UTP23

Summary

UTP23 (UTP23 small subunit processome component, HGNC:28224) is a protein-coding gene on chromosome 8q24.11, encoding rRNA-processing protein UTP23 homolog (Q9BRU9). Involved in rRNA-processing and ribosome biogenesis. It is a selective cancer dependency (DepMap: 88.3% of cell lines).

Enables mRNA 3’-UTR binding activity and mRNA 5’-UTR binding activity. Predicted to be involved in rRNA processing. Predicted to act upstream of or within endonucleolytic cleavage in 5’-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleus. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Implicated in colorectal adenocarcinoma.

Source: NCBI Gene 84294 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• Cancer dependency (DepMap): dependent in 88.3% of screened cell lines
• MANE Select transcript: NM_032334

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28224
Approved symbol	UTP23
Name	UTP23 small subunit processome component
Location	8q24.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC14595
Ensembl gene	ENSG00000147679
Ensembl biotype	protein_coding
Entrez	84294

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000309822, ENST00000517814, ENST00000517820, ENST00000519443, ENST00000520733, ENST00000521071, ENST00000521703, ENST00000521974, ENST00000524128, ENST00000940242

RefSeq mRNA: 1 — MANE Select: NM_032334 NM_032334

CCDS: CCDS6320

Canonical transcript exons

ENST00000309822 — 3 exons

Exon	Start	End
ENSE00000981304	116770192	116770366
ENSE00001196281	116771456	116774684
ENSE00001196285	116766524	116766791

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 96.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7004 / max 304.3934, expressed in 1786 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
90322	16.7004	1786

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	96.54	silver quality
pancreatic ductal cell	CL:0002079	95.27	silver quality
calcaneal tendon	UBERON:0003701	94.94	gold quality
epithelial cell of pancreas	CL:0000083	91.76	silver quality
cardia of stomach	UBERON:0001162	91.72	gold quality
pericardium	UBERON:0002407	91.63	gold quality
layer of synovial tissue	UBERON:0007616	91.51	gold quality
corpus callosum	UBERON:0002336	90.83	gold quality
nipple	UBERON:0002030	90.61	gold quality
vena cava	UBERON:0004087	90.44	silver quality
pylorus	UBERON:0001166	90.37	gold quality
parietal pleura	UBERON:0002400	90.30	gold quality
tibialis anterior	UBERON:0001385	90.25	gold quality
myocardium	UBERON:0002349	89.65	gold quality
synovial joint	UBERON:0002217	89.53	gold quality
secondary oocyte	CL:0000655	89.44	gold quality
cardiac muscle of right atrium	UBERON:0003379	89.39	gold quality
left ventricle myocardium	UBERON:0006566	89.33	gold quality
tendon	UBERON:0000043	89.12	gold quality
deltoid	UBERON:0001476	88.66	silver quality
mammary duct	UBERON:0001765	88.65	gold quality
superior surface of tongue	UBERON:0007371	88.61	gold quality
epithelium of mammary gland	UBERON:0003244	88.60	gold quality
visceral pleura	UBERON:0002401	88.49	gold quality
inferior vagus X ganglion	UBERON:0005363	88.46	gold quality
oocyte	CL:0000023	88.44	gold quality
buccal mucosa cell	CL:0002336	88.14	silver quality
upper arm skin	UBERON:0004263	88.13	gold quality
nasal cavity epithelium	UBERON:0005384	87.75	silver quality
pharyngeal mucosa	UBERON:0000355	87.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-110499	no	1788.69
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

141 targeting UTP23, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-23A-3P	99.95	74.24	3163

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 88.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

• yUtp23/hUTP23 could therefore be central to the coordinated integration and release of ES6 binding factors and likely plays a pivotal role in remodeling this pre-rRNA region in both yeast and humans. Finally, studies using RNAi-rescue systems in human cells revealed that intact PIN domain and Zinc finger motifs in human hUTP23 are essential for 18S rRNA maturation. (PMID:28082392)
• Our findings elucidated a previously unknown function for UTP23 in regulating paclitaxel sensitivity and UTP23 could serve as a potential prognostic predictor for ovarian cancer (PMID:31540773)
• UTP23 Functions in Breast Cancer Progression and Predicts Poor Prognosis of Luminal a Breast Cancer. (PMID:37880005)
• UTP23 Is a Promising Prognostic Biomarker and Is Associated with Immune Infiltration in Breast Cancer. (PMID:38305284)
• Cytoplasmic expression of UTP23 promotes colorectal cancer progression. (PMID:38372088)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	utp23	ENSDARG00000105012
mus_musculus	Utp23	ENSMUSG00000022313
rattus_norvegicus	Utp23	ENSRNOG00000063314
drosophila_melanogaster	CG17652	FBGN0031361
caenorhabditis_elegans		WBGENE00016411

