PNO1

protein-coding

partner of NOB1 homolog, the group of Ribosomal biogenesis factors

Gene summary

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in nucleolus. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KHRBP1

MANE transcript

NM_020143.4

Inheritance

—

ClinVar variants

U:46B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr2:68,157,888-68,176,238

External References & Databases

Ensembl (ENSG00000115946)

Transcript & Mutation Effects

hg38 • Region Span ~18.4 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 PNO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020143.4. 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			44 clinvar		1 clinvar	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	46	1	1	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020143.4	RefSeq	NP_064528.1	7	MANE Select
ENST00000263657.7	Ensembl	ENSP00000263657.2	7	MANE Select
NM_001329916.2	RefSeq	NP_001316845.1	6	Standard
NM_001329917.2	RefSeq	NP_001316846.1	6	Standard

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

Molecular Function

RNA binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263657
Coding exons: 7
Length: 18395
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125747
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.234	147	139	1.06	0.00000649	1638
Missense (PolyPhen)		33	41.817	0.78915		517
Synonymous	-0.445	54	50.0	1.08	0.00000233	502
Loss of Function	2.33	3	11.5	0.260	5.00e-7	148

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000048	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA (PubMed:25851604). {ECO:0000269|PubMed:25851604}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.321
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.956

Gene Damage Prediction

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