UTP6

protein-coding

UTP6 small subunit processome component, the group of UTPb subcomplex

Gene summary

Predicted to enable snoRNA binding activity. Involved in ribosomal small subunit biogenesis. Located in chromosome and nucleolus. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C17orf40

MANE transcript

NM_018428.3

Inheritance

—

ClinVar variants

U:84B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr17:31,860,904-31,901,708

External References & Databases

Ensembl (ENSG00000108651)

Transcript & Mutation Effects

hg38 • Region Span ~40.8 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 UTP6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018428.3. 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			2 clinvar		2 clinvar	4
missense			79 clinvar	3 clinvar	2 clinvar	84
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	84	3	4	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018428.3	RefSeq	NP_060898.2	19	MANE Select
ENST00000261708.9	Ensembl	ENSP00000261708.4	19	MANE Select
ENST00000579459.1	Ensembl	ENSP00000464599.1	2	Standard
ENST00000581012.6	Ensembl	ENSP00000462135.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
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)
rRNA processing

Cellular Component

nucleoplasm
nucleolus
small-subunit processome
Pwp2p-containing subcomplex of 90S preribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261708
Coding exons: 19
Length: 40862
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125748
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.444	292	314	0.930	0.0000160	3934
Missense (PolyPhen)		54	65.304	0.8269		850
Synonymous	0.858	100	112	0.897	0.00000601	1038
Loss of Function	3.30	20	43.5	0.460	0.00000230	512

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00038	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in nucleolar processing of pre-18S ribosomal RNA. {ECO:0000250}.;

Recessive Scores

pRec: 0.0988

Intolerance Scores

LoFtool: 0.904
RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.962

Gene Damage Prediction

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