NOL10

Summary

NOL10 (nucleolar protein 10, HGNC:25862) is a protein-coding gene on chromosome 2p25.1, encoding Nucleolar protein 10 (Q9BSC4). It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in nucleolus.

Source: NCBI Gene 79954 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 96 total
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_024894

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25862
Approved symbol	NOL10
Name	nucleolar protein 10
Location	2p25.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14075
Ensembl gene	ENSG00000115761
Ensembl biotype	protein_coding
OMIM	616197
Entrez	79954

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 10 protein_coding, 6 retained_intron, 6 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined

ENST00000345985, ENST00000381685, ENST00000431319, ENST00000473087, ENST00000538384, ENST00000695464, ENST00000695465, ENST00000695466, ENST00000695467, ENST00000695468, ENST00000695469, ENST00000695470, ENST00000695471, ENST00000695472, ENST00000695473, ENST00000695474, ENST00000695475, ENST00000695476, ENST00000695477, ENST00000695478, ENST00000695479, ENST00000695480, ENST00000900361, ENST00000928634, ENST00000928635, ENST00000971267

RefSeq mRNA: 3 — MANE Select: NM_024894 NM_001261392, NM_001261394, NM_024894

CCDS: CCDS1673, CCDS58697, CCDS58698

Canonical transcript exons

ENST00000381685 — 21 exons

Exon	Start	End
ENSE00000710613	10600853	10600942
ENSE00000710614	10602776	10602874
ENSE00000710617	10607185	10607311
ENSE00000710699	10657742	10657891
ENSE00000710701	10659172	10659250
ENSE00000804743	10654481	10654547
ENSE00000804746	10662959	10663044
ENSE00000804748	10667218	10667278
ENSE00001137526	10644320	10644372
ENSE00001137560	10673520	10673557
ENSE00001137597	10603078	10603157
ENSE00001137627	10668658	10668723
ENSE00001137656	10684567	10684612
ENSE00001203548	10671554	10671690
ENSE00003581913	10675794	10675871
ENSE00003612925	10681971	10682069
ENSE00003963894	10589043	10589290
ENSE00003963898	10589578	10589751
ENSE00003963913	10577636	10577738
ENSE00003963922	10570754	10572190
ENSE00003963934	10689796	10689975

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 97.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.2618 / max 354.5567, expressed in 1810 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26879	17.2618	1810

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.88	gold quality
male germ cell	CL:0000015	95.47	gold quality
parotid gland	UBERON:0001831	90.49	gold quality
adrenal tissue	UBERON:0018303	90.49	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.55	gold quality
calcaneal tendon	UBERON:0003701	89.29	gold quality
epithelium of nasopharynx	UBERON:0001951	88.02	gold quality
tendon	UBERON:0000043	87.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.53	gold quality
islet of Langerhans	UBERON:0000006	86.35	gold quality
sural nerve	UBERON:0015488	85.73	gold quality
gastrocnemius	UBERON:0001388	84.88	gold quality
cardia of stomach	UBERON:0001162	84.74	gold quality
muscle of leg	UBERON:0001383	84.42	gold quality
pancreas	UBERON:0001264	84.25	gold quality
body of pancreas	UBERON:0001150	84.03	gold quality
gingival epithelium	UBERON:0001949	83.97	gold quality
tendon of biceps brachii	UBERON:0008188	83.93	gold quality
adrenal gland	UBERON:0002369	83.88	gold quality
stromal cell of endometrium	CL:0002255	83.68	gold quality
mammary duct	UBERON:0001765	83.60	gold quality
gingiva	UBERON:0001828	83.46	gold quality
ventricular zone	UBERON:0003053	83.36	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.36	gold quality
saphenous vein	UBERON:0007318	83.35	gold quality
tonsil	UBERON:0002372	83.29	gold quality
left adrenal gland	UBERON:0001234	83.26	gold quality
pharyngeal mucosa	UBERON:0000355	83.25	gold quality
right adrenal gland	UBERON:0001233	83.24	gold quality
right adrenal gland cortex	UBERON:0035827	83.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.67
E-MTAB-6678	no	3.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

72 targeting NOL10, 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-1193	100.00	65.93	529
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 1)

• PQBP5/NOL10 maintains and anchors the nucleolus under physiological and osmotic stress conditions. (PMID:36599853)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nol10	ENSDARG00000020077
mus_musculus	Nol10	ENSMUSG00000061458
rattus_norvegicus	Nol10	ENSRNOG00000005344
drosophila_melanogaster	l(2)34Fd	FBGN0261535
caenorhabditis_elegans		WBGENE00017989

Protein

Protein identifiers

Nucleolar protein 10 — Q9BSC4 (reviewed: Q9BSC4)

All UniProt accessions (10): Q9BSC4, A0A8Q3SHS4, A0A8Q3SHT1, A0A8Q3SHT2, A0A8Q3SHT6, A0A8Q3SHW5, A0A8Q3SHX7, A0A8Q3SHY9, A0A8Q3SHZ5, A0A8Q3SIR1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the WD repeat NOL10/ENP2 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9BSC4-1	1	yes
Q9BSC4-2	2
Q9BSC4-3	3
Q9BSC4-4	4

