NOP58

Summary

NOP58 (NOP58 ribonucleoprotein, HGNC:29926) is a protein-coding gene on chromosome 2q33.1, encoding Nucleolar protein 58 (Q9Y2X3). Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

The protein encoded by this gene is a core component of box C/D small nucleolar ribonucleoproteins. Some box C/D small nucleolar RNAs (snoRNAs), such as U3, U8, and U14, are dependent upon the encoded protein for their synthesis. This protein is SUMOylated, which is necessary for high affinity binding to snoRNAs.

Source: NCBI Gene 51602 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 82 total — 1 pathogenic
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_015934

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29926
Approved symbol	NOP58
Name	NOP58 ribonucleoprotein
Location	2q33.1
Locus type	gene with protein product
Status	Approved
Aliases	NOP5, HSPC120
Ensembl gene	ENSG00000055044
Ensembl biotype	protein_coding
OMIM	616742
Entrez	51602

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 6 protein_coding, 4 protein_coding_CDS_not_defined, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000264279, ENST00000426814, ENST00000433543, ENST00000467734, ENST00000472050, ENST00000478508, ENST00000478941, ENST00000488403, ENST00000492688, ENST00000492740, ENST00000919440, ENST00000919441, ENST00000919442, ENST00000919443, ENST00000919444

RefSeq mRNA: 1 — MANE Select: NM_015934 NM_015934

CCDS: CCDS2353

Canonical transcript exons

ENST00000264279 — 15 exons

Exon	Start	End
ENSE00000803415	202295674	202295837
ENSE00000964999	202291125	202291270
ENSE00000965000	202292777	202292903
ENSE00001246796	202303386	202303661
ENSE00001828228	202265763	202265986
ENSE00003489936	202300234	202300367
ENSE00003524173	202277950	202278002
ENSE00003539065	202284345	202284481
ENSE00003555874	202290323	202290457
ENSE00003556578	202287660	202287724
ENSE00003564944	202302921	202303057
ENSE00003575999	202275113	202275189
ENSE00003611174	202282351	202282472
ENSE00003645254	202297845	202297906
ENSE00003670262	202297379	202297513

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 99.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 94.9908 / max 1285.2682, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24708	93.9903	1822
24714	1.0005	459

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	99.42	gold quality
pancreatic ductal cell	CL:0002079	98.74	gold quality
gingival epithelium	UBERON:0001949	97.41	gold quality
sural nerve	UBERON:0015488	97.34	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.32	gold quality
body of pancreas	UBERON:0001150	97.25	gold quality
calcaneal tendon	UBERON:0003701	97.09	gold quality
tonsil	UBERON:0002372	97.06	gold quality
left ovary	UBERON:0002119	96.96	gold quality
adenohypophysis	UBERON:0002196	96.89	gold quality
right ovary	UBERON:0002118	96.73	gold quality
pituitary gland	UBERON:0000007	96.71	gold quality
thymus	UBERON:0002370	96.69	gold quality
left uterine tube	UBERON:0001303	96.68	gold quality
ileal mucosa	UBERON:0000331	96.61	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.61	gold quality
colonic mucosa	UBERON:0000317	96.60	gold quality
trabecular bone tissue	UBERON:0002483	96.55	gold quality
lymph node	UBERON:0000029	96.52	gold quality
gingiva	UBERON:0001828	96.49	gold quality
epithelium of nasopharynx	UBERON:0001951	96.48	gold quality
nasopharynx	UBERON:0001728	96.47	gold quality
adrenal tissue	UBERON:0018303	96.41	gold quality
endometrium	UBERON:0001295	96.35	gold quality
cauda epididymis	UBERON:0004360	96.34	gold quality
vermiform appendix	UBERON:0001154	96.33	gold quality
rectum	UBERON:0001052	96.25	gold quality
oral cavity	UBERON:0000167	96.24	gold quality
seminal vesicle	UBERON:0000998	96.23	gold quality
pancreas	UBERON:0001264	96.23	gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-7	yes	1406.57
E-MTAB-9067	yes	20.44
E-MTAB-10042	yes	14.11
E-GEOD-93593	yes	6.95
E-MTAB-7606	no	1212.23
E-MTAB-6911	no	1102.71
E-GEOD-110499	no	1020.62
E-ENAD-21	no	766.51
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting NOP58, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-1272	99.34	68.79	878
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-6780B-3P	99.13	67.18	622
HSA-MIR-4464	98.95	67.73	820
HSA-MIR-4748	98.95	67.53	810
HSA-MIR-4780	98.57	64.75	611
HSA-MIR-3689A-5P	98.35	70.12	1049
HSA-MIR-3689B-5P	98.35	70.12	1049
HSA-MIR-3689E	98.35	70.12	1049
HSA-MIR-3689F	98.35	70.08	1052
HSA-MIR-4669	97.94	62.71	224
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-4432	97.80	67.87	705
HSA-MIR-4670-3P	97.37	68.35	1378

