NOP9

Summary

NOP9 (NOP9 nucleolar protein, HGNC:19826) is a protein-coding gene on chromosome 14q12, encoding Nucleolar protein 9 (Q86U38).

Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. Predicted to be active in nucleolus.

Source: NCBI Gene 161424 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 121 total
• MANE Select transcript: NM_174913

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19826
Approved symbol	NOP9
Name	NOP9 nucleolar protein
Location	14q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196943
Ensembl biotype	protein_coding
OMIM	618308
Entrez	161424

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000267425, ENST00000396802, ENST00000557362, ENST00000650565

RefSeq mRNA: 2 — MANE Select: NM_174913 NM_001286367, NM_174913

CCDS: CCDS66616, CCDS9624

Canonical transcript exons

ENST00000267425 — 10 exons

Exon	Start	End
ENSE00000940736	24304041	24304277
ENSE00001032211	24303732	24303857
ENSE00001032225	24300408	24300857
ENSE00001032252	24301965	24302106
ENSE00001032259	24299850	24300201
ENSE00001032264	24302232	24302424
ENSE00001032274	24301612	24301722
ENSE00001101284	24303074	24303214
ENSE00001300449	24304493	24304598
ENSE00001616260	24304938	24309124

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 89.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.1894 / max 73.3363, expressed in 1790 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139026	12.7416	1789
139027	0.4478	253

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skeletal muscle tissue	UBERON:0001134	89.13	gold quality
gastrocnemius	UBERON:0001388	88.73	gold quality
muscle of leg	UBERON:0001383	88.60	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.10	gold quality
muscle tissue	UBERON:0002385	86.55	gold quality
ganglionic eminence	UBERON:0004023	86.23	gold quality
granulocyte	CL:0000094	86.01	gold quality
ventricular zone	UBERON:0003053	85.70	gold quality
islet of Langerhans	UBERON:0000006	85.23	gold quality
duodenum	UBERON:0002114	85.06	gold quality
cortical plate	UBERON:0005343	84.70	gold quality
esophagus mucosa	UBERON:0002469	84.34	gold quality
mucosa of transverse colon	UBERON:0004991	84.31	gold quality
leukocyte	CL:0000738	84.17	gold quality
spleen	UBERON:0002106	84.16	gold quality
stromal cell of endometrium	CL:0002255	84.15	gold quality
apex of heart	UBERON:0002098	84.11	gold quality
monocyte	CL:0000576	84.01	gold quality
heart left ventricle	UBERON:0002084	83.88	gold quality
prefrontal cortex	UBERON:0000451	83.31	gold quality
esophagus	UBERON:0001043	83.23	gold quality
left adrenal gland cortex	UBERON:0035825	83.12	gold quality
pancreas	UBERON:0001264	83.06	gold quality
right adrenal gland	UBERON:0001233	82.89	gold quality
left adrenal gland	UBERON:0001234	82.85	gold quality
right adrenal gland cortex	UBERON:0035827	82.57	gold quality
adrenal gland	UBERON:0002369	82.47	gold quality
right lobe of liver	UBERON:0001114	82.44	gold quality
blood	UBERON:0000178	82.32	gold quality
tonsil	UBERON:0002372	82.30	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-9543	yes	1643.02
E-ANND-3	no	1.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting NOP9, 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-4481	100.00	66.42	1669
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000078442
mus_musculus	Nop9	ENSMUSG00000019297
rattus_norvegicus	Nop9	ENSRNOG00000020321
drosophila_melanogaster	CG11123	FBGN0033169
caenorhabditis_elegans		WBGENE00014078

Protein

Protein identifiers

Nucleolar protein 9 — Q86U38 (reviewed: Q86U38)

All UniProt accessions (3): A0A3B3ISH6, Q86U38, H0YJP7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NOP9 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86U38-1	1	yes
Q86U38-2	2

RefSeq proteins (2): NP_001273296, NP_777573* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001313	Pumilio_RNA-bd_rpt	Repeat
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR040000	NOP9	Family

Pfam: PF22493

UniProt features (19 total): repeat 6, sequence variant 4, compositionally biased region 2, splice variant 2, region of interest 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86U38-F1	86.53	0.76

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 7

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 84 (showing top): GOBP_RIBOSOME_BIOGENESIS, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, chr14q12, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_NUCLEAR_TRANSPORT, GOBP_MATURATION_OF_5_8S_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_NUCLEAR_EXPORT, GOBP_MATURATION_OF_5_8S_RRNA, GOBP_ORGANELLE_LOCALIZATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOCC_90S_PRERIBOSOME

GO Biological Process (5): ribosomal small subunit export from nucleus (GO:0000056), endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447), endonucleolytic cleavage to generate mature 5’-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472), endonucleolytic cleavage in 5’-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480), biological_process (GO:0008150)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (4): nucleolus (GO:0005730), 90S preribosome (GO:0030686), preribosome, small subunit precursor (GO:0030688), cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	3
endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	3
preribosome	2
ribosomal subunit export from nucleus	1
maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
rRNA 5’-end processing	1
nucleic acid binding	1
nuclear lumen	1
intracellular membraneless organelle	1
t-UTP complex	1

Protein interactions and networks

STRING

1783 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NOP9	PUM3	Q15397	678
NOP9	NOB1	Q9ULX3	508
NOP9	ANKRD18A	Q8IVF6	474
NOP9	PUM1	Q14671	470
NOP9	ZNF280D	Q6N043	433
NOP9	RIMKLB	Q9ULI2	397
NOP9	PUM2	Q8TB72	367
NOP9	ARHGEF19	Q8IW93	358
NOP9	CEBPZ	Q03701	352
NOP9	DDX49	Q9Y6V7	351
NOP9	DDX18	Q9NVP1	350
NOP9	DDX52	Q9Y2R4	350
NOP9	DKC1	O60832	349
NOP9	BYSL	Q13895	348
NOP9	RRP8	O43159	348

