UTP3

protein-coding

UTP3 small subunit processome component, the group of SSU processome

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, Jul 2025]

MANE transcript

NM_020368.3

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr4:70,688,532-70,690,551

External References & Databases

Ensembl (ENSG00000132467)

Transcript & Mutation Effects

hg38 • Region Span ~2.0 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 UTP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020368.3. 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
missense			42 clinvar		2 clinvar	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	0	3	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020368.3	RefSeq	NP_065101.1	1	MANE Select
ENST00000254803.4	Ensembl	ENSP00000254803.2	1	MANE Select

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

maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
chromatin organization
rRNA processing
brain development

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254803
Coding exons: 1
Length: 2072
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.15	203	255	0.796	0.0000124	3116
Missense (PolyPhen)		57	73.987	0.7704		880
Synonymous	-0.429	105	99.6	1.05	0.00000463	939
Loss of Function	1.56	10	16.9	0.591	8.58e-7	227

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for gene silencing: has a role in the structure of silenced chromatin. Plays a role in the developing brain (By similarity). {ECO:0000250|UniProtKB:Q12136, ECO:0000250|UniProtKB:Q9JI13}.;

Recessive Scores

pRec: 0.0955

Intolerance Scores

LoFtool: 0.718
RVIS EVS: 0.8
RVIS percentile EVS: 87.49

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.914

Gene Damage Prediction

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