RRP15

gene
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Also known as CGI-115

Summary

RRP15 (ribosomal RNA processing 15 homolog, HGNC:24255) is a protein-coding gene on chromosome 1q41, encoding RRP15-like protein (Q9Y3B9). It is a common-essential gene (DepMap: required in 94.2% of cancer cell lines).

This gene encodes a protein that co-purifies with human nucleoli. A similar protein in budding yeast is a component of pre-60S ribosomal particles, and is required for the early maturation steps of the 60S subunit.

Source: NCBI Gene 51018 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 45 total — 2 pathogenic
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 94.2% of screened cell lines (common-essential)
  • MANE Select transcript: NM_016052

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24255
Approved symbolRRP15
Nameribosomal RNA processing 15 homolog
Location1q41
Locus typegene with protein product
StatusApproved
AliasesCGI-115
Ensembl geneENSG00000067533
Ensembl biotypeprotein_coding
OMIM611193
Entrez51018

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000366932, ENST00000491428, ENST00000925041, ENST00000925042, ENST00000925043, ENST00000925044, ENST00000925045

RefSeq mRNA: 1 — MANE Select: NM_016052 NM_016052

CCDS: CCDS1520

Canonical transcript exons

ENST00000366932 — 5 exons

ExonStartEnd
ENSE00001000133218305028218305125
ENSE00001000134218307431218307632
ENSE00001000135218302294218302559
ENSE00001443017218330948218337983
ENSE00001443018218285293218285455

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 91.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.4053 / max 997.1908, expressed in 1782 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
859424.40531782

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065591.50gold quality
oocyteCL:000002390.00gold quality
calcaneal tendonUBERON:000370189.74gold quality
cartilage tissueUBERON:000241887.01gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.12gold quality
germinal epithelium of ovaryUBERON:000130485.51gold quality
gastrocnemiusUBERON:000138885.35gold quality
esophagus squamous epitheliumUBERON:000692085.18gold quality
heart right ventricleUBERON:000208085.11gold quality
muscle of legUBERON:000138384.98gold quality
palpebral conjunctivaUBERON:000181284.29gold quality
squamous epitheliumUBERON:000691484.19gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.86gold quality
biceps brachiiUBERON:000150783.85gold quality
myocardiumUBERON:000234983.64silver quality
adrenal tissueUBERON:001830383.35gold quality
muscle organUBERON:000163083.13gold quality
gingival epitheliumUBERON:000194983.05gold quality
tendonUBERON:000004383.02gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450282.86gold quality
oviduct epitheliumUBERON:000480482.41gold quality
amniotic fluidUBERON:000017382.20gold quality
islet of LangerhansUBERON:000000682.11gold quality
hindlimb stylopod muscleUBERON:000425282.04gold quality
nephron tubuleUBERON:000123181.95gold quality
ventricular zoneUBERON:000305381.89gold quality
mucosa of sigmoid colonUBERON:000499381.86gold quality
epithelium of esophagusUBERON:000197681.84gold quality
oral cavityUBERON:000016781.56gold quality
gingivaUBERON:000182881.49gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-13yes729.84
E-CURD-7yes589.96
E-ENAD-21yes534.35
E-ANND-3yes8.31
E-MTAB-6142no53.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

315 targeting RRP15, 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-6867-5P100.0082.213464
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3163100.0077.238605
HSA-MIR-656-3P100.0072.152788
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5692A100.0074.406850
HSA-MIR-4262100.0073.263931
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3646100.0073.565283
HSA-MIR-340-5P100.0072.504437
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548AW99.9972.573559
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.2% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 5)

