UTP15

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

Basic information

Region (hg38): 5:73565443-73583380

Links

ENSG00000164338NCBI:84135OMIM:616194HGNC:25758Uniprot:Q8TED0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)2542391
5-73568253-G-A not specified Uncertain significance (Aug 12, 2021)2225514
5-73568290-A-G not specified Uncertain significance (Jan 26, 2023)2473267
5-73568301-A-G not specified Uncertain significance (Jun 05, 2024)3331710
5-73568308-C-T not specified Uncertain significance (Feb 27, 2023)2489760
5-73568310-G-A not specified Uncertain significance (Aug 14, 2024)3467403
5-73570643-C-T not specified Uncertain significance (Jul 31, 2024)3467401
5-73570645-G-A not specified Uncertain significance (Jan 03, 2024)2343863
5-73570668-G-C not specified Uncertain significance (Feb 03, 2022)2275739
5-73570688-C-G not specified Uncertain significance (Jan 23, 2024)3187894
5-73572564-C-A not specified Uncertain significance (Aug 04, 2023)2600895
5-73572572-T-G not specified Uncertain significance (Jun 24, 2022)2257642
5-73572597-A-G not specified Uncertain significance (Jul 11, 2023)2610366
5-73576974-A-G not specified Uncertain significance (Jun 11, 2021)2232562
5-73576995-A-G not specified Uncertain significance (Feb 15, 2023)2484452
5-73577023-G-A not specified Uncertain significance (Aug 01, 2024)3467402
5-73577856-C-T not specified Uncertain significance (Dec 27, 2023)3187895
5-73577877-G-A not specified Uncertain significance (Jan 07, 2022)3187896
5-73577877-G-C not specified Uncertain significance (May 14, 2024)3331711
5-73577905-T-C not specified Uncertain significance (Sep 09, 2024)3467400
5-73577988-A-C not specified Uncertain significance (Jul 06, 2021)2378701
5-73578820-C-T not specified Uncertain significance (Apr 13, 2023)2520645
5-73578821-G-A not specified Uncertain significance (Jan 03, 2024)3187891
5-73579072-A-G not specified Uncertain significance (May 26, 2022)2291550
5-73580050-C-T not specified Uncertain significance (Dec 13, 2022)3187892

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UTP15protein_codingprotein_codingENST00000296792 1216527
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000072200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.442072740.7560.00001373370
Missense in Polyphen61102.640.594281272
Synonymous0.1649597.10.9790.00000491997
Loss of Function4.82027.00.000.00000160334

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
Phenotype

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