NOP14

protein-coding

NOP14 nucleolar protein, the group of SSU processome

Gene summary

This gene encodes a protein that plays a role in pre-18s rRNA processing and small ribosomal subunit assembly. The encoded protein may be involved in the regulation of pancreatic cancer cell proliferation and migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

Previous symbols:

C4orf9
NOL14

MANE transcript

NM_001291978.2

Inheritance

—

ClinVar variants

U:189B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr4:2,937,933-2,963,406

External References & Databases

Ensembl (ENSG00000087269)

Transcript & Mutation Effects

hg38 • Region Span ~25.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NOP14 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 186

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001291978.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense			180 clinvar	15 clinvar	1 clinvar	196
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	189	15	1	205

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001291978.2	RefSeq	NP_001278907.1	18	MANE Select
ENST00000416614.7	Ensembl	ENSP00000405068.2	18	MANE Select
NM_001291979.2	RefSeq	NP_001278908.1	17	Standard
NM_003703.3	RefSeq	NP_003694.1	18	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nop14	Danio rerio	Structure: ventral wall of dorsal aorta Quality: absent abnormal

Gene / Model

Organism

Observed Phenotype

nop14

Danio rerio

Structure: ventral wall of dorsal aorta

Quality: absent

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

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

Molecular Function

RNA binding
enzyme binding
snoRNA binding

Cellular Component

nucleus
nucleoplasm
nucleolus
membrane
90S preribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000416614
Coding exons: 18
Length: 25453
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 65
Defined: 125748
p: 0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.835	544	492	1.11	0.0000283	5632
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00038	0.00038	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00040	0.00039	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.672
RVIS EVS: 0.57
RVIS percentile EVS: 81.73

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.836

Gene Damage Prediction

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