UTP18

UTP18 small subunit processome component, the group of WD repeat domain containing|UTPb subcomplex

Basic information

Region (hg38): 17:51260546-51297936

Previous symbols: [ "WDR50" ]

Links

ENSG00000011260 ∙ NCBI:51096 ∙ OMIM:612816 ∙ HGNC:24274 ∙ Uniprot:Q9Y5J1 ∙ 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 UTP18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP18 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			39	2		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in UTP18

This is a list of pathogenic ClinVar variants found in the UTP18 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-51260595-A-G		not specified	Uncertain significance (Jan 03, 2022)
17-51260612-A-G		not specified	Uncertain significance (May 15, 2024)
17-51260631-G-A		not specified	Uncertain significance (Feb 11, 2022)
17-51260650-G-T		not specified	Uncertain significance (Aug 12, 2021)
17-51260678-G-A		not specified	Likely benign (Mar 23, 2023)
17-51260721-C-T		not specified	Uncertain significance (Nov 03, 2023)
17-51260745-C-A		not specified	Uncertain significance (Mar 08, 2025)
17-51260759-G-A		not specified	Uncertain significance (Mar 04, 2024)
17-51260762-G-A		not specified	Uncertain significance (Oct 16, 2024)
17-51260783-G-A		not specified	Uncertain significance (Dec 17, 2024)
17-51260807-C-T		not specified	Uncertain significance (Apr 01, 2024)
17-51260814-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-51260841-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-51260888-G-A		not specified	Uncertain significance (Dec 04, 2024)
17-51260901-T-C		not specified	Uncertain significance (Mar 03, 2025)
17-51260921-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-51260922-C-G		not specified	Uncertain significance (Jan 17, 2025)
17-51263295-G-C		not specified	Uncertain significance (Jan 06, 2023)
17-51263337-C-T		not specified	Uncertain significance (May 06, 2024)
17-51266192-A-G		not specified	Uncertain significance (Jan 03, 2024)
17-51266208-G-A		not specified	Uncertain significance (May 25, 2022)
17-51266208-G-C		not specified	Uncertain significance (Jan 09, 2025)
17-51266270-C-T		not specified	Uncertain significance (Jun 21, 2022)
17-51268843-A-C		not specified	Uncertain significance (Aug 05, 2024)
17-51268886-C-T		not specified	Uncertain significance (Feb 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP18	protein_coding	protein_coding	ENST00000225298	13	37409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00233	0.997	124759	0	36	124795	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.208	304	294	1.03	0.0000143	3631
Missense in Polyphen		54	60.253	0.89622		812
Synonymous	-1.20	125	109	1.15	0.00000543	1051
Loss of Function	2.97	9	25.0	0.359	0.00000106	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000417	0.000417
Ashkenazi Jewish	0.00	0.00
East Asian	0.000344	0.000334
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000717	0.0000706
Middle Eastern	0.000344	0.000334
South Asian	0.000235	0.000229
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in nucleolar processing of pre-18S ribosomal RNA. {ECO:0000250}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.0839

Intolerance Scores

• loftool: 0.445
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.738
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp18

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;nuclear membrane;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
• Molecular function: RNA binding