  • The budding yeast homolog of human RRP15 is required for maturation of 60S ribosomal particles (PMID:15769876)
  • Data suggest that ribosomal RNA-processing protein 15 (RRP15) might be a potential target for cancer therapy. (PMID:28099941)
  • Inhibition of ribosomal RNA processing 15 Homolog (RRP15), which is overexpressed in hepatocellular carcinoma, suppresses tumour growth via induction of senescence and apoptosis. (PMID:34343634)
  • RRP15 deficiency induces ribosome stress to inhibit colorectal cancer proliferation and metastasis via LZTS2-mediated beta-catenin suppression. (PMID:36750557)
  • Inhibition of Ribosomal RNA Processing 15 Homolog (RRP15) Suppressed Tumor Growth, Invasion and Epithelial to Mesenchymal Transition (EMT) of Colon Cancer. (PMID:36834940)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorrp15ENSDARG00000013478
mus_musculusRrp15ENSMUSG00000001305
rattus_norvegicusRrp15ENSRNOG00000002450
drosophila_melanogasterCG3817FBGN0038275

Protein

Protein identifiers

RRP15-like proteinQ9Y3B9 (reviewed: Q9Y3B9)

Alternative names: Ribosomal RNA-processing protein 15

All UniProt accessions (1): Q9Y3B9

UniProt curated annotations — full annotation on UniProt →

Post-translational modifications. Citrullinated by PADI4.

Similarity. Belongs to the RRP15 family.

RefSeq proteins (1): NP_057136* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012459Rrp15Family

Pfam: PF07890

UniProt features (29 total): modified residue 11, cross-link 5, compositionally biased region 4, sequence variant 3, region of interest 2, initiator methionine 1, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
8FKQELECTRON MICROSCOPY2.76
8FKPELECTRON MICROSCOPY2.85
8FKSELECTRON MICROSCOPY2.88
8FKRELECTRON MICROSCOPY2.89

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y3B9-F167.760.15

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 (16): 9, 11, 19, 58, 67, 104, 206, 266, 276, 280, 108, 179, 208, 239, 239, 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 235 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, ELVIDGE_HYPOXIA_DN, GOBP_RIBOSOME_BIOGENESIS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_MATURATION_OF_LSU_RRNA, MODULE_171, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GARY_CD5_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, GOBP_MATURATION_OF_5_8S_RRNA, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS

GO Biological Process (3): maturation of 5.8S rRNA (GO:0000460), maturation of LSU-rRNA (GO:0000470), rRNA processing (GO:0006364)

GO Molecular Function (0):

GO Cellular Component (1): preribosome, large subunit precursor (GO:0030687)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
rRNA processing2
ribosomal large subunit biogenesis1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
preribosome1

Protein interactions and networks

STRING

2296 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RRP15CSNK2A1P19138780
RRP15SURF6O75683774
RRP15PAK1IP1Q9NWT1696
RRP15GNL2Q13823676
RRP15NSA2O95478666
RRP15EBNA1BP2Q99848657
RRP15NOP2P46087647
RRP15WDR12Q9GZL7626
RRP15SPATA17Q96L03625
RRP15WDR74Q6RFH5614
RRP15GPATCH2Q9NW75608
RRP15NMD3Q96D46591
RRP15RRP12Q5JTH9568
RRP15PWP1Q13610558
RRP15SDAD1Q9NVU7557

IntAct

85 interactions, top by confidence:

ABTypeScore
SART3PRPF4psi-mi:“MI:0914”(association)0.730
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
PPANPPM1Gpsi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPL10RPS6psi-mi:“MI:0914”(association)0.350
NOP56C12orf43psi-mi:“MI:0914”(association)0.350
HNRNPUpsi-mi:“MI:0914”(association)0.350
SGTBARHGAP32psi-mi:“MI:0914”(association)0.350
SYNCRIPARHGAP32psi-mi:“MI:0914”(association)0.350
JUNpsi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
MKI67ARHGAP10psi-mi:“MI:0914”(association)0.350
OASLLARP1psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
PPANIGF2BP3psi-mi:“MI:0914”(association)0.350
C6orf11RRP8psi-mi:“MI:0914”(association)0.350
TAF1Dpsi-mi:“MI:0914”(association)0.350
USP2LONP1psi-mi:“MI:0914”(association)0.350
PTPN6RPL35Apsi-mi:“MI:0914”(association)0.350
NPOLRMTpsi-mi:“MI:0914”(association)0.350
NMRPL45psi-mi:“MI:0914”(association)0.350
EIF2AK2NKRFpsi-mi:“MI:0914”(association)0.350
SYKPLEKHD1psi-mi:“MI:0914”(association)0.350
SRPK1SNRPGP15psi-mi:“MI:0914”(association)0.350