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

• Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. (PMID:12032086)
• snoRNP assembly factor NUFIP can regulate the interactions between TIP48 and TIP49 and the core box C/D proteins. (PMID:19620283)
• SUMOylation is essential for high-affinity Nop58 binding to small nucleolar riboproteins. (PMID:20797632)
• Bcd1p controls RNA loading of the core protein Nop58 during C/D box snoRNP biogenesis. (PMID:30700579)
• Long noncoding RNA FAM83A-AS1 facilitates hepatocellular carcinoma progression by binding with NOP58 to enhance the mRNA stability of FAM83A. (PMID:31696213)
• NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis. (PMID:33367824)
• Overexpression of NOP58 as a Prognostic Marker in Hepatocellular Carcinoma: A TCGA Data-Based Analysis. (PMID:34014550)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nop58	ENSDARG00000104353
mus_musculus	Nop58	ENSMUSG00000026020
rattus_norvegicus	Nop58	ENSRNOG00000016486
drosophila_melanogaster	nop5	FBGN0026196
caenorhabditis_elegans	nol-58	WBGENE00020915

Paralogs (1): NOP56 (ENSG00000101361)

Protein

Protein identifiers

Nucleolar protein 58 — Q9Y2X3 (reviewed: Q9Y2X3)

Alternative names: Nucleolar protein 5

All UniProt accessions (3): Q9Y2X3, F8WED0, H7BZ72

UniProt curated annotations — full annotation on UniProt →

Function. Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs. 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. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes that function in methylation of multiple sites on ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs).

Subunit / interactions. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles; the core proteins SNU13, NOP56, NOP58 and FBL or FBLL1 assemble stepwise onto the snoRNA. Interacts with NOLC1/Nopp140. Interacts with NOPCHAP1, NUFIP1, RUVBL1 and RUVBL2; NOPCHAP1 bridges the association of NOP58 with RUVBL1:RUVBL2 and NUFIP1. Interacts with PIH1D1. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3.

Subcellular location. Nucleus. Nucleolus. Nucleoplasm.

Tissue specificity. Ubiquitous.

Post-translational modifications. Sumoylation is essential for high-affinity binding to snoRNAs.

Similarity. Belongs to the NOP5/NOP56 family.

RefSeq proteins (1): NP_057018* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002687	Nop_dom	Domain
IPR012974	NOP58/56_N	Domain
IPR012976	NOSIC	Domain
IPR036070	Nop_dom_sf	Homologous_superfamily
IPR042239	Nop_C	Homologous_superfamily
IPR045056	Nop56/Nop58	Family

Pfam: PF01798, PF08156

UniProt features (41 total): cross-link 15, modified residue 7, sequence conflict 5, sequence variant 4, compositionally biased region 4, region of interest 2, mutagenesis site 2, chain 1, domain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7MQA	ELECTRON MICROSCOPY	2.7
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2X3-F1	75.38	0.35

