NOP9

protein-coding

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

Gene summary

Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf21

MANE transcript

NM_174913.3

Inheritance

—

ClinVar variants

U:110B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr14:24,299,850-24,309,124

External References & Databases

Ensembl (ENSG00000196943)

Transcript & Mutation Effects

hg38 • Region Span ~9.3 kb

Loading mutation effect viewer...

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 NOP9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174913.3. 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			1 clinvar	1 clinvar		2
missense			105 clinvar	1 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	110	2	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174913.3	RefSeq	NP_777573.1	10	MANE Select
ENST00000267425.8	Ensembl	ENSP00000267425.3	10	MANE Select
NM_001286367.2	RefSeq	NP_001273296.1	10	Standard
ENST00000396802.7	Ensembl	ENSP00000380020.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

RNA binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267425
Coding exons: 10
Length: 9263
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 60
Defined: 125748
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.449	340	364	0.934	0.0000202	4015
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00026	0.00024	rare
South Asian	0.00033	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.153

Intolerance Scores

RVIS EVS: 0.98
RVIS percentile EVS: 90.46

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E

Gene Damage Prediction

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