NOP9

NOP9 nucleolar protein, the group of Armadillo like helical domain containing|SSU processome

Basic information

Region (hg38): 14:24299849-24309124

Previous symbols: [ "C14orf21" ]

Links

ENSG00000196943 ∙ NCBI:161424 ∙ OMIM:618308 ∙ HGNC:19826 ∙ Uniprot:Q86U38 ∙ 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 NOP9 gene.

• Inborn genetic diseases (35 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP9 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				1		1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9			9
Total	0	0	35	1	0

Variants in NOP9

This is a list of pathogenic ClinVar variants found in the NOP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24299995-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-24300003-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-24300068-A-C		not specified	Uncertain significance (May 18, 2023)
14-24300075-C-T		not specified	Uncertain significance (Dec 20, 2022)
14-24300094-C-T		not specified	Uncertain significance (Nov 01, 2022)
14-24300408-A-T		not specified	Uncertain significance (Jan 23, 2024)
14-24300456-C-T		not specified	Uncertain significance (Mar 06, 2023)
14-24300492-A-G		not specified	Uncertain significance (Sep 14, 2022)
14-24300494-G-C		not specified	Uncertain significance (Nov 10, 2022)
14-24300522-C-T		not specified	Uncertain significance (Jan 09, 2024)
14-24300556-C-G		not specified	Uncertain significance (Aug 02, 2021)
14-24300687-C-T		not specified	Uncertain significance (May 08, 2023)
14-24301636-A-T		not specified	Uncertain significance (Jul 29, 2022)
14-24301994-T-C		not specified	Uncertain significance (Jan 23, 2024)
14-24302024-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-24302028-A-G		not specified	Uncertain significance (Jan 22, 2024)
14-24302048-C-A		not specified	Uncertain significance (Feb 28, 2024)
14-24302067-T-C		not specified	Uncertain significance (Nov 22, 2022)
14-24302076-T-C		not specified	Uncertain significance (Sep 06, 2022)
14-24302081-A-G		not specified	Uncertain significance (Feb 03, 2022)
14-24302261-C-T		not specified	Uncertain significance (Oct 06, 2022)
14-24302308-A-G		not specified	Uncertain significance (Sep 13, 2023)
14-24302333-A-G		not specified	Uncertain significance (Nov 09, 2023)
14-24302350-C-A		not specified	Uncertain significance (Oct 26, 2021)
14-24302351-A-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP9	protein_coding	protein_coding	ENST00000267425	10	9263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-11	0.589	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.449	340	364	0.934	0.0000202	4015
Missense in Polyphen		90	100.43	0.89617		1137
Synonymous	-0.177	154	151	1.02	0.00000777	1399
Loss of Function	1.41	21	29.3	0.718	0.00000164	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000409	0.000394
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000261	0.000237
Middle Eastern	0.000599	0.000598
South Asian	0.000330	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.153

Intolerance Scores

• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.46

Haploinsufficiency Scores

• pHI: 0.0200
• hipred: N
• hipred_score: 0.399
• ghis: 0.442

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nop9

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: RNA binding