NOP58

NOP58 ribonucleoprotein, the group of U3 small nucleolar ribonucleoprotein|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:202265735-202303661

Links

ENSG00000055044 ∙ NCBI:51602 ∙ OMIM:616742 ∙ HGNC:29926 ∙ Uniprot:Q9Y2X3 ∙ 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 NOP58 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP58 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in NOP58

This is a list of pathogenic ClinVar variants found in the NOP58 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-202265966-G-C		not specified	Uncertain significance (Mar 11, 2024)
2-202277958-T-G		not specified	Uncertain significance (Dec 17, 2023)
2-202277981-G-C		not specified	Uncertain significance (Jul 05, 2023)
2-202282432-C-A		not specified	Uncertain significance (Jun 09, 2022)
2-202284445-G-T		not specified	Uncertain significance (Nov 27, 2023)
2-202290334-G-T		not specified	Uncertain significance (Apr 11, 2023)
2-202290440-A-G		not specified	Uncertain significance (Feb 27, 2023)
2-202292778-T-C		not specified	Uncertain significance (Aug 02, 2022)
2-202295712-G-A		not specified	Uncertain significance (May 16, 2022)
2-202295802-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-202297430-T-C		not specified	Uncertain significance (Mar 24, 2023)
2-202297473-C-T		not specified	Uncertain significance (May 27, 2022)
2-202300280-T-C		not specified	Uncertain significance (Oct 05, 2023)
2-202300347-A-G		not specified	Uncertain significance (Sep 22, 2023)
2-202302986-A-G		not specified	Uncertain significance (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP58	protein_coding	protein_coding	ENST00000264279	15	37951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00365	0.996	125713	0	30	125743	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	202	274	0.737	0.0000137	3460
Missense in Polyphen		38	91.461	0.41548		1119
Synonymous	-0.333	93	89.0	1.04	0.00000435	944
Loss of Function	3.46	10	30.6	0.326	0.00000164	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000254	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.000118	0.000109
South Asian	0.000165	0.000163
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for 60S ribosomal subunit biogenesis (By similarity). Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs. {ECO:0000250, ECO:0000269|PubMed:15574333, ECO:0000269|PubMed:17636026, ECO:0000269|PubMed:19620283}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;Metabolism of RNA;SUMOylation;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.746
• ghis: 0.661

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.740

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nop58

Zebrafish Information Network

• Gene name: nop58
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: rRNA processing;snoRNA localization
• Cellular component: fibrillar center;nucleus;nucleoplasm;nucleolus;small nucleolar ribonucleoprotein complex;cytosol;Cajal body;membrane;box C/D snoRNP complex;small-subunit processome;pre-snoRNP complex
• Molecular function: TFIID-class transcription factor complex binding;RNA binding;protein binding;snoRNA binding;ATPase binding