UTP23

UTP23 small subunit processome component, the group of SSU processome

Basic information

Region (hg38): 8:116766505-116849463

Previous symbols: [ "C8orf53" ]

Links

ENSG00000147679 ∙ NCBI:84294 ∙ ∙ HGNC:28224 ∙ Uniprot:Q9BRU9 ∙ 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 UTP23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP23 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			12		2	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	2

Variants in UTP23

This is a list of pathogenic ClinVar variants found in the UTP23 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-116766611-T-A		not specified	Uncertain significance (May 28, 2023)
8-116766639-T-G		not specified	Uncertain significance (May 29, 2024)
8-116766764-T-G		not specified	Uncertain significance (Jun 29, 2022)
8-116770269-G-A		not specified	Uncertain significance (Jul 26, 2022)
8-116770326-T-C		not specified	Uncertain significance (May 27, 2022)
8-116770356-T-C		not specified	Uncertain significance (Nov 12, 2021)
8-116771486-A-C		not specified	Uncertain significance (Jun 29, 2022)
8-116771520-A-T		not specified	Uncertain significance (Feb 28, 2023)
8-116771601-A-G			Benign (Feb 20, 2018)
8-116771616-T-C		not specified	Uncertain significance (Oct 10, 2023)
8-116771619-A-G		not specified	Uncertain significance (Jan 11, 2023)
8-116771630-G-C		not specified	Uncertain significance (Nov 10, 2022)
8-116771635-A-T		not specified	Uncertain significance (Apr 06, 2024)
8-116771732-G-T		not specified	Uncertain significance (Aug 17, 2022)
8-116771736-C-T			Benign (Jul 13, 2018)
8-116771820-A-G		not specified	Uncertain significance (Nov 29, 2023)
8-116847469-A-T			Likely benign (Oct 16, 2018)
8-116847501-T-C		Cornelia de Lange syndrome 4 • not specified	Conflicting classifications of pathogenicity (Jul 23, 2024)
8-116847506-A-C		Cornelia de Lange syndrome 4	Uncertain significance (May 05, 2023)
8-116847508-T-C			Uncertain significance (Mar 01, 2024)
8-116847532-C-T		Mungan syndrome	Pathogenic (Dec 13, 2018)
8-116847533-G-A		Cornelia de Lange syndrome 4	Likely benign (Jun 11, 2023)
8-116847533-G-C		Cornelia de Lange syndrome 4	Uncertain significance (Dec 02, 2021)
8-116847538-T-A		Cornelia de Lange syndrome 4	Likely pathogenic (Oct 28, 2021)
8-116847544-T-C		Cornelia de Lange syndrome 4	Uncertain significance (Dec 12, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP23	protein_coding	protein_coding	ENST00000309822	3	82961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0864	0.875	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.691	100	121	0.824	0.00000561	1611
Missense in Polyphen		22	27.081	0.81237		362
Synonymous	-0.711	51	44.9	1.13	0.00000204	471
Loss of Function	1.77	3	8.59	0.349	4.25e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000724	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000727	0.000719
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in rRNA-processing and ribosome biogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.781
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: Y
• hipred_score: 0.599
• ghis: 0.561

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp23

Gene ontology

• Biological process: endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• Cellular component: nucleolus;small-subunit processome
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;mRNA 5'-UTR binding;small ribosomal subunit rRNA binding