NOP14

NOP14 nucleolar protein, the group of SSU processome

Basic information

Region (hg38): 4:2937933-2963406

Previous symbols: [ "C4orf9", "NOL14" ]

Links

ENSG00000087269 ∙ NCBI:8602 ∙ OMIM:611526 ∙ HGNC:16821 ∙ Uniprot:P78316 ∙ 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 NOP14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOP14 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			53	8	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	8	1

Variants in NOP14

This is a list of pathogenic ClinVar variants found in the NOP14 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-2938899-G-C		not specified	Uncertain significance (Apr 01, 2024)
4-2938908-C-T		not specified	Uncertain significance (Aug 05, 2024)
4-2938913-C-T		not specified	Uncertain significance (Oct 29, 2021)
4-2938914-G-A		not specified	Uncertain significance (Jun 03, 2022)
4-2938925-G-A		not specified	Uncertain significance (Nov 17, 2022)
4-2939193-C-T		not specified	Uncertain significance (Dec 19, 2023)
4-2939239-C-T		not specified	Uncertain significance (Oct 21, 2024)
4-2939240-G-A		not specified	Uncertain significance (Nov 01, 2021)
4-2939261-T-C		not specified	Uncertain significance (Feb 10, 2023)
4-2939270-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-2939339-C-G			Likely benign (May 24, 2018)
4-2939339-C-T		not specified	Uncertain significance (Sep 14, 2022)
4-2939542-G-A		not specified	Uncertain significance (Aug 19, 2024)
4-2939561-G-A		not specified	Uncertain significance (Jun 16, 2024)
4-2939572-C-G		not specified	Uncertain significance (Sep 09, 2021)
4-2939577-C-G		not specified	Uncertain significance (Mar 20, 2024)
4-2939587-A-G		not specified	Uncertain significance (Jun 22, 2024)
4-2939594-G-A		not specified	Uncertain significance (Sep 02, 2024)
4-2939600-G-A		not specified	Conflicting classifications of pathogenicity (Feb 01, 2024)
4-2939621-C-T		not specified	Uncertain significance (Oct 04, 2022)
4-2941596-G-C		not specified	Uncertain significance (Oct 05, 2021)
4-2941647-T-C		not specified	Likely benign (Mar 23, 2022)
4-2941679-A-G		not specified	Uncertain significance (Jun 23, 2023)
4-2941691-C-T		not specified	Uncertain significance (Nov 14, 2023)
4-2942228-A-T		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOP14	protein_coding	protein_coding	ENST00000416614	18	25453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000214	1.00	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.835	544	492	1.11	0.0000283	5632
Missense in Polyphen		175	172.95	1.0119		1998
Synonymous	-0.807	219	204	1.07	0.0000133	1593
Loss of Function	3.83	18	46.0	0.391	0.00000251	536

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000633	0.000630
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000382	0.000381
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000382	0.000381
South Asian	0.000396	0.000392
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in nucleolar processing of pre-18S ribosomal RNA. Has a role in the nuclear export of 40S pre-ribosomal subunit to the cytoplasm (By similarity). {ECO:0000250}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.672
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.73

Haploinsufficiency Scores

• pHI: 0.134
• hipred: Y
• hipred_score: 0.648
• ghis: 0.525

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.836

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nop14

Zebrafish Information Network

• Gene name: nop14
• Affected structure: ventral wall of dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;ribosomal small subunit biogenesis
• Cellular component: nucleus;nucleoplasm;nucleolus;membrane;90S preribosome;Noc4p-Nop14p complex;small-subunit processome
• Molecular function: RNA binding;enzyme binding;snoRNA binding