UTP23

protein-coding

UTP23 small subunit processome component, the group of SSU processome

Gene summary

Enables mRNA 3'-UTR binding activity and mRNA 5'-UTR binding activity. Predicted to be involved in rRNA processing. Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C8orf53

MANE transcript

NM_032334.3

Inheritance

—

ClinVar variants

U:35B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr8:116,766,505-116,849,463

External References & Databases

Ensembl (ENSG00000147679)

Transcript & Mutation Effects

hg38 • Region Span ~83.0 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 UTP23 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032334.3. 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			33 clinvar		1 clinvar	34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	0	1	36

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032334.3	RefSeq	NP_115710.2	3	MANE Select
ENST00000309822.7	Ensembl	ENSP00000308332.2	3	MANE Select
ENST00000517814.1	Ensembl	ENSP00000429962.1	3	Standard
ENST00000517820.1	Ensembl	ENSP00000427767.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Molecular Function

RNA binding
mRNA 3'-UTR binding
protein binding
mRNA 5'-UTR binding
small ribosomal subunit rRNA binding

Cellular Component

nucleolus
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309822
Coding exons: 3
Length: 82961
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125746
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.691	100	121	0.824	0.00000561	1611
Missense (PolyPhen)		22	27.081	0.81237		362
Synonymous	-0.711	51	44.9	1.13	0.00000204	471
Loss of Function	1.77	3	8.59	0.349	4.25e-7	124

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	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.00073	0.00072	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in rRNA-processing and ribosome biogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.781
RVIS EVS: 0.42
RVIS percentile EVS: 76.81

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.296

Gene Damage Prediction

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