UTP18

gene
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Also known as CGI-48

Summary

UTP18 (UTP18 small subunit processome component, HGNC:24274) is a protein-coding gene on chromosome 17q21.33, encoding U3 small nucleolar RNA-associated protein 18 homolog (Q9Y5J1). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. It is a common-essential gene (DepMap: required in 96.9% of cancer cell lines).

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in nuclear membrane; nucleolus; and nucleoplasm. Part of small-subunit processome.

Source: NCBI Gene 51096 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 82 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 96.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_016001

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24274
Approved symbolUTP18
NameUTP18 small subunit processome component
Location17q21.33
Locus typegene with protein product
StatusApproved
AliasesCGI-48
Ensembl geneENSG00000011260
Ensembl biotypeprotein_coding
OMIM612816
Entrez51096

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000225298, ENST00000508506, ENST00000579261, ENST00000582150, ENST00000582832, ENST00000583205, ENST00000583725, ENST00000854754, ENST00000854755, ENST00000854756, ENST00000932455, ENST00000932456, ENST00000932457, ENST00000942771, ENST00000942772, ENST00000942773

RefSeq mRNA: 1 — MANE Select: NM_016001 NM_016001

CCDS: CCDS42362

Canonical transcript exons

ENST00000225298 — 14 exons

ExonStartEnd
ENSE000007377955126327451263386
ENSE000007378075126618251266280
ENSE000007378105127586651275991
ENSE000007378135127713051277304
ENSE000007378225128802951288203
ENSE000008201065126054651260926
ENSE000022404695126883751268904
ENSE000022595755127336251273450
ENSE000026862335129778251297933
ENSE000034609805128038951280479
ENSE000034894875129696551297003
ENSE000035545985129390351294045
ENSE000035977105128000551280105
ENSE000036166605128524551285368

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 96.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.1893 / max 237.8671, expressed in 1810 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16174527.12551807
1617441.0638693

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453496.10gold quality
left testisUBERON:000453395.88gold quality
spermCL:000001995.78gold quality
esophagus squamous epitheliumUBERON:000692095.66gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099195.61gold quality
male germ cellCL:000001595.25gold quality
testisUBERON:000047395.22gold quality
adult organismUBERON:000702395.20gold quality
calcaneal tendonUBERON:000370195.09gold quality
cartilage tissueUBERON:000241894.98gold quality
gingival epitheliumUBERON:000194994.54gold quality
tibiaUBERON:000097994.45gold quality
squamous epitheliumUBERON:000691494.23gold quality
visceral pleuraUBERON:000240194.20gold quality
germinal epithelium of ovaryUBERON:000130494.12gold quality
gingivaUBERON:000182894.00gold quality
epithelium of esophagusUBERON:000197694.00gold quality
pleuraUBERON:000097793.85gold quality
parietal pleuraUBERON:000240093.80gold quality
palpebral conjunctivaUBERON:000181293.51gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047393.45gold quality
placentaUBERON:000198793.42gold quality
mucosa of sigmoid colonUBERON:000499393.25gold quality
oral cavityUBERON:000016793.23gold quality
skin of hipUBERON:000155493.21gold quality
eyeUBERON:000097093.19gold quality
monocyteCL:000057693.11gold quality
middle temporal gyrusUBERON:000277193.04gold quality
mononuclear cellCL:000084293.03gold quality
leukocyteCL:000073892.91gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting UTP18, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-656-3P100.0072.152788
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-22-3P99.9368.13917
HSA-MIR-1211999.8768.351653
HSA-MIR-58799.6470.862611
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-942-5P99.4168.401977
HSA-MIR-608899.2968.451284
HSA-MIR-149-5P99.2567.161315
HSA-MIR-422A99.1865.83550
HSA-MIR-6815-3P99.1368.981530
HSA-MIR-1207-3P98.9966.221532
HSA-MIR-4477A98.8369.752952
HSA-MIR-378A-3P98.4366.10548
HSA-MIR-378B98.4365.36573
HSA-MIR-378C98.4366.10548
HSA-MIR-378D98.4366.10548
HSA-MIR-378E98.4365.99551
HSA-MIR-378F98.4365.66554
HSA-MIR-378H98.4366.16545
HSA-MIR-378I98.4366.10548
HSA-MIR-506-5P98.0267.411065
HSA-MIR-430398.0168.132304
HSA-MIR-892B98.0067.11821
HSA-MIR-365496.4366.55646
HSA-MIR-208A-3P95.8766.51397
HSA-MIR-208B-3P95.8766.56396

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.9% of screened cell lines, common-essential.

