UTP3

UTP3 small subunit processome component, the group of SSU processome

Basic information

Region (hg38): 4:70688532-70690551

Links

ENSG00000132467 ∙ NCBI:57050 ∙ OMIM:611614 ∙ HGNC:24477 ∙ Uniprot:Q9NQZ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UTP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			23		2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	3

Variants in UTP3

This is a list of pathogenic ClinVar variants found in the UTP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-70688745-C-T			Benign (May 29, 2018)
4-70688761-T-C			Benign (May 29, 2018)
4-70688789-C-T		not specified	Uncertain significance (Jan 20, 2025)
4-70688841-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-70688857-A-T		not specified	Uncertain significance (Nov 10, 2021)
4-70688859-C-T		not specified	Uncertain significance (Dec 25, 2024)
4-70688976-A-G		not specified	Uncertain significance (Mar 08, 2025)
4-70689015-G-A		not specified	Uncertain significance (Feb 24, 2025)
4-70689037-G-C		not specified	Uncertain significance (Jan 08, 2024)
4-70689282-G-A		not specified	Uncertain significance (Feb 08, 2025)
4-70689336-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-70689347-C-G		not specified	Uncertain significance (Sep 01, 2024)
4-70689353-C-T		not specified	Uncertain significance (Oct 12, 2021)
4-70689390-C-T		not specified	Uncertain significance (Jan 26, 2022)
4-70689395-G-A		not specified	Uncertain significance (Apr 17, 2023)
4-70689488-C-T		not specified	Uncertain significance (Jun 05, 2024)
4-70689521-T-C		not specified	Uncertain significance (Dec 21, 2023)
4-70689599-A-T		not specified	Uncertain significance (Dec 17, 2023)
4-70689654-T-C		not specified	Uncertain significance (Jan 12, 2024)
4-70689714-C-T		not specified	Uncertain significance (Jun 13, 2023)
4-70689744-C-G		not specified	Uncertain significance (Aug 12, 2021)
4-70689777-A-G		not specified	Uncertain significance (Jul 25, 2024)
4-70689790-T-A			Benign (May 29, 2018)
4-70689878-G-A		not specified	Uncertain significance (Mar 19, 2024)
4-70689911-A-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP3	protein_coding	protein_coding	ENST00000254803	1	2072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000194	0.901	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	203	255	0.796	0.0000124	3116
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.718
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.0593
• hipred: N
• hipred_score: 0.484
• ghis: 0.417

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp3

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);chromatin organization;rRNA processing;brain development
• Cellular component: nucleus;nucleoplasm;nucleolus;small-subunit processome
• Molecular function: RNA binding;protein binding