NOL6

nucleolar protein 6, the group of UTPc subcomplex|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:33461353-33473930

Links

ENSG00000165271 ∙ NCBI:65083 ∙ OMIM:611532 ∙ HGNC:19910 ∙ Uniprot:Q9H6R4 ∙ 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 NOL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOL6 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	3	0

Variants in NOL6

This is a list of pathogenic ClinVar variants found in the NOL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-33463417-T-C		not specified	Uncertain significance (Sep 27, 2021)
9-33464085-G-T			Likely benign (Sep 01, 2022)
9-33466090-G-A		not specified	Uncertain significance (Aug 17, 2021)
9-33466105-C-A		not specified	Uncertain significance (Oct 29, 2021)
9-33466144-C-T			Likely benign (Sep 01, 2022)
9-33466349-C-T		not specified	Uncertain significance (Nov 15, 2021)
9-33466350-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-33466374-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-33466393-G-A			Likely benign (Mar 01, 2023)
9-33466675-G-A		not specified	Uncertain significance (May 14, 2024)
9-33467228-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-33467782-G-A		not specified	Uncertain significance (Jan 20, 2025)
9-33468977-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-33469098-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOL6	protein_coding	protein_coding	ENST00000297990	26	12490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000266	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.864	633	697	0.908	0.0000450	7279
Missense in Polyphen		188	249.98	0.75205		2602
Synonymous	0.496	269	280	0.962	0.0000160	2492
Loss of Function	6.44	5	57.9	0.0863	0.00000295	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000914	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.399
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.36

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.639
• ghis: 0.551

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nol6

Gene ontology

• Biological process: rRNA processing;tRNA export from nucleus
• Cellular component: condensed nuclear chromosome;nucleus;nucleoplasm;nucleolus;mitochondrion;small-subunit processome;CURI complex;UTP-C complex
• Molecular function: RNA binding