UTP20

UTP20 small subunit processome component, the group of Armadillo like helical domain containing|SSU processome

Basic information

Region (hg38): 12:101280104-101386618

Links

ENSG00000120800 ∙ NCBI:27340 ∙ OMIM:612822 ∙ HGNC:17897 ∙ Uniprot:O75691 ∙ 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 UTP20 gene.

• Inborn genetic diseases (86 variants)
• not provided (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP20 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				5	5	10
missense			79	9	7	95
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	79	14	12

Variants in UTP20

This is a list of pathogenic ClinVar variants found in the UTP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-101280289-A-C		not specified	Likely benign (Nov 05, 2021)
12-101280305-A-G		not specified	Uncertain significance (Oct 14, 2023)
12-101281124-A-G			Benign (Jul 31, 2018)
12-101281167-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-101285817-A-G		not specified	Uncertain significance (Aug 09, 2021)
12-101285874-C-G		not specified	Uncertain significance (Sep 29, 2022)
12-101286343-G-T		not specified	Uncertain significance (Mar 07, 2024)
12-101286398-C-T		not specified	Uncertain significance (Nov 17, 2023)
12-101286399-G-A			Benign/Likely benign (May 01, 2022)
12-101286409-A-G		not specified	Uncertain significance (Mar 06, 2023)
12-101286494-T-C		not specified	Uncertain significance (Dec 27, 2022)
12-101286495-G-A			Benign (May 21, 2018)
12-101288997-A-G		not specified	Uncertain significance (Mar 27, 2023)
12-101290192-C-G		not specified	Uncertain significance (Aug 22, 2023)
12-101290282-A-C			Benign (Dec 31, 2019)
12-101290752-G-A		not specified	Likely benign (Nov 15, 2021)
12-101290793-T-C		not specified	Uncertain significance (Aug 15, 2023)
12-101290806-G-A		not specified	Uncertain significance (Jan 05, 2022)
12-101290816-C-T			Likely benign (Jul 23, 2018)
12-101290832-T-A		not specified	Uncertain significance (Jul 06, 2021)
12-101291762-C-T			Benign (Jul 31, 2018)
12-101291808-A-C		not specified	Uncertain significance (Oct 12, 2021)
12-101291822-A-T		not specified	Uncertain significance (Nov 27, 2023)
12-101291865-C-A			Benign (Jul 31, 2018)
12-101291874-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP20	protein_coding	protein_coding	ENST00000261637	62	106508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-15	1.00	125648	0	99	125747	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.524	1366	1.42e+3	0.961	0.0000747	18321
Missense in Polyphen		306	373.73	0.81876		4946
Synonymous	-0.0345	529	528	1.00	0.0000290	5199
Loss of Function	6.97	52	141	0.368	0.00000691	1906

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000765	0.000764
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000661	0.000598
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000481	0.000475
Middle Eastern	0.000661	0.000598
South Asian	0.000337	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in 18S pre-rRNA processing. Associates with U3 snoRNA. {ECO:0000269|PubMed:17498821}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.752
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.13

Haploinsufficiency Scores

• pHI: 0.587
• hipred: Y
• hipred_score: 0.637
• ghis: 0.504

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.377

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp20

Gene ontology

• Biological process: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;negative regulation of cell population proliferation
• Cellular component: nucleoplasm;nucleolus;cytoplasm;plasma membrane;90S preribosome;preribosome, small subunit precursor;small-subunit processome
• Molecular function: RNA binding;protein binding