BioGRID (183): RRP15 (Affinity Capture-MS), RRP15 (Affinity Capture-MS), DDX27 (Co-fractionation), DDX54 (Co-fractionation), NIFK (Co-fractionation), PAK1IP1 (Co-fractionation), RBM28 (Co-fractionation), RPF2 (Co-fractionation), RRP15 (Co-fractionation), RRP15 (Co-fractionation), RRP15 (Co-fractionation), RRP15 (Co-fractionation), RRP15 (Proximity Label-MS), RRP15 (Affinity Capture-MS), RRP15 (Affinity Capture-MS)

ESM2 similar proteins: A0AUP1, A4II15, A7MCB7, E1C760, F6RRD7, F7AEX0, P14629, P78316, Q1L8X2, Q28DG8, Q2IA00, Q3T071, Q3U155, Q3ZCI6, Q4R6T7, Q4R8R3, Q4R8V8, Q4V7N4, Q5PQS7, Q5R939, Q5RA37, Q5XI65, Q5ZIH9, Q5ZIM6, Q6DFL5, Q6IEG0, Q6PBE2, Q6PII3, Q7SYB2, Q7ZXA8, Q80VN0, Q8C6C7, Q8C9J3, Q8CIL4, Q8IXW5, Q8R3N1, Q8R3N6, Q8VYD3, Q93VM9, Q95JM8

Diamond homologs: P91318, Q3T062, Q5M947, Q61RF0, Q7ZV20, Q9CYX7, Q9Y3B9, Q296J6, Q9VFE6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 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
Peptide chain elongation1728.8×9e-19
Viral mRNA Translation1728.8×9e-19
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1728.4×9e-19
Selenocysteine synthesis1727.2×1e-18
Eukaryotic Translation Termination1727.2×1e-18
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1726.7×1e-18
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1726.7×1e-18
Formation of a pool of free 40S subunits1725.4×3e-18

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1933.8×2e-21
ribosomal large subunit biogenesis729.9×4e-07
ribosomal small subunit biogenesis1021.9×5e-09
translation1918.8×1e-16
negative regulation of viral genome replication518.0×6e-04
rRNA processing1317.7×9e-11
negative regulation of translation815.1×6e-06
RNA processing612.6×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance33
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1199385Single allelePathogenic
565226GRCh37/hg19 1q41(chr1:218486800-218632368)x1Pathogenic

SpliceAI

1297 predictions. Top by Δscore:

VariantEffectΔscore
1:218285453:AAG:Adonor_gain1.0000
1:218285453:AAGGT:Adonor_loss1.0000
1:218285454:AG:Adonor_loss1.0000
1:218285455:GGTAA:Gdonor_loss1.0000
1:218285456:G:Cdonor_loss1.0000
1:218285457:T:Gdonor_loss1.0000
1:218302283:T:TAacceptor_gain1.0000
1:218302284:G:Aacceptor_gain1.0000
1:218302289:TATA:Tacceptor_loss1.0000
1:218302290:A:AGacceptor_gain1.0000
1:218302291:T:Gacceptor_gain1.0000
1:218302292:A:AGacceptor_gain1.0000
1:218302292:AG:Aacceptor_gain1.0000
1:218302293:G:GTacceptor_gain1.0000
1:218302293:GG:Gacceptor_gain1.0000
1:218302293:GGA:Gacceptor_gain1.0000
1:218302293:GGAA:Gacceptor_gain1.0000
1:218307425:CTACA:Cacceptor_loss1.0000
1:218307430:GGGGT:Gacceptor_gain1.0000
1:218307611:G:GTdonor_gain1.0000
1:218307630:CAGGT:Cdonor_loss1.0000
1:218307631:AGGT:Adonor_loss1.0000
1:218307632:GGTAA:Gdonor_loss1.0000
1:218307633:G:Tdonor_loss1.0000
1:218307634:T:Adonor_loss1.0000
1:218317413:G:GTdonor_gain1.0000
1:218330936:A:AGacceptor_gain1.0000
1:218331036:A:Tdonor_gain1.0000
1:218331102:G:GTdonor_gain1.0000
1:218331103:A:Tdonor_gain1.0000

