NOL9

nucleolar protein 9, the group of Large ribosomal subunit biogenesis complex

Basic information

Region (hg38): 1:6521347-6554513

Links

ENSG00000162408 ∙ NCBI:79707 ∙ OMIM:620304 ∙ HGNC:26265 ∙ Uniprot:Q5SY16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NOL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOL9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			52	4		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	4	0

Variants in NOL9

This is a list of pathogenic ClinVar variants found in the NOL9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-6525949-G-C		not specified	Uncertain significance (Jun 29, 2023)
1-6525970-T-C		not specified	Uncertain significance (Dec 17, 2024)
1-6525993-T-C		not specified	Uncertain significance (Nov 13, 2024)
1-6526003-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-6526003-G-T		not specified	Uncertain significance (Aug 09, 2021)
1-6526722-T-G		not specified	Uncertain significance (May 29, 2024)
1-6529104-G-A		not specified	Uncertain significance (Apr 09, 2024)
1-6529126-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-6529126-C-T		not specified	Uncertain significance (Nov 12, 2021)
1-6529153-C-A		not specified	Uncertain significance (Nov 03, 2023)
1-6532014-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-6532015-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-6532045-T-C		not specified	Likely benign (Nov 25, 2024)
1-6532077-T-C		not specified	Uncertain significance (Jul 27, 2024)
1-6532605-T-C		not specified	Uncertain significance (Jul 11, 2023)
1-6532623-T-C		not specified	Uncertain significance (Oct 09, 2024)
1-6532643-T-C		not specified	Uncertain significance (Jan 22, 2024)
1-6532658-G-A		not specified	Uncertain significance (Feb 10, 2025)
1-6532700-T-C		not specified	Uncertain significance (Dec 05, 2022)
1-6532727-C-G		not specified	Uncertain significance (Oct 01, 2024)
1-6532734-G-C		not specified	Uncertain significance (Mar 05, 2025)
1-6532739-A-T		not specified	Uncertain significance (Jun 01, 2022)
1-6532757-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-6533411-T-A		not specified	Uncertain significance (Aug 16, 2022)
1-6533417-G-A		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOL9	protein_coding	protein_coding	ENST00000377705	12	33189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00888	0.991	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	283	366	0.773	0.0000194	4448
Missense in Polyphen		73	112.42	0.64932		1381
Synonymous	-0.714	155	144	1.08	0.00000782	1425
Loss of Function	3.40	9	28.6	0.314	0.00000143	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polynucleotide 5'-kinase involved in rRNA processing. The kinase activity is required for the processing of the 32S precursor into 5.8S and 28S rRNAs, more specifically for the generation of the major 5.8S(S) form. In vitro, has both DNA and RNA 5'-kinase activities. Probably binds RNA. {ECO:0000269|PubMed:21063389}.

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• loftool: 0.576
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.429
• ghis: 0.541

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nol9

Zebrafish Information Network

• Gene name: nol9
• Affected structure: hematopoietic multipotent progenitor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of 5.8S rRNA;rRNA processing;phosphorylation
• Cellular component: nucleoplasm;nucleolus;membrane;intermediate filament cytoskeleton
• Molecular function: RNA binding;protein binding;ATP binding;polynucleotide 5'-hydroxyl-kinase activity