incorporation by autoradiography	ic50	7.4000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	4
sodium arsenite	increases expression, affects binding, decreases reaction, decreases expression, affects reaction	4
Valproic Acid	affects cotreatment, increases expression, increases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
TAK-243	increases sumoylation	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
decabromobiphenyl ether	decreases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
cobaltous chloride	increases expression	1
tetrabromobisphenol A	decreases expression	1
N-benzyloxycarbonylprolylprolinal	increases expression	1
chloropicrin	increases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol B	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Bortezomib	increases expression	1

ChEMBL screening assays

90 unique, capped per target: 90 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1920845	Binding	Induction of ribosome to readthrough in human A-T lymphoblastoid cells assessed as ATM ser1981 autophosphorylation at 30 uM after 4 days by PTT-ELISA assay	Synthesis and evaluation of compounds that induce readthrough of premature termination codons. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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