AlphaMissense

1900 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:218307453:G:CA176P0.999
1:218307457:T:AV177D0.999
1:218305119:C:AA166E0.998
1:218307433:G:AG169D0.998
1:218307445:T:CL173S0.998
1:218307447:T:CF174L0.998
1:218307449:T:AF174L0.998
1:218307449:T:GF174L0.998
1:218330978:T:AW246R0.998
1:218330978:T:CW246R0.998
1:218331028:G:CW262C0.998
1:218331028:G:TW262C0.998
1:218305107:T:CL162P0.997
1:218305118:G:CA166P0.997
1:218307432:G:CG169R0.997
1:218307448:T:CF174S0.997
1:218307555:T:CF210L0.997
1:218307556:T:CF210S0.997
1:218307557:C:AF210L0.997
1:218307557:C:GF210L0.997
1:218330980:G:CW246C0.997
1:218330980:G:TW246C0.997
1:218331026:T:AW262R0.997
1:218331026:T:CW262R0.997
1:218307447:T:AF174I0.996
1:218307454:C:AA176D0.996
1:218307568:T:CL214S0.996
1:218302428:T:AW92R0.995
1:218302428:T:CW92R0.995
1:218307439:T:AV171E0.995

dbSNP variants (sampled 300 via entrez): RS1000084257 (1:218334567 A>G,T), RS1000119690 (1:218314450 G>A,T), RS1000172028 (1:218318303 CT>C), RS1000174107 (1:218314132 G>A,T), RS1000212412 (1:218294503 A>G,T), RS1000346425 (1:218333433 A>G), RS1000401757 (1:218320497 A>T), RS1000439863 (1:218299141 A>C), RS1000453435 (1:218315652 C>T), RS1000491125 (1:218296312 T>G), RS1000510777 (1:218316904 T>C), RS1000682541 (1:218322677 C>G), RS1000749644 (1:218320807 C>A), RS1000811660 (1:218328589 G>C), RS1000913554 (1:218302950 G>A,C)

Disease associations

OMIM: gene MIM:611193 | disease phenotypes: MIM:614816

GenCC curated gene-disease

Mondo (1): Loeys-Dietz syndrome 4 (MONDO:0013897)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002481_4Acne (severe)4.000000e-08
GCST007692_9Chronic obstructive pulmonary disease5.000000e-06
GCST90000025_852Appendicular lean mass3.000000e-11
GCST90020028_457Hip circumference adjusted for BMI3.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004980appendicular lean mass
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067113 (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
5.93Kd1177nMCHEMBL5653589
5.93ED501177nMCHEMBL5653589

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]benzamide2149323: Binding affinity to human RRP15 incubated for 45 mins by Kinobead based pull down assaykd1.1768uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects cotreatment, increases expression, affects expression6
bisphenol Adecreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression2
Estradiolincreases expression2
Tetrachlorodibenzodioxinaffects expression, decreases expression2
Tretinoindecreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
afuresertibdecreases expression1
FR900359affects phosphorylation1
alpha phellandrenedecreases expression1
trichostatin Adecreases expression, increases expression1
2-butenaldecreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
zinc chloridedecreases expression, decreases reaction1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression, decreases reaction1
butyraldehydedecreases expression1
coumarindecreases phosphorylation1
CGP 52608affects binding, increases reaction1
dorsomorphinaffects cotreatment, increases expression1
LDN 193189affects cotreatment, decreases expression1
MT19c compoundincreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Ethanolaffects cotreatment, decreases expression, increases abundance1
Atrazinedecreases expression1
Caffeinedecreases phosphorylation1
Cisplatindecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652365BindingBinding affinity to human RRP15 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.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Loeys-Dietz syndrome 4