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 (22): 304, 351, 483, 502, 514, 157, 353, 411, 415, 422, 426, 441, 444, 465, 467, 467, 467, 485, 497, 497 …

Mutagenesis-validated functional residues (2):

Position	Phenotype
283	restricted to nucleoplasm. abolishes interaction with nopchap1.
310–313	restricted to nucleoplasm. decreases interaction with nopchap1.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-4570464	SUMOylation of RNA binding proteins
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 185 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, PAL_PRMT5_TARGETS_UP, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_NEUROGENESIS, GOBP_RNA_METHYLATION, GOBP_MRNA_MODIFICATION, GHO_ATF5_TARGETS_UP, WEI_MYCN_TARGETS_WITH_E_BOX, MUELLER_PLURINET, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1

GO Biological Process (4): rRNA processing (GO:0006364), ribosomal small subunit biogenesis (GO:0042274), snoRNA localization (GO:0048254), ribosome biogenesis (GO:0042254)

GO Molecular Function (5): TFIID-class transcription factor complex binding (GO:0001094), RNA binding (GO:0003723), snoRNA binding (GO:0030515), ATPase binding (GO:0051117), protein binding (GO:0005515)

GO Cellular Component (12): fibrillar center (GO:0001650), nucleoplasm (GO:0005654), nucleolus (GO:0005730), sno(s)RNA-containing ribonucleoprotein complex (GO:0005732), cytosol (GO:0005829), Cajal body (GO:0015030), membrane (GO:0016020), box C/D methylation guide snoRNP complex (GO:0031428), small-subunit processome (GO:0032040), pre-snoRNP complex (GO:0070761), nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
SUMO E3 ligases SUMOylate target proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
ribosome biogenesis	2
ribonucleoprotein complex biogenesis	2
nucleolus	2
nuclear lumen	2
ribonucleoprotein complex	2
RNA processing	1
rRNA metabolic process	1
RNA localization	1
RNA polymerase II general transcription initiation factor binding	1
nucleic acid binding	1
RNA binding	1
enzyme binding	1
binding	1
intracellular membraneless organelle	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
box C/D RNP complex	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

3670 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NOP58	FBL	P22087	999
NOP58	SNU13	P55769	998
NOP58	NOP56	O00567	989
NOP58	RRP9	O43818	964
NOP58	NHP2	Q9NX24	963
NOP58	DKC1	O60832	917
NOP58	PIH1D1	Q9NWS0	864
NOP58	RUVBL2	Q9Y230	820
NOP58	NOP10	Q9NPE3	811
NOP58	RUVBL1	P82276	809
NOP58	PWP2	Q15269	767
NOP58	UTP15	Q8TED0	753
NOP58	BMS1	Q14692	749
NOP58	TBL3	Q12788	748
NOP58	UTP4	Q969X6	743

IntAct

168 interactions, top by confidence:

A	B	Type	Score
MED29	MED19	psi-mi:“MI:0914”(association)	0.890
NOP58	FBL	psi-mi:“MI:0914”(association)	0.800
FBL	NOP56	psi-mi:“MI:0914”(association)	0.800
MED9	MED19	psi-mi:“MI:0914”(association)	0.790
XPC	CETN3	psi-mi:“MI:0914”(association)	0.730
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
TGS1	NOP58	psi-mi:“MI:0407”(direct interaction)	0.660
TGS1	NOP58	psi-mi:“MI:0915”(physical association)	0.660
DDX21	DKC1	psi-mi:“MI:0914”(association)	0.640
NEMP1	RGPD8	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
RUVBL2	POLR3A	psi-mi:“MI:0914”(association)	0.640
NOP58	NOP56	psi-mi:“MI:0914”(association)	0.640
NUFIP1	NOP58	psi-mi:“MI:0914”(association)	0.600
NOP58	SNU13	psi-mi:“MI:0915”(physical association)	0.560
NOP58	NOPCHAP1	psi-mi:“MI:0915”(physical association)	0.560
NP	KPNA6	psi-mi:“MI:0914”(association)	0.550
BCOR	CBX4	psi-mi:“MI:0914”(association)	0.530
FBL	ZNF316	psi-mi:“MI:0914”(association)	0.530
TGS1	SNRNP70	psi-mi:“MI:0914”(association)	0.530
CUL3	ACOT7	psi-mi:“MI:0914”(association)	0.500
CSNK2A1	NOP58	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
NOP58	SERPINH1	psi-mi:“MI:0915”(physical association)	0.400
THUMPD2	NOP58	psi-mi:“MI:0915”(physical association)	0.400
Ybx1	MRPS18B	psi-mi:“MI:0915”(physical association)	0.400
Snu13		psi-mi:“MI:0915”(physical association)	0.400

