UTP15

protein-coding

UTP15 small subunit processome component, the group of WD repeat domain containing|UTPa subcomplex

Gene summary

Enables RNA binding activity. Involved in positive regulation of rRNA processing; positive regulation of transcription by RNA polymerase I; and ribosomal small subunit biogenesis. Located in cytoplasm and fibrillar center. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032175.4

Inheritance

—

ClinVar variants

U:61

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:73,565,443-73,583,380

External References & Databases

Ensembl (ENSG00000164338)

Transcript & Mutation Effects

hg38 • Region Span ~17.9 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 UTP15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032175.4. 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
missense			59 clinvar			59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	61	0	0	61

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032175.4	RefSeq	NP_115551.2	12	MANE Select
ENST00000296792.9	Ensembl	ENSP00000296792.4	12	MANE Select
NM_001284430.1	RefSeq	NP_001271359.1	12	Standard
NM_001284431.1	RefSeq	NP_001271360.1	8	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
utp15	Danio rerio	Structure: dorsal longitudinal anastomotic vessel Quality: aplastic abnormal

Gene / Model

Organism

Observed Phenotype

utp15

Danio rerio

Structure: dorsal longitudinal anastomotic vessel

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
rRNA processing
Metabolism of RNA

Biological Process

rRNA processing
positive regulation of transcription by RNA polymerase I
positive regulation of rRNA processing

Molecular Function

RNA binding
protein binding

Cellular Component

fibrillar center
nucleoplasm
nucleolus
cytoplasm
endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296792
Coding exons: 12
Length: 16527
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	1.44	207	274	0.756	0.0000137	3370
Missense (PolyPhen)		61	102.64	0.59428		1272
Synonymous	0.164	95	97.1	0.979	0.00000491	997
Loss of Function	4.82	0	27.0	0.00	0.00000160	334

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: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre- ribosomal RNA transcription by RNA polymerase I. {ECO:0000269|PubMed:17699751}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.0799
RVIS EVS: 0.09
RVIS percentile EVS: 60.57

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.221