IntAct

138 interactions, top by confidence:

A	B	Type	Score
IGBP1	PPP6C	psi-mi:“MI:0914”(association)	0.940
RBM8A	CASC3	psi-mi:“MI:0914”(association)	0.900
BYSL	PARN	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
B3GAT3	GOLIM4	psi-mi:“MI:0914”(association)	0.640
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
PDGFRB	PIK3R2	psi-mi:“MI:0914”(association)	0.610
SPINT2	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
EPHA1	EXOC5	psi-mi:“MI:0914”(association)	0.530
PTGER3	PIK3R2	psi-mi:“MI:0914”(association)	0.530
LRRC4C	DVL2	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
CXCR4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
CXCR4	FANCA	psi-mi:“MI:0914”(association)	0.530
RBM19	KRR1	psi-mi:“MI:0914”(association)	0.530
CD44	PDPK1	psi-mi:“MI:0914”(association)	0.530
CSGALNACT2	TPST1	psi-mi:“MI:0914”(association)	0.530
EDA	AP3B1	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
LRRTM4	AP3B1	psi-mi:“MI:0914”(association)	0.530
SLC30A4	OPA1	psi-mi:“MI:0914”(association)	0.530

BioGRID (154): NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), NOP9 (Co-fractionation), NOP9 (Co-fractionation), NOP9 (Co-fractionation), POLR1D (Co-fractionation)

ESM2 similar proteins: A4FV45, A4IG72, A7E2Y6, D3ZUM2, E0CZ22, E1BP36, I3L5V6, O75127, Q0IHP3, Q0P5H9, Q14296, Q14CZ7, Q15021, Q28DE0, Q3SZK4, Q53R41, Q58CX2, Q5BK48, Q5M9G9, Q5R655, Q5RFI6, Q68FN9, Q6DI86, Q6DJ55, Q6GQ66, Q6PA48, Q6PDS3, Q6SZW1, Q7L8L6, Q7TMV3, Q7YS91, Q86U38, Q8BMC4, Q8BSN9, Q8C3S2, Q8K2Z4, Q8N0Z6, Q8NDA8, Q91V83, Q91YM4

Diamond homologs: Q86U38, Q8BMC4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 177 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
rRNA processing in the nucleus and cytosol	8	11.2×	3e-04
rRNA processing	8	10.2×	4e-04
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	9	7.6×	4e-04
Signaling by ROBO receptors	7	7.6×	4e-03
Eukaryotic Translation Termination	7	7.3×	4e-03
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	7	7.2×	4e-03
Formation of a pool of free 40S subunits	7	6.8×	5e-03
L13a-mediated translational silencing of Ceruloplasmin expression	7	6.2×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal small subunit biogenesis	6	9.0×	9e-03
cytoplasmic translation	7	8.5×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	104
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

4044 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:24300770:A:C	S204R	0.995
14:24300772:C:A	S204R	0.995
14:24300772:C:G	S204R	0.995
14:24304512:C:A	A556D	0.993
14:24301988:A:C	S278R	0.992
14:24301990:C:A	S278R	0.992
14:24301990:C:G	S278R	0.992
14:24305032:G:C	W616C	0.992
14:24305032:G:T	W616C	0.992
14:24304974:G:A	G597D	0.991
14:24300585:G:A	G142E	0.990
14:24300768:G:A	G203D	0.989
14:24300789:T:C	L210P	0.988
14:24301994:T:C	C280R	0.988
14:24302375:C:A	A365D	0.988
14:24305030:T:A	W616R	0.988
14:24305030:T:C	W616R	0.988
14:24304587:C:A	A581D	0.987
14:24300584:G:T	G142W	0.986
14:24304527:G:A	G561D	0.986
14:24300773:T:C	F205L	0.985
14:24300775:C:A	F205L	0.985
14:24300775:C:G	F205L	0.985
14:24302380:T:C	F367L	0.984
14:24302382:C:A	F367L	0.984
14:24302382:C:G	F367L	0.984
14:24304550:T:A	W569R	0.984
14:24304550:T:C	W569R	0.984
14:24304143:A:C	S505R	0.983
14:24304145:T:A	S505R	0.983

dbSNP variants (sampled 300 via entrez): RS1000004430 (14:24280870 G>A), RS1000065403 (14:24290706 G>GCACCCCAGAACT), RS1000076387 (14:24308808 C>A), RS1000119979 (14:24280612 G>A), RS1000147165 (14:24297185 G>A), RS1000203991 (14:24299737 T>G), RS1000414917 (14:24277653 A>C), RS1000519268 (14:24309126 A>C), RS1000752062 (14:24291312 C>T), RS1000827936 (14:24299871 C>G,T), RS1000838877 (14:24274385 A>T), RS1000870456 (14:24277942 T>A), RS1000935069 (14:24298441 C>G), RS1001042178 (14:24303871 G>A), RS1001151761 (14:24276276 C>A)

Disease associations

OMIM: gene MIM:618308 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002371_1	Parent of origin effect on language impairment (paternal)	4.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
mono(carboxy-isooctyl)phthalate	affects expression	1
Cadmium	increases abundance, increases expression	1
Estradiol	increases expression	1
Quercetin	decreases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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