UTP20

protein-coding

UTP20 small subunit processome component, the group of Armadillo like helical domain containing|SSU processome

Gene summary

UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and is involved in 18S rRNA processing (Wang et al., 2007 [PubMed 17498821]).[supplied by OMIM, Jun 2009]

MANE transcript

NM_014503.3

Inheritance

—

ClinVar variants

U:386B:38

Top phenotype

UTP20-related condition

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr12:101,280,105-101,386,618

External References & Databases

Ensembl (ENSG00000120800)

Transcript & Mutation Effects

hg38 • Region Span ~106.5 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 UTP20 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 384

not providedTotal: 22

UTP20-related conditionTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014503.3. 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			3 clinvar	7 clinvar	6 clinvar	16
missense			375 clinvar	19 clinvar	6 clinvar	400
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	386	26	12	424

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014503.3	RefSeq	NP_055318.2	62	MANE Select
ENST00000261637.5	Ensembl	ENSP00000261637.4	62	MANE Select
ENST00000923496.1	Ensembl	ENSP00000593555.1	61	Standard
ENST00000923496.2	Ensembl	ENSP00000593555.1	61	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

Biological Process

endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
rRNA processing
negative regulation of cell population proliferation

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
nucleolus
cytoplasm
plasma membrane
90S preribosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261637
Coding exons: 62
Length: 106508
Individuals with no LoFs: 125648
Homozygous LoFs: 0
Heterozygous LoFs: 99
Defined: 125747
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.524	1366	1.42e+3	0.961	0.0000747	18321
Missense (PolyPhen)		306	373.73	0.81876		4946
Synonymous	-0.0345	529	528	1.00	0.0000290	5199
Loss of Function	6.97	52	141	0.368	0.00000691	1906

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00052	0.00040	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00066	0.00060	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00048	0.00047	rare
South Asian	0.00034	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in 18S pre-rRNA processing. Associates with U3 snoRNA. {ECO:0000269|PubMed:17498821}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.752
RVIS EVS: 1.33
RVIS percentile EVS: 94.13

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.377

Gene Damage Prediction

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