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusUtp18ENSMUSG00000054079
rattus_norvegicusUtp18ENSRNOG00000002644

Protein

Protein identifiers

U3 small nucleolar RNA-associated protein 18 homologQ9Y5J1 (reviewed: Q9Y5J1)

Alternative names: WD repeat-containing protein 50

All UniProt accessions (6): Q9Y5J1, F6VJE8, J3KSR7, J3QLD6, J3QR85, J3QRG0

UniProt curated annotations — full annotation on UniProt →

Function. 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. Involved in nucleolar processing of pre-18S ribosomal RNA.

Subunit / interactions. 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.

Similarity. Belongs to the WD repeat UTP18 family.

RefSeq proteins (1): NP_057085* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR045161Utp18Family

Pfam: PF00400

UniProt features (25 total): modified residue 7, repeat 6, cross-link 4, compositionally biased region 3, region of interest 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
7MQAELECTRON MICROSCOPY2.7
7MQ8ELECTRON MICROSCOPY3.6
7MQ9ELECTRON MICROSCOPY3.87

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5J1-F177.920.45

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 (11): 121, 124, 204, 205, 206, 210, 221, 84, 183, 201, 517

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-6790901rRNA modification in the nucleus and cytosol
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 225 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, RNGTGGGC_UNKNOWN, GOBP_RIBOSOME_BIOGENESIS, MORF_MBD4, GOBP_MATURATION_OF_SSU_RRNA, MORF_RAD21, GGGTGGRR_PAX4_03, USF_C, SP1_Q2_01, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, MORF_SKP1A, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, ZIC1_01, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN

GO Biological Process (2): rRNA processing (GO:0006364), ribosomal small subunit biogenesis (GO:0042274)

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

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), nuclear membrane (GO:0031965), small-subunit processome (GO:0032040), Pwp2p-containing subcomplex of 90S preribosome (GO:0034388), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
rRNA processing in the nucleus and cytosol2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ribosome biogenesis2
nuclear lumen2
cellular anatomical structure2
nucleolus2
nuclear protein-containing complex2
RNA processing1
rRNA metabolic process1
ribonucleoprotein complex biogenesis1
nucleic acid binding1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
nucleus1
nuclear envelope1
organelle membrane1
preribosome1
t-UTP complex1
90S preribosome1

Protein interactions and networks

STRING

2309 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
UTP18TBL3Q12788986
UTP18WDR36Q8NI36972
UTP18UTP6Q9NYH9968
UTP18PWP2Q15269963
UTP18MTREXP42285954
UTP18WDR3Q9UNX4929
UTP18UTP4Q969X6846
UTP18HEATR1Q9H583836
UTP18UTP3Q9NQZ2833
UTP18WDR43Q15061759
UTP18UTP11Q9Y3A2742
UTP18NOP53Q9NZM5729
UTP18UTP15Q8TED0728
UTP18UTP20O75691709
UTP18NOL6Q9H6R4708

IntAct

109 interactions, top by confidence:

