NOP2

NOP2 nucleolar protein, the group of NOP2/Sun RNA methyltransferase family

Basic information

Region (hg38): 12:6556863-6568691

Previous symbols: [ "NOL1" ]

Links

ENSG00000111641 ∙ NCBI:4839 ∙ OMIM:164031 ∙ HGNC:7867 ∙ Uniprot:P46087 ∙ 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 NOP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP2 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				3	1	4
missense			64	6	4	74
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	64	9	6

Variants in NOP2

This is a list of pathogenic ClinVar variants found in the NOP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6557020-C-A		not specified	Uncertain significance (Feb 27, 2023)
12-6557033-T-G		not specified	Uncertain significance (Feb 22, 2025)
12-6557034-T-G		not specified	Uncertain significance (Nov 12, 2021)
12-6557057-C-T		not specified	Uncertain significance (Feb 07, 2023)
12-6557077-C-CA			Benign (Nov 13, 2017)
12-6557093-G-C		not specified	Uncertain significance (Jul 05, 2022)
12-6557110-A-T		not specified	Uncertain significance (Dec 25, 2024)
12-6557124-A-G		not specified	Uncertain significance (Nov 10, 2024)
12-6557213-A-G		not specified	Likely benign (Sep 22, 2022)
12-6557219-G-C		not specified	Uncertain significance (Aug 11, 2024)
12-6557226-T-A		not specified	Uncertain significance (Feb 22, 2023)
12-6557235-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-6557256-G-C		not specified	Likely benign (Jul 07, 2024)
12-6557258-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-6557269-C-G		not specified	Uncertain significance (Aug 01, 2024)
12-6557330-C-T			Benign (Aug 16, 2018)
12-6557373-C-T		not specified	Uncertain significance (Apr 08, 2024)
12-6557408-C-A		not specified	Uncertain significance (Aug 26, 2022)
12-6557483-A-G		not specified	Likely benign (Feb 10, 2022)
12-6557492-A-T		not specified	Uncertain significance (Nov 17, 2022)
12-6557498-G-A		not specified	Uncertain significance (Apr 17, 2023)
12-6557550-C-G		not specified	Uncertain significance (Oct 20, 2023)
12-6557552-T-C		not specified	Likely benign (Aug 12, 2021)
12-6557607-A-C		not specified	Uncertain significance (Dec 16, 2024)
12-6560113-G-A		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP2	protein_coding	protein_coding	ENST00000382421	16	11829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000380	124635	0	3	124638	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.638	431	470	0.917	0.0000261	5436
Missense in Polyphen		110	167.49	0.65677		1832
Synonymous	1.31	157	179	0.876	0.00000926	1702
Loss of Function	5.38	2	37.6	0.0532	0.00000232	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000949	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ribosomal large subunit assembly (PubMed:24120868). S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C(5) position of cytosine 4447 in 28S rRNA (Probable). May play a role in the regulation of the cell cycle and the increased nucleolar activity that is associated with the cell proliferation (Probable). {ECO:0000269|PubMed:24120868, ECO:0000305, ECO:0000305|PubMed:23913415}.
• Pathway: Imatinib and Chronic Myeloid Leukemia;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;rRNA processing;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Metabolism of RNA;TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.702
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.63

Haploinsufficiency Scores

• pHI: 0.987
• hipred: Y
• hipred_score: 0.573
• ghis: 0.499

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nop2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ribosomal large subunit assembly;regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;rRNA base methylation;regulation of signal transduction by p53 class mediator
• Cellular component: nucleoplasm;nucleolus
• Molecular function: RNA binding;protein binding;rRNA (cytosine-C5-)-methyltransferase activity