Paralogs (1): FCF1 (ENSG00000119616)

Protein

Protein identifiers

rRNA-processing protein UTP23 homolog — Q9BRU9 (reviewed: Q9BRU9)

All UniProt accessions (7): Q9BRU9, E5RG01, E5RGP0, E5RH13, E5RIC4, E5RIM0, G3XAM4

UniProt curated annotations — full annotation on UniProt →

Function. Involved in rRNA-processing and ribosome biogenesis.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the UTP23/FCF1 family. UTP23 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BRU9-1	1	yes
Q9BRU9-2	2

RefSeq proteins (1): NP_115710* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006984	Fcf1/UTP23	Family
IPR029060	PIN-like_dom_sf	Homologous_superfamily
IPR057776	UTP23_sensor	Domain

Pfam: PF04900, PF24779

UniProt features (12 total): sequence variant 3, compositionally biased region 2, splice variant 2, chain 1, region of interest 1, sequence conflict 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRU9-F1	82.09	0.59

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 (2): 174, 179

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_RIBOSOME_BIOGENESIS, 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, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, SENESE_HDAC1_TARGETS_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GOMF_MRNA_BINDING

GO Biological Process (3): endonucleolytic cleavage in 5’-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (5): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), mRNA 5’-UTR binding (GO:0048027), small ribosomal subunit rRNA binding (GO:0070181), 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
mRNA binding	2
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
ribonucleoprotein complex biogenesis	1
nucleic acid binding	1
rRNA 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

1666 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UTP23	EIF3H	O15372	675
UTP23	DDX52	Q9Y2R4	674
UTP23	KRI1	Q8N9T8	648
UTP23	MED30	Q96HR3	614
UTP23	RCL1	Q9Y2P8	608
UTP23	EMG1	Q92979	606
UTP23	UTP3	Q9NQZ2	593
UTP23	UTP15	Q8TED0	560
UTP23	BMS1	Q14692	549
UTP23	WDR46	O15213	535
UTP23	PDCD11	Q14690	535
UTP23	KRR1	Q13601	526
UTP23	ABT1	Q9ULW3	510
UTP23	RAD21	O60216	504
UTP23	NOP14	P78316	490

IntAct

160 interactions, top by confidence:

A	B	Type	Score
KRTAP10-8	UTP23	psi-mi:“MI:0915”(physical association)	0.720
H1-1	RRP8	psi-mi:“MI:0914”(association)	0.640
	UTP23	psi-mi:“MI:0915”(physical association)	0.600
UTP23		psi-mi:“MI:0915”(physical association)	0.600
UTP23	PDE9A	psi-mi:“MI:0915”(physical association)	0.560
TRIM27	UTP23	psi-mi:“MI:0915”(physical association)	0.560
TCF4	UTP23	psi-mi:“MI:0915”(physical association)	0.560
TRIM23	UTP23	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	UTP23	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	UTP23	psi-mi:“MI:0915”(physical association)	0.560
KRT31	UTP23	psi-mi:“MI:0915”(physical association)	0.560
KRT40	UTP23	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLA	UTP23	psi-mi:“MI:0915”(physical association)	0.560
MID2	UTP23	psi-mi:“MI:0915”(physical association)	0.560
PDE9A	UTP23	psi-mi:“MI:0915”(physical association)	0.560
UTP23	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
UTP23	TCF4	psi-mi:“MI:0915”(physical association)	0.560
UTP23	TRIM23	psi-mi:“MI:0915”(physical association)	0.560
UTP23	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.560
UTP23	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (220): UTP23 (Two-hybrid), UTP23 (Two-hybrid), UTP23 (Two-hybrid), UTP23 (Two-hybrid), UTP23 (Two-hybrid), UTP23 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), UTP23 (Affinity Capture-RNA), UTP23 (Affinity Capture-MS), UTP23 (Affinity Capture-MS)

ESM2 similar proteins: A4IHS0, A5WUX7, A6ZND9, B1P1W2, B3LIY9, B4KPG8, B5XAM2, D2HD32, E7EXT2, O44568, O94443, P25642, P34511, P82673, Q05863, Q08230, Q08DT6, Q08DU1, Q09691, Q12322, Q14197, Q2KI45, Q3T116, Q3UFY8, Q497V5, Q498P2, Q5RDI0, Q5U2R4, Q60R52, Q7JUX9, Q80VP5, Q8C1Z8, Q8K2Y7, Q8MT06, Q8N5C6, Q8R035, Q8VCE1, Q95Q11, Q9BRU9, Q9BVP2