ABTypeScore
CCT2TXNDC9psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
PTK2TGFB1I1psi-mi:“MI:0914”(association)0.680
CCT5TXNDC9psi-mi:“MI:0914”(association)0.640
KMT2AMEN1psi-mi:“MI:0914”(association)0.640
C1DZFC3H1psi-mi:“MI:0914”(association)0.640
RPS14CCZ1Bpsi-mi:“MI:0914”(association)0.640
PWP2FBLpsi-mi:“MI:0914”(association)0.610
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
UTP18PWP2psi-mi:“MI:0915”(physical association)0.560
HAVCR2TCAF2psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
WDR43WDR75psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
CCT7PEX7psi-mi:“MI:0914”(association)0.530
EXOSC4ZFC3H1psi-mi:“MI:0914”(association)0.530
ADARB1SPTY2D1psi-mi:“MI:0914”(association)0.530
TOMM20TPP1psi-mi:“MI:0914”(association)0.480
UTP18CSNK2A1psi-mi:“MI:0217”(phosphorylation reaction)0.440
UTP18H1-5psi-mi:“MI:0915”(physical association)0.400
HCFC2MEN1psi-mi:“MI:0915”(physical association)0.400
UTP18ERBB2psi-mi:“MI:0915”(physical association)0.370
HNRNPUpsi-mi:“MI:0914”(association)0.350
Eif3eRPSApsi-mi:“MI:0914”(association)0.350
Eif3iCBX4psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350

BioGRID (166): UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), MPHOSPH10 (Co-fractionation), RBM19 (Co-fractionation), UTP18 (Co-fractionation), UTP18 (Affinity Capture-MS), UTP18 (Two-hybrid), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS), UTP18 (Affinity Capture-MS)

ESM2 similar proteins: A0JMQ0, A4IHS2, A9UZS7, B0WC36, B3MHX6, B3NLK7, B4GIU9, B4HN85, B4J9K1, B4KQU8, B4LKS9, B4MYI5, B4P528, F4IH25, O00423, O13046, O75717, P59328, P97452, Q05BC3, Q0D6V7, Q0VA16, Q14137, Q17LZ2, Q28XF0, Q2TAF3, Q32LB0, Q3TWF6, Q4V8C3, Q562C2, Q5EB92, Q5RAS1, Q5RJT2, Q5SSI6, Q5U2Z5, Q6DIP5, Q6GPP0, Q6GQ76, Q7K0Y1, Q7PTC5

Diamond homologs: Q5SSI6, Q9FMU5, Q9V7P1, Q9Y5J1, P40362, P78750, Q54MH6, Q9P4X3

SIGNOR signaling

1 interactions.

AEffectBMechanism
UTP18“form complex”“UTP-B complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 144 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:

PathwayPartnersFoldFDR
rRNA modification in the nucleus and cytosol917.6×4e-07
Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding515.7×1e-03
rRNA processing in the nucleus and cytosol711.7×3e-04
rRNA processing710.7×3e-04
Major pathway of rRNA processing in the nucleolus and cytosol1610.3×1e-09
mRNA Polyadenylation76.4×5e-03
Processing of Capped Intron-Containing Pre-mRNA76.0×6e-03
Metabolism of RNA125.2×3e-04

GO biological processes:

GO termPartnersFoldFDR
positive regulation of transcription by RNA polymerase I630.9×1e-05
positive regulation of telomere maintenance via telomerase529.1×1e-04
ribosomal small subunit biogenesis1221.7×2e-10
ribosomal large subunit biogenesis517.6×7e-04
regulation of alternative mRNA splicing, via spliceosome713.6×1e-04
RNA processing712.2×2e-04
negative regulation of translation69.3×3e-03
antiviral innate immune response59.0×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance65
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2463 predictions. Top by Δscore:

VariantEffectΔscore
17:51260894:G:GTdonor_gain1.0000
17:51260925:GG:Gdonor_gain1.0000
17:51260926:GG:Gdonor_gain1.0000
17:51260927:G:GGdonor_gain1.0000
17:51260932:G:GTdonor_gain1.0000
17:51260933:G:Tdonor_gain1.0000
17:51263268:CTGTA:Cacceptor_loss1.0000
17:51263270:GTAGG:Gacceptor_loss1.0000
17:51263271:TAG:Tacceptor_loss1.0000
17:51263272:A:Cacceptor_loss1.0000
17:51263382:GAAAT:Gdonor_gain1.0000
17:51263384:AAT:Adonor_gain1.0000
17:51263385:AT:Adonor_gain1.0000
17:51263386:TGTAA:Tdonor_loss1.0000
17:51263387:G:GAdonor_loss1.0000
17:51263387:G:GGdonor_gain1.0000
17:51263388:TAA:Tdonor_loss1.0000
17:51266179:TA:Tacceptor_loss1.0000
17:51266180:A:AGacceptor_gain1.0000
17:51266180:AG:Aacceptor_gain1.0000
17:51266180:AGG:Aacceptor_gain1.0000
17:51266180:AGGGT:Aacceptor_loss1.0000
17:51266181:G:Aacceptor_gain1.0000
17:51266181:G:GGacceptor_gain1.0000
17:51266181:GGG:Gacceptor_gain1.0000
17:51266181:GGGT:Gacceptor_gain1.0000
17:51266181:GGGTT:Gacceptor_gain1.0000
17:51266276:GAAGA:Gdonor_gain1.0000
17:51266277:AAGA:Adonor_gain1.0000
17:51266278:AGA:Adonor_gain1.0000

