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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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NOL9
nucleolar protein 9
Chromosome 1 · 1p36.31
NCBI Gene: 79707Ensembl: ENSG00000162408.12HGNC: HGNC:26265UniProt: Q5SY16
108PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Kinase
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activitymaturation of 5.8S rRNAnucleusplacenta praeviapreeclampsiahepatocellular carcinomaGriscelli disease
✦AI Summary

NOL9 (nucleolar protein 9) is a polynucleotide kinase essential for ribosome biogenesis 1. It phosphorylates 5'-hydroxyl groups on single-stranded and double-stranded RNA/DNA substrates and is required for efficient pre-rRNA processing, particularly ITS2 cleavage and maturation of 5.8S and 28S rRNAs 1. NOL9 associates with the endoribonuclease LAS1L to form a catalytic endonuclease-kinase complex that marks ITS2 for degradation 2. This complex is recruited to the rixosome core scaffold, a multi-subunit complex containing PELP1, WDR18, and TEX10 3. NOL9 contains a nucleolar localization sequence responsible for transporting the assembled Las1L-NOL9 complex into the nucleolus 2. Dysregulation of NOL9 has significant disease implications. In hepatocellular carcinoma, NOL9 is upregulated and correlates with poor prognosis, larger tumors, and advanced pathological grades; its expression is epigenetically regulated by DNA methylation 4. NOL9 promotes HCC growth through Wnt/β-catenin pathway activation 4. In acute myeloid leukemia with NPM1 mutations, elevated LAS1-NOL9 levels affect prognosis, and targeting this axis via LAS1 inhibition impairs 28S rRNA maturation and stabilizes p53 5. NOL9 mutations are recurrent in EBV-positive diffuse large B-cell lymphoma 6. A zebrafish nol9 loss-of-function model demonstrates that NOL9 deficiency causes 28S rRNA processing defects, resulting in hypoplastic pancreas/liver and impaired hematopoiesis, establishing it as central to tissue-specific ribosome biogenesis 7.

Sources cited
1
NOL9 is a polynucleotide kinase that phosphorylates 5'-hydroxyl groups and is required for ITS2 processing and 5.8S/28S rRNA maturation
PMID: 21063389
2
NOL9 forms an endonuclease-kinase complex with LAS1L and contains a nucleolar localization sequence for complex transport
PMID: 31288032
3
NOL9 provides RNA 5' kinase activity within the rixosome multi-subunit complex containing PELP1, WDR18, TEX10, and LAS1L
PMID: 40195365
4
NOL9 is upregulated in hepatocellular carcinoma, regulates cell proliferation via Wnt/β-catenin pathway, and is epigenetically regulated by DNA methylation
PMID: 39955289
5
In NPM1-mutant AML, LAS1-NOL9 axis targeting by inhibiting LAS1 impairs 28S rRNA maturation and stabilizes p53
PMID: 36796466
6
NOL9 loss-of-function in zebrafish causes 28S rRNA processing defects and impaired hematopoiesis and pancreas development
PMID: 26624285
7
NOL9 mutations are recurrent in EBV-positive diffuse large B-cell lymphoma
PMID: 38457199
8
NOL9/Grc3 belongs to the Clp1 family of polynucleotide kinases with 5' kinase activity
PMID: 37606665
Disease Associationsⓘ20
placenta praeviaOpen Targets
0.28Weak
preeclampsiaOpen Targets
0.28Weak
hepatocellular carcinomaOpen Targets
0.07Suggestive
Griscelli diseaseOpen Targets
0.05Suggestive
uncombable hair syndromeOpen Targets
0.04Suggestive
Griscelli disease type 3Open Targets
0.04Suggestive
Griscelli syndrome type 3Open Targets
0.04Suggestive
Griscelli disease type 1Open Targets
0.04Suggestive
Griscelli syndrome type 1Open Targets
0.04Suggestive
hypotrichosis 8Open Targets
0.03Suggestive
isolated familial wooly hair disorderOpen Targets
0.03Suggestive
Woolly hairOpen Targets
0.03Suggestive
Clouston syndromeOpen Targets
0.03Suggestive
Waardenburg syndrome, IIa 2FOpen Targets
0.03Suggestive
schizophreniaOpen Targets
0.02Suggestive
neoplasmOpen Targets
0.02Suggestive
breast cancerOpen Targets
0.01Suggestive
acute myeloid leukemiaOpen Targets
0.01Suggestive
ileal neoplasmOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HEATR1Protein interaction100%UTP15Protein interaction100%NOP56Protein interaction100%WDR36Protein interaction100%UTP14AProtein interaction100%UTP20Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
64%
Ovary
59%
Liver
59%
Lung
45%
Heart
42%
Gene Interaction Network
Click a node to explore
NOL9HEATR1UTP15NOP56WDR36UTP14AUTP20
PROTEIN STRUCTURE
Preparing viewer…
PDB9DUN · 3.32 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.63LoF Tolerant
pLIⓘ
0.01Tolerant
Observed/Expected LoF0.46 [0.34–0.63]
RankingsWhere NOL9 stands among ~20K protein-coding genes
  • #4,409of 20,598
    Most Researched108 · top quartile
  • #4,430of 17,882
    Most Constrained (LOEUF)0.63 · top quartile
Genes detectedNOL9
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
USP36 SUMOylates Las1L and Promotes Its Function in Pre-Ribosomal RNA ITS2 Processing.
PMID: 39356143
Cancer Res Commun · 2024
1.00
2
Molecular insights into the overall architecture of human rixosome.
PMID: 40195365
Nat Commun · 2025
0.90
3
Nucleolar NOL9 regulated by DNA methylation promotes hepatocellular carcinoma growth through activation of Wnt/β-catenin signaling pathway.
PMID: 39955289
Cell Death Dis · 2025
0.80
4
Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei.
PMID: 37606665
J Mol Evol · 2023
0.70
5
Nol9 Is a Spatial Regulator for the Human ITS2 Pre-rRNA Endonuclease-Kinase Complex.
PMID: 31288032
J Mol Biol · 2019
0.60