NOP16

NOP16 nucleolar protein

Basic information

Region (hg38): 5:176383946-176388927

Links

ENSG00000048162 ∙ NCBI:51491 ∙ OMIM:612861 ∙ HGNC:26934 ∙ Uniprot:Q9Y3C1 ∙ 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 NOP16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP16 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1		4
Total	0	0	16	1	0

Variants in NOP16

This is a list of pathogenic ClinVar variants found in the NOP16 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176384248-T-G		not specified	Uncertain significance (Mar 05, 2024)
5-176384260-A-C		not specified	Uncertain significance (Oct 05, 2023)
5-176384262-G-T		not specified	Uncertain significance (Feb 05, 2024)
5-176384323-G-A		not specified	Uncertain significance (May 03, 2023)
5-176384329-G-C		not specified	Uncertain significance (Jan 06, 2023)
5-176384361-T-C		not specified	Uncertain significance (Dec 06, 2021)
5-176384364-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-176385248-C-T		not specified	Uncertain significance (Sep 14, 2023)
5-176385255-C-T		not specified	Uncertain significance (Jun 22, 2021)
5-176385296-C-G		not specified	Uncertain significance (Feb 17, 2023)
5-176386845-A-G		not specified	Uncertain significance (Jan 23, 2024)
5-176388245-C-A		not specified	Uncertain significance (Sep 13, 2023)
5-176388303-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-176388844-C-A		not specified	Uncertain significance (Apr 22, 2022)
5-176388893-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-176388909-G-C		not specified	Likely benign (Feb 27, 2023)
5-176388917-A-C		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP16	protein_coding	protein_coding	ENST00000510123	5	5028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0120	0.860	124779	0	17	124796	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	120	136	0.881	0.00000706	1524
Missense in Polyphen		30	39.157	0.76614		471
Synonymous	0.382	49	52.5	0.933	0.00000273	473
Loss of Function	1.25	4	7.75	0.516	3.41e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.0000971	0.0000971
Middle Eastern	0.000278	0.000278
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.488
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.179
• ghis: 0.413

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nop16

Gene ontology

• Biological process: ribosomal large subunit biogenesis
• Cellular component: nucleus;nucleolus;intracellular membrane-bounded organelle
• Molecular function: RNA binding