AlphaMissense

3662 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:51268868:T:AW196R0.996
17:51268868:T:CW196R0.996
17:51268870:G:CW196C0.996
17:51268870:G:TW196C0.996
17:51285265:T:AW409R0.996
17:51285265:T:CW409R0.996
17:51285362:C:AA441D0.996
17:51275929:T:CF259L0.995
17:51275931:C:AF259L0.995
17:51275931:C:GF259L0.995
17:51268838:T:CF186L0.994
17:51268840:C:AF186L0.994
17:51268840:C:GF186L0.994
17:51293904:T:AV502D0.994
17:51263355:T:AW142R0.992
17:51263355:T:CW142R0.992
17:51277227:C:AA312D0.992
17:51285361:G:CA441P0.990
17:51288166:C:AA489E0.990
17:51263357:G:CW142C0.989
17:51263357:G:TW142C0.989
17:51277232:A:CS314R0.989
17:51277234:T:AS314R0.989
17:51277234:T:GS314R0.989
17:51275930:T:CF259S0.988
17:51275986:T:CF278L0.988
17:51275988:T:AF278L0.988
17:51275988:T:GF278L0.988
17:51288046:T:AV449E0.988
17:51285368:G:AG443D0.987

dbSNP variants (sampled 300 via entrez): RS1000022706 (17:51279601 G>A,C), RS1000075663 (17:51274385 C>G), RS1000152256 (17:51291013 A>G), RS1000240467 (17:51259316 A>G), RS1000375758 (17:51297414 A>G), RS1000505999 (17:51278322 A>G), RS1000556238 (17:51291999 G>T), RS1000607304 (17:51291751 AAAG>A), RS1000611090 (17:51297913 G>A), RS1000619069 (17:51278113 A>G), RS1000629771 (17:51280579 C>T), RS1000745672 (17:51285017 C>T), RS1000938097 (17:51267454 T>A), RS1000967136 (17:51270150 C>T), RS1001004120 (17:51272635 A>G)

Disease associations

OMIM: gene MIM:612816 | 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):

StudyTraitp-value
GCST003993_14Menarche (age at onset)1.000000e-10
GCST008103_55Bipolar disorder4.000000e-07
GCST009391_505Metabolite levels2.000000e-07
GCST90020028_1424Hip circumference adjusted for BMI1.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004703age at menarche
EFO:0010527pyridoxate measurement
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067108 (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).

pChemblTypeValueUnitMolecule
7.52Kd30.24nMCHEMBL5653589
7.52ED5030.24nMCHEMBL5653589

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.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149748: Binding affinity to human UTP18 incubated for 45 mins by Kinobead based pull down assaykd0.0302uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, affects cotreatment2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Aflatoxin B1affects cotreatment, decreases expression, increases methylation2
Particulate Matterincreases abundance, increases expression, decreases expression2
FR900359increases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
coumarinincreases phosphorylation1
nivalenolincreases expression1
beta-methylcholineaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001affects expression1
dorsomorphinaffects cotreatment, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Vorinostataffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Benzo(a)pyreneincreases expression1
Benztropineincreases expression1
Cannabidiolincreases expression1
Clozapineincreases expression1
Diazinonincreases methylation1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradiolincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652790BindingBinding affinity to human UTP18 incubated for 45 mins by Kinobead based pull down assayNVP-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.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.