NOL10

nucleolar protein 10, the group of WD repeat domain containing

Basic information

Region (hg38): 2:10562346-10689987

Previous symbols: [ "PQBP5" ]

Links

ENSG00000115761 ∙ NCBI:79954 ∙ OMIM:616197 ∙ HGNC:25862 ∙ Uniprot:Q9BSC4 ∙ 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 NOL10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOL10 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				2		2
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	0

Variants in NOL10

This is a list of pathogenic ClinVar variants found in the NOL10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10572115-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-10572120-G-A		not specified	Uncertain significance (Aug 30, 2021)
2-10572126-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-10589073-T-C		not specified	Uncertain significance (Feb 28, 2024)
2-10589090-T-C			Likely benign (Nov 01, 2022)
2-10589129-T-C			Likely benign (Nov 01, 2022)
2-10589142-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-10589177-C-G		not specified	Uncertain significance (Jul 14, 2023)
2-10589194-G-A		not specified	Uncertain significance (Apr 26, 2023)
2-10589232-T-C		not specified	Uncertain significance (Jun 02, 2023)
2-10589238-C-T		not specified	Uncertain significance (Nov 30, 2021)
2-10589248-T-G		not specified	Uncertain significance (Jul 25, 2023)
2-10589263-G-A		not specified	Uncertain significance (Jul 21, 2021)
2-10589274-G-T		not specified	Uncertain significance (Oct 26, 2021)
2-10589586-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-10589593-T-G		not specified	Uncertain significance (Nov 18, 2022)
2-10589744-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-10600858-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-10600891-C-G		not specified	Uncertain significance (Jun 27, 2022)
2-10602819-C-T		not specified	Uncertain significance (Apr 22, 2024)
2-10603125-G-A		not specified	Uncertain significance (Aug 10, 2023)
2-10607293-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-10607305-C-G		not specified	Uncertain significance (Dec 20, 2021)
2-10607311-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-10644341-C-G		not specified	Uncertain significance (Jun 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOL10	protein_coding	protein_coding	ENST00000381685	21	119210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0507	0.949	125576	0	17	125593	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	259	316	0.819	0.0000165	4449
Missense in Polyphen		61	83.638	0.72934		1177
Synonymous	0.383	110	115	0.955	0.00000607	1184
Loss of Function	4.45	11	42.2	0.261	0.00000235	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000284	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.000284	0.000272
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0975

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.756
• ghis: 0.519

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nol10

Zebrafish Information Network

• Gene name: nol10
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• Cellular component: nucleolus;small-subunit processome
• Molecular function: RNA binding