BioGRID (438): NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), NOP58 (Biochemical Activity), NOP58 (Affinity Capture-MS), NOP58 (Biochemical Activity), NOP58 (Affinity Capture-MS), NOP58 (Affinity Capture-MS), DCAF13 (Co-fractionation), DDX24 (Co-fractionation), DDX27 (Co-fractionation)

ESM2 similar proteins: A1CL70, A1D688, A2QE38, A3LUT0, A5DHW0, A5E4V9, A6QYH8, A6RMY5, A6ZPE5, A7F2R6, A7TIF5, O00567, O04658, O94514, P0CP02, P0CP03, P0CP26, P0CP27, P0CP58, P0CP59, P39730, Q0CQH1, Q10251, Q12460, Q12499, Q1E1Q5, Q21276, Q2UC04, Q3SZ63, Q4PBF2, Q4R779, Q4WYK9, Q54MT2, Q55FI4, Q59S06, Q5B8G3, Q5RA29, Q6BIX6, Q6CG46, Q6CKR8

Diamond homologs: A1CL70, A1D688, A2QE38, A3LUT0, A5DHW0, A5E4V9, A6QYH8, A6RMY5, A6ZPE5, A7F2R6, A7TIF5, O00567, O04656, O04658, O94514, P0CP26, P0CP27, Q0CQH1, Q12460, Q12499, Q1E1Q5, Q21276, Q2UC04, Q3SZ63, Q4PBF2, Q4R779, Q4WYK9, Q54MT2, Q55FI4, Q58105, Q59S06, Q5B8G3, Q5RA29, Q6BIX6, Q6CG46, Q6CKR8, Q6DFW4, Q6FQ21, Q753I4, Q8X066

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
NOP58	“form complex”	“U3 snoRNP”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 179 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.

GO biological processes:

GO term	Partners	Fold	FDR
NLS-bearing protein import into nucleus	7	38.7×	3e-07
positive regulation of transcription elongation by RNA polymerase II	7	14.5×	3e-04
mRNA stabilization	5	12.6×	8e-03
rRNA processing	8	7.8×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	56
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1455397	NC_000002.11:g.(?202566574)(203424669_?)del	Pathogenic

SpliceAI

2311 predictions. Top by Δscore:

Variant	Effect	Δscore
2:202275102:T:G	acceptor_gain	1.0000
2:202275106:A:AG	acceptor_gain	1.0000
2:202275107:TTACA:T	acceptor_loss	1.0000
2:202275108:TACA:T	acceptor_loss	1.0000
2:202275109:A:AG	acceptor_gain	1.0000
2:202275110:CAGG:C	acceptor_loss	1.0000
2:202275111:A:AG	acceptor_gain	1.0000
2:202275111:AG:A	acceptor_gain	1.0000
2:202275111:AGGTT:A	acceptor_loss	1.0000
2:202275112:G:GG	acceptor_gain	1.0000
2:202275112:GG:G	acceptor_gain	1.0000
2:202275112:GGT:G	acceptor_gain	1.0000
2:202275112:GGTT:G	acceptor_gain	1.0000
2:202275112:GGTTC:G	acceptor_gain	1.0000
2:202275185:AAAAT:A	donor_gain	1.0000
2:202275186:AAAT:A	donor_gain	1.0000
2:202275187:AAT:A	donor_gain	1.0000
2:202275187:AATGT:A	donor_loss	1.0000
2:202275188:AT:A	donor_gain	1.0000
2:202275189:TG:T	donor_loss	1.0000
2:202275190:G:GG	donor_gain	1.0000
2:202277942:A:AG	acceptor_gain	1.0000
2:202277943:A:G	acceptor_gain	1.0000
2:202277948:A:AG	acceptor_gain	1.0000
2:202277949:G:GG	acceptor_gain	1.0000
2:202277949:GA:G	acceptor_gain	1.0000
2:202278001:AGG:A	donor_loss	1.0000
2:202278002:GGTAA:G	donor_loss	1.0000
2:202278003:G:C	donor_loss	1.0000
2:202278004:T:G	donor_loss	1.0000

