UTP15

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

Basic information

Region (hg38): 5:73565443-73583380

Links

ENSG00000164338 ∙ NCBI:84135 ∙ OMIM:616194 ∙ HGNC:25758 ∙ Uniprot:Q8TED0 ∙ 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 UTP15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP15 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						0
missense			25			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	25	0	0

Variants in UTP15

This is a list of pathogenic ClinVar variants found in the UTP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-73567360-C-A		not specified	Uncertain significance (May 03, 2023)
5-73568253-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-73568290-A-G		not specified	Uncertain significance (Jan 26, 2023)
5-73568301-A-G		not specified	Uncertain significance (Jun 05, 2024)
5-73568308-C-T		not specified	Uncertain significance (Feb 27, 2023)
5-73568310-G-A		not specified	Uncertain significance (Aug 14, 2024)
5-73568469-G-A		not specified	Uncertain significance (Dec 11, 2024)
5-73570643-C-T		not specified	Uncertain significance (Jul 31, 2024)
5-73570645-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-73570668-G-C		not specified	Uncertain significance (Feb 03, 2022)
5-73570685-C-G		not specified	Uncertain significance (Feb 13, 2025)
5-73570688-C-G		not specified	Uncertain significance (Jan 23, 2024)
5-73572564-C-A		not specified	Uncertain significance (Aug 04, 2023)
5-73572566-G-A		not specified	Uncertain significance (Feb 07, 2025)
5-73572572-T-G		not specified	Uncertain significance (Jan 19, 2025)
5-73572597-A-G		not specified	Uncertain significance (Jul 11, 2023)
5-73576974-A-G		not specified	Uncertain significance (Jun 11, 2021)
5-73576995-A-G		not specified	Uncertain significance (Feb 15, 2023)
5-73577023-G-A		not specified	Uncertain significance (Aug 01, 2024)
5-73577856-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-73577877-G-A		not specified	Uncertain significance (Jan 07, 2022)
5-73577877-G-C		not specified	Uncertain significance (May 14, 2024)
5-73577905-T-C		not specified	Uncertain significance (Sep 09, 2024)
5-73577988-A-C		not specified	Uncertain significance (Jul 06, 2021)
5-73578004-G-A		not specified	Uncertain significance (Mar 14, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP15	protein_coding	protein_coding	ENST00000296792	12	16527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000722	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	207	274	0.756	0.0000137	3370
Missense in 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

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: 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}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.0799
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.794
• ghis: 0.584

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Mouse Genome Informatics

• Gene name: Utp15

Zebrafish Information Network

• Gene name: utp15
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: rRNA processing;positive regulation of transcription by RNA polymerase I;positive regulation of rRNA processing
• Cellular component: fibrillar center;nucleoplasm;nucleolus;cytoplasm;endoplasmic reticulum
• Molecular function: RNA binding;protein binding