NOL4

nucleolar protein 4

Basic information

Region (hg38): 18:33851100-34224952

Links

ENSG00000101746 ∙ NCBI:8715 ∙ OMIM:603577 ∙ HGNC:7870 ∙ Uniprot:O94818 ∙ 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 NOL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOL4 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in NOL4

This is a list of pathogenic ClinVar variants found in the NOL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-33853002-G-A		not specified	Uncertain significance (Aug 16, 2021)
18-33883351-G-A		not specified	Uncertain significance (Dec 16, 2023)
18-33883385-C-T		not specified	Uncertain significance (Jan 29, 2024)
18-33943082-G-A		not specified	Uncertain significance (Dec 19, 2023)
18-33957414-T-G		not specified	Uncertain significance (Jun 18, 2024)
18-33958276-G-A		not specified	Uncertain significance (Mar 24, 2023)
18-33958412-C-T		not specified	Uncertain significance (Dec 02, 2021)
18-34019343-C-T		not specified	Uncertain significance (Jun 22, 2021)
18-34019344-G-C		not specified	Uncertain significance (Oct 03, 2022)
18-34019364-A-G		not specified	Uncertain significance (Nov 15, 2021)
18-34019413-T-C		not specified	Uncertain significance (Apr 04, 2023)
18-34019422-C-G		not specified	Uncertain significance (Nov 17, 2022)
18-34019427-G-A		not specified	Uncertain significance (Jul 08, 2022)
18-34093585-T-C		not specified	Uncertain significance (Aug 02, 2023)
18-34105061-T-C		not specified	Uncertain significance (Mar 30, 2024)
18-34105150-C-G		not specified	Uncertain significance (Mar 30, 2024)
18-34129894-C-T		not specified	Uncertain significance (Apr 20, 2024)
18-34129983-C-T		not specified	Uncertain significance (Oct 21, 2021)
18-34129984-G-A			Uncertain significance (Oct 01, 2022)
18-34222991-G-A		not specified	Uncertain significance (Nov 15, 2023)
18-34223030-C-A		not specified	Uncertain significance (May 03, 2023)
18-34223031-C-A		not specified	Uncertain significance (May 03, 2023)
18-34223120-G-A		not specified	Uncertain significance (Apr 04, 2023)
18-34223132-T-C		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOL4	protein_coding	protein_coding	ENST00000261592	11	373853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000513	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	240	361	0.664	0.0000193	4200
Missense in Polyphen		85	199.98	0.42504		2420
Synonymous	-1.28	154	135	1.14	0.00000743	1195
Loss of Function	5.02	3	35.0	0.0856	0.00000210	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0701
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.338
• hipred: Y
• hipred_score: 0.800
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nol4

Gene ontology

• Cellular component: nucleolus
• Molecular function: RNA binding