Diamond homologs: O13610, O74862, Q08DU1, Q12339, Q9BRU9, Q9CX11, Q32PD0, Q5RFQ0, Q9Y324, Q05498, Q55GM5, Q9CTH6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 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
Eukaryotic Translation Initiation	8	29.8×	3e-09
Cap-dependent Translation Initiation	8	29.8×	3e-09
SARS-CoV-1 modulates host translation machinery	8	29.8×	3e-09
Peptide chain elongation	19	29.1×	3e-21
Viral mRNA Translation	19	29.1×	3e-21
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	19	28.7×	3e-21
Selenocysteine synthesis	19	27.5×	4e-21
Eukaryotic Translation Termination	19	27.5×	4e-21

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	20	36.7×	2e-23
ribosomal small subunit biogenesis	9	20.3×	1e-07
translation	18	18.3×	2e-15
rRNA processing	10	14.0×	4e-07
RNA processing	6	13.0×	6e-04
regulation of alternative mRNA splicing, via spliceosome	5	12.1×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

459 predictions. Top by Δscore:

Variant	Effect	Δscore
8:116766787:ACAAG:A	donor_loss	1.0000
8:116766788:CAAGG:C	donor_loss	1.0000
8:116766789:AAGG:A	donor_loss	1.0000
8:116766790:AGG:A	donor_loss	1.0000
8:116766791:GGT:G	donor_loss	1.0000
8:116766792:G:A	donor_loss	1.0000
8:116766793:T:G	donor_loss	1.0000
8:116770186:TTTCA:T	acceptor_loss	1.0000
8:116770187:TTCA:T	acceptor_loss	1.0000
8:116770188:TCAG:T	acceptor_loss	1.0000
8:116770189:CAGAT:C	acceptor_loss	1.0000
8:116770190:A:G	acceptor_loss	1.0000
8:116770191:GAT:G	acceptor_gain	1.0000
8:116770191:GATGT:G	acceptor_gain	1.0000
8:116770295:G:GG	donor_gain	1.0000
8:116770326:TTG:T	donor_gain	1.0000
8:116770335:G:T	donor_gain	1.0000
8:116847688:CACG:C	acceptor_gain	1.0000
8:116847689:ACGC:A	acceptor_loss	1.0000
8:116847690:CG:C	acceptor_gain	1.0000
8:116847690:CGCT:C	acceptor_loss	1.0000
8:116847691:GCTG:G	acceptor_loss	1.0000
8:116847692:C:CC	acceptor_gain	1.0000
8:116847692:CTG:C	acceptor_loss	1.0000
8:116847693:T:A	acceptor_loss	1.0000
8:116848947:TGAAG:T	donor_gain	1.0000
8:116766741:G:GT	donor_gain	0.9900
8:116766768:G:GT	donor_gain	0.9900
8:116766768:G:T	donor_gain	0.9900
8:116766778:C:G	donor_gain	0.9900

AlphaMissense

1630 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:116770359:C:A	A119E	0.999
8:116766706:T:C	C35R	0.998
8:116766715:G:C	A38P	0.997
8:116766716:C:A	A38E	0.997
8:116770193:T:C	C64R	0.997
8:116766617:G:T	R5M	0.996
8:116766712:G:C	A37P	0.996
8:116770209:T:C	L69P	0.996
8:116766788:C:T	T62I	0.995
8:116770274:T:C	C91R	0.995
8:116770310:T:C	C103R	0.995
8:116770358:G:C	A119P	0.995
8:116766617:G:C	R5T	0.994
8:116766618:G:C	R5S	0.994
8:116766618:G:T	R5S	0.994
8:116766703:T:C	F34L	0.994
8:116766705:C:A	F34L	0.994
8:116766705:C:G	F34L	0.994
8:116770251:C:A	A83E	0.994
8:116770310:T:A	C103S	0.994
8:116770311:G:C	C103S	0.994
8:116770362:C:A	T120K	0.994
8:116766689:T:C	L29P	0.993
8:116766695:A:T	D31V	0.993
8:116770193:T:A	C64S	0.993
8:116770194:G:C	C64S	0.993
8:116770250:G:C	A83P	0.993
8:116770312:T:G	C103W	0.993
8:116771507:T:C	F139L	0.993
8:116771509:T:A	F139L	0.993

dbSNP variants (sampled 300 via entrez): RS1000294330 (8:116765679 T>C,G), RS1001256865 (8:116773965 T>A), RS1001791055 (8:116766797 C>G,T), RS1001948125 (8:116768051 A>G), RS1002044343 (8:116774801 A>G,T), RS1003549564 (8:116772045 G>A), RS1003576642 (8:116764860 T>C), RS1003603500 (8:116772388 T>C), RS1003799729 (8:116768032 A>C), RS1004007291 (8:116774449 G>A), RS1004021088 (8:116769400 T>C), RS1004357538 (8:116774756 A>G), RS1004360879 (8:116764705 G>A,C), RS1004418574 (8:116768301 T>C), RS1004747798 (8:116769661 T>C)

Disease associations

OMIM: gene `` | 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: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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