AlphaMissense

3474 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:202290379:T:A	W186R	1.000
2:202290379:T:C	W186R	1.000
2:202290388:T:A	W189R	1.000
2:202290388:T:C	W189R	1.000
2:202291217:G:A	G243R	1.000
2:202291217:G:C	G243R	1.000
2:202292799:G:C	R268P	1.000
2:202295742:T:C	F326L	1.000
2:202295744:C:A	F326L	1.000
2:202295744:C:G	F326L	1.000
2:202295782:G:A	G339D	1.000
2:202265969:G:C	G10R	0.999
2:202265970:G:A	G10D	0.999
2:202284391:T:C	L115P	0.999
2:202284406:G:C	R120P	0.999
2:202284477:C:G	H144D	0.999
2:202287682:T:C	F153L	0.999
2:202287684:T:A	F153L	0.999
2:202287684:T:G	F153L	0.999
2:202287700:G:C	D159H	0.999
2:202287708:G:A	M161I	0.999
2:202287708:G:C	M161I	0.999
2:202287708:G:T	M161I	0.999
2:202287718:G:C	A165P	0.999
2:202290350:T:C	L176P	0.999
2:202290354:C:A	N177K	0.999
2:202290354:C:G	N177K	0.999
2:202290366:G:A	M181I	0.999
2:202290366:G:C	M181I	0.999
2:202290366:G:T	M181I	0.999

dbSNP variants (sampled 300 via entrez): RS1000026848 (2:202293614 C>G,T), RS1000053207 (2:202280513 A>C,G), RS1000126627 (2:202280668 T>C), RS1000136804 (2:202287357 C>T), RS1000174334 (2:202276201 G>A), RS1000221571 (2:202269823 C>A,G,T), RS1000273846 (2:202270243 G>C), RS1000293485 (2:202268605 G>A), RS1000299017 (2:202287592 T>C,G), RS1000390041 (2:202282503 C>T), RS1000481689 (2:202301666 G>A,T), RS1000624449 (2:202269897 C>T), RS1000656927 (2:202270187 A>C), RS1000726453 (2:202303809 G>A), RS1000817585 (2:202264543 C>T)

Disease associations

OMIM: gene MIM:616742 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067121 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.54	Kd	28.69	nM	CHEMBL3752910
7.54	ED50	28.69	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 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-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149899: Binding affinity to human NOP58 incubated for 45 mins by Kinobead based pull down assay	kd	0.0287	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases expression	3
deoxynivalenol	increases expression	2
sodium arsenite	decreases expression	2
nivalenol	increases expression	2
Plant Extracts	increases expression, decreases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	decreases sumoylation	1
TL8-506	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization	1
coumarin	increases phosphorylation	1
15-acetyldeoxynivalenol	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
chloropicrin	increases expression	1
deguelin	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
pyrimidifen	increases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
bisphenol S	increases expression	1
jinfukang	decreases expression, affects cotreatment	1
LDN 193189	affects cotreatment, decreases expression	1
picoxystrobin	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652941	Binding	Binding affinity to human NOP58 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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