RefSeq proteins (3): NP_001248321, NP_001248323, NP_079170* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR012580	NUC153	Domain
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR040382	NOL10/Enp2	Family
IPR056550	NOL10_2nd	Domain
IPR056551	Beta-prop_NOL10_N	Domain

Pfam: PF08159, PF23097, PF23098

UniProt features (29 total): repeat 7, splice variant 6, modified residue 5, coiled-coil region 3, compositionally biased region 2, sequence conflict 2, region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

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

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSC4-F1	77.60	0.31

Functional residue map

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

Post-translational modifications (5): 1, 25, 475, 481, 514

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_RIBOSOME_BIOGENESIS, chr2p25, GOBP_MATURATION_OF_SSU_RRNA, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, BACH2_01, LASTOWSKA_COAMPLIFIED_WITH_MYCN, CREB_Q3, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP

GO Biological Process (1): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): nucleolus (GO:0005730), small-subunit processome (GO:0032040), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
maturation of SSU-rRNA	1
nucleic acid binding	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2093 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NOL10	NGDN	Q8NEJ9	862
NOL10	AATF	Q9NY61	796
NOL10	UTP15	Q8TED0	699
NOL10	NOP58	Q9Y2X3	663
NOL10	WDR36	Q8NI36	640
NOL10	RBM34	P42696	597
NOL10	UTP14A	Q9BVJ6	597
NOL10	PDCD11	Q14690	572
NOL10	BMS1	Q14692	567
NOL10	DDX51	Q8N8A6	563
NOL10	SLC66A3	Q8N755	514
NOL10	KIAA0513	O60268	506
NOL10	TBC1D31	Q96DN5	492
NOL10	NAT10	Q9H0A0	491
NOL10	KCNF1	Q9H3M0	476

IntAct

94 interactions, top by confidence:

A	B	Type	Score
LARP7	CCNT1	psi-mi:“MI:0914”(association)	0.850
CCT2	TXNDC9	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
rep	MPHOSPH10	psi-mi:“MI:0914”(association)	0.660
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
CCT7	PEX7	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
NOL10	DDX10	psi-mi:“MI:0914”(association)	0.530
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
NOL10	HNRNPM	psi-mi:“MI:0915”(physical association)	0.400
NELL1	NOL10	psi-mi:“MI:0915”(physical association)	0.400
Shoc2	GABPB1	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
		psi-mi:“MI:0914”(association)	0.350
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
rep	NVL	psi-mi:“MI:0914”(association)	0.350
rep	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
SRPK2	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
NOL10	SRI	psi-mi:“MI:0914”(association)	0.350

BioGRID (207): NOL10 (Affinity Capture-MS), NOL10 (Affinity Capture-MS), NOL10 (Affinity Capture-MS), AATF (Co-fractionation), GRWD1 (Co-fractionation), NOL10 (Co-fractionation), NOL10 (Co-fractionation), NOL10 (Co-fractionation), NOL10 (Co-fractionation), NOL10 (Co-fractionation), NOL10 (Co-fractionation), NOL6 (Co-fractionation), PPP5C (Co-fractionation), RBM19 (Co-fractionation), WDR36 (Co-fractionation)

ESM2 similar proteins: A4IG32, A4QNE6, A5D7H2, A7MB16, A8WGE3, F1LNJ2, O43172, O43815, O55106, O60508, O75643, P55884, P58405, P79987, Q13033, Q15542, Q29RZ9, Q3MHE2, Q4G061, Q561Y0, Q569Z1, Q5E9I8, Q5M7F6, Q5M9G8, Q5NVD0, Q5R7H5, Q5RAC9, Q5RJG1, Q5VQ78, Q66H99, Q676U5, Q6DJD8, Q6H8D5, Q6H8D6, Q6NVM6, Q6P4T2, Q7T0Q5, Q8BGF3, Q8C092, Q8C0J2

Diamond homologs: G0S902, O74879, P48234, Q5RJG1, Q66H99, Q6NVM6, Q7T0Q5, Q802W4, Q9BSC4, Q5XGE2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 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 modification in the nucleus and cytosol	8	20.8×	4e-07
rRNA processing in the nucleus and cytosol	7	15.6×	7e-06
Influenza Viral RNA Transcription and Replication	5	15.0×	3e-04
rRNA processing	7	14.2×	1e-05
Peptide chain elongation	8	14.1×	5e-06
Viral mRNA Translation	8	14.1×	5e-06
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	8	13.9×	5e-06
Major pathway of rRNA processing in the nucleolus and cytosol	16	13.7×	7e-12

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal small subunit biogenesis	10	23.5×	7e-09
cytoplasmic translation	9	17.2×	6e-07
rRNA processing	9	13.1×	5e-06
regulation of alternative mRNA splicing, via spliceosome	5	12.6×	2e-03
translation	9	9.5×	4e-05
mRNA processing	9	7.3×	3e-04
RNA splicing	7	6.4×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3806 predictions. Top by Δscore:

Variant	Effect	Δscore
2:10572187:CAGA:C	acceptor_gain	1.0000
2:10572191:C:CC	acceptor_gain	1.0000
2:10577631:CTCA:C	donor_loss	1.0000
2:10577632:TCA:T	donor_loss	1.0000
2:10577633:CA:C	donor_loss	1.0000
2:10577634:A:AC	donor_gain	1.0000
2:10577634:A:AG	donor_loss	1.0000
2:10577634:AC:A	donor_gain	1.0000
2:10577634:ACC:A	donor_gain	1.0000
2:10577634:ACCCT:A	donor_gain	1.0000
2:10577635:C:CC	donor_gain	1.0000
2:10577635:CC:C	donor_gain	1.0000
2:10577635:CCC:C	donor_gain	1.0000
2:10577635:CCCT:C	donor_gain	1.0000
2:10577635:CCCTC:C	donor_gain	1.0000
2:10577734:TTTTG:T	acceptor_gain	1.0000
2:10577735:TTTG:T	acceptor_gain	1.0000
2:10577736:TTG:T	acceptor_gain	1.0000
2:10577736:TTGC:T	acceptor_loss	1.0000
2:10577737:TG:T	acceptor_gain	1.0000
2:10577737:TGCTA:T	acceptor_loss	1.0000
2:10577738:GCTAT:G	acceptor_loss	1.0000
2:10577739:C:CC	acceptor_gain	1.0000
2:10577741:A:AC	acceptor_gain	1.0000
2:10577741:A:C	acceptor_gain	1.0000
2:10589037:AC:A	donor_loss	1.0000
2:10589038:C:CA	donor_loss	1.0000
2:10589039:TCA:T	donor_loss	1.0000
2:10589040:CAC:C	donor_loss	1.0000
2:10589041:A:AC	donor_gain	1.0000

AlphaMissense

4530 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:10603109:C:T	G401E	1.000
2:10607196:A:G	L381P	1.000
2:10607211:A:T	V376D	1.000
2:10607213:A:C	F375L	1.000
2:10607213:A:T	F375L	1.000
2:10607215:A:G	F375L	1.000
2:10607290:A:G	W350R	1.000
2:10607290:A:T	W350R	1.000
2:10607298:G:T	A347D	1.000
2:10675846:A:C	C79W	1.000
2:10603110:C:A	G401W	0.999
2:10603110:C:G	G401R	0.999
2:10603110:C:T	G401R	0.999
2:10603127:A:G	L395P	0.999
2:10603127:A:T	L395H	0.999
2:10603145:A:G	L389P	0.999
2:10603154:A:G	L386P	0.999
2:10607196:A:T	L381H	0.999
2:10607214:A:C	F375C	0.999
2:10607214:A:G	F375S	0.999
2:10607277:A:G	L354S	0.999
2:10607285:A:C	C351W	0.999
2:10607287:A:G	C351R	0.999
2:10607288:C:A	W350C	0.999
2:10607288:C:G	W350C	0.999
2:10644372:C:T	G325D	0.999
2:10657756:A:G	W298R	0.999
2:10657756:A:T	W298R	0.999
2:10657872:C:G	R259P	0.999
2:10659176:C:A	G251V	0.999

dbSNP variants (sampled 300 via entrez): RS1000004395 (2:10597625 A>G), RS1000005088 (2:10635902 T>A,C), RS1000062597 (2:10586801 GCTTAT>G), RS1000081486 (2:10611656 C>T), RS1000115025 (2:10666415 T>G), RS1000116983 (2:10591874 A>G), RS1000117092 (2:10627280 T>C), RS1000150186 (2:10577526 TC>T), RS1000211799 (2:10683022 A>T), RS1000225402 (2:10689505 G>A), RS1000251323 (2:10681334 A>G), RS1000270258 (2:10687966 C>T), RS1000316938 (2:10581009 A>G), RS1000342026 (2:10653231 T>C), RS1000382944 (2:10654954 A>C)

Disease associations

OMIM: gene MIM:616197 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002606_28	Prostate cancer	3.000000e-08
GCST002606_9	Prostate cancer	2.000000e-08
GCST008403_33	Arterial stiffness index	5.000000e-06
GCST010677_2	Liver fibrogenesis (alpha smooth muscle actin levels)	7.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004517	arterial stiffness measurement
EFO:0010576	liver fibrosis measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
TAK-243	increases sumoylation	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
methacrylaldehyde	increases abundance, affects cotreatment, increases oxidation	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
eprenetapopt	affects reaction, affects expression	1
Erlotinib Hydrochloride	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Catechin	decreases expression, affects cotreatment	1
Diethylstilbestrol	increases expression	1
Doxorubicin	increases expression	1
Estradiol	increases expression	1
Ethyl Methanesulfonate	decreases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1

Clinical trials (associated diseases)

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