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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RRP9
ribosomal RNA processing 9, U3 small nucleolar RNA binding protein
Chromosome 3 · 3p21.2
NCBI Gene: 9136Ensembl: ENSG00000114767.8HGNC: HGNC:16829UniProt: O43818
104PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
U3 snoRNA bindingRNA bindingprotein bindingribosomal small subunit biogenesisneurodegenerative diseaseneoplasmpachyonychia congenitaHerpes Zoster
✦AI Summary

RRP9 (ribosomal RNA processing 9) is a core component of the U3 small nucleolar ribonucleoprotein (snoRNP) complex that plays essential roles in ribosomal RNA processing and ribosome biogenesis 12. The protein contains a seven-bladed WD repeat propeller domain and an N-terminal region with a nuclear localization signal 2. RRP9 specifically binds to the unique B/C motif of U3 snoRNA, with its conserved 7bc loop being crucial for this interaction and proper nucleolar localization 2. The protein undergoes neddylation modification at lysine 221 by the E3 ligase Smurf1, which is essential for pre-rRNA processing and ribosome biogenesis 1. Clinically, RRP9 is significantly overexpressed in multiple cancers including colorectal, breast, thyroid, and acute myeloid leukemia, where high expression correlates with poor prognosis and promotes tumor progression 3456. In breast cancer, RRP9 promotes progression through interaction with JUN protein and activation of AKT signaling 4. The protein's stability is enhanced by METTL1-mediated m7G methylation in colorectal cancer 7. These findings establish RRP9 as both a fundamental ribosome biogenesis factor and an important oncogene across multiple cancer types.

Sources cited
1
RRP9 is a core component of U3 snoRNP complex, undergoes neddylation at K221 by Smurf1, and this modification is essential for pre-rRNA processing
PMID: 34662580
2
RRP9 contains WD repeat domain with seven-bladed propeller structure, binds U3 snoRNA B/C motif, and has conserved 7bc loop crucial for U3 recognition
PMID: 23509373
3
RRP9 is highly expressed in colorectal cancer tissues and high expression correlates with poor prognosis
PMID: 37904456
4
RRP9 is upregulated in breast cancer, promotes cancer progression, and functions through JUN protein interaction and AKT signaling
PMID: 39702367
5
Ribosome biogenesis is a hallmark of anaplastic thyroid cancer and RRP9 silencing dramatically inhibits tumor growth
PMID: 40234451
6
RRP9 is regulated by MYC signaling in acute myeloid leukemia and is essential for ribosome biogenesis
PMID: 40781078
7
METTL1 enhances RRP9 mRNA stability through m7G methylation modification in colorectal cancer
PMID: 39960239
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.49Moderate
neoplasmOpen Targets
0.10Weak
pachyonychia congenitaOpen Targets
0.08Suggestive
Herpes ZosterOpen Targets
0.08Suggestive
nervous system diseaseOpen Targets
0.08Suggestive
posterior cortical atrophyOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.07Suggestive
acute myeloid leukemiaOpen Targets
0.07Suggestive
esophageal squamous cell carcinomaOpen Targets
0.07Suggestive
complicationOpen Targets
0.07Suggestive
colorectal cancerOpen Targets
0.04Suggestive
prostate cancerOpen Targets
0.02Suggestive
colorectal carcinomaOpen Targets
0.02Suggestive
Ehlers-Danlos syndrome, musculocontractural typeOpen Targets
0.02Suggestive
cancerOpen Targets
0.02Suggestive
KeloidOpen Targets
0.02Suggestive
head and neck squamous cell carcinomaOpen Targets
0.01Suggestive
pancreatic adenocarcinomaOpen Targets
0.01Suggestive
esophageal cancerOpen Targets
0.01Suggestive
skin squamous cell carcinomaOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
NOB1Shared pathway100%DKC1Protein interaction100%SNU13Protein interaction100%RRP1Protein interaction100%RTCAProtein interaction100%NOLC1Protein interaction100%
Tissue Expression6 tissues
Ovary
100%
Lung
99%
Liver
90%
Heart
57%
Bone Marrow
56%
Brain
51%
Gene Interaction Network
Click a node to explore
RRP9NOB1DKC1SNU13RRP1RTCANOLC1
PROTEIN STRUCTURE
Preparing viewer…
PDB4J0W · 1.70 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.70LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.53 [0.40–0.70]
RankingsWhere RRP9 stands among ~20K protein-coding genes
  • #4,616of 20,598
    Most Researched104 · top quartile
  • #5,337of 17,882
    Most Constrained (LOEUF)0.70
Genes detectedRRP9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Integrative proteogenomic characterization reveals therapeutic targets in poorly differentiated and anaplastic thyroid cancers.
PMID: 40234451
Nat Commun · 2025
1.00
2
Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid.
PMID: 37988222
Aging (Albany NY) · 2023
0.90
3
METTL1 Enhances RRP9 mRNA Stability Through m7G Modification to Drive Colorectal Tumorigenesis.
PMID: 39960239
Mol Carcinog · 2025
0.80
4
RRP9 and DDX21 as new biomarkers of colorectal cancer.
PMID: 37904456
Medicine (Baltimore) · 2023
0.70
5
Chidamide and cytarabine synergistically treat acute myeloid leukemia: inhibiting ribosome biogenesis via the MYC-RRP9 pathway.
PMID: 40781078
Cell Death Dis · 2025
0.60