UTP6

UTP6 small subunit processome component, the group of UTPb subcomplex

Basic information

Region (hg38): 17:31860904-31901708

Previous symbols: [ "C17orf40" ]

Links

ENSG00000108651 ∙ NCBI:55813 ∙ ∙ HGNC:18279 ∙ Uniprot:Q9NYH9 ∙ 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 UTP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP6 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					2	2
missense			42	2	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	4

Variants in UTP6

This is a list of pathogenic ClinVar variants found in the UTP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-31863379-G-A		not specified	Uncertain significance (Dec 02, 2021)
17-31863380-C-T		not specified	Uncertain significance (Dec 02, 2021)
17-31863382-T-C		not specified	Uncertain significance (Feb 19, 2025)
17-31863384-G-C		not specified	Uncertain significance (Jul 06, 2021)
17-31865372-C-G		not specified	Uncertain significance (Oct 25, 2023)
17-31865398-C-G		not specified	Uncertain significance (Feb 16, 2023)
17-31865404-T-C		not specified	Uncertain significance (May 08, 2023)
17-31868096-G-A		not specified	Uncertain significance (Feb 19, 2025)
17-31868098-C-T		not specified	Uncertain significance (Nov 24, 2024)
17-31868103-C-G		not specified	Uncertain significance (Apr 25, 2023)
17-31873394-T-C		not specified	Uncertain significance (May 08, 2024)
17-31873430-C-G		not specified	Uncertain significance (Jan 10, 2025)
17-31873467-T-C		not specified	Uncertain significance (Oct 12, 2021)
17-31873483-G-C		not specified	Uncertain significance (Jan 16, 2025)
17-31873684-C-T		not specified	Uncertain significance (Dec 20, 2022)
17-31875256-G-T		not specified	Uncertain significance (Aug 19, 2024)
17-31875258-T-G		not specified	Uncertain significance (Feb 25, 2025)
17-31875288-C-A		not specified	Uncertain significance (Jun 22, 2021)
17-31875305-C-A		not specified	Uncertain significance (Nov 17, 2022)
17-31875318-C-G		not specified	Uncertain significance (May 31, 2023)
17-31878253-C-G		not specified	Uncertain significance (Feb 14, 2025)
17-31878707-C-G		not specified	Uncertain significance (Jul 11, 2023)
17-31878718-C-A		not specified	Uncertain significance (Oct 26, 2022)
17-31878779-C-T		not specified	Uncertain significance (Aug 28, 2023)
17-31880587-T-C		not specified	Uncertain significance (Jan 10, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP6	protein_coding	protein_coding	ENST00000261708	19	40862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.11e-8	1.00	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.444	292	314	0.930	0.0000160	3934
Missense in Polyphen		54	65.304	0.8269		850
Synonymous	0.858	100	112	0.897	0.00000601	1038
Loss of Function	3.30	20	43.5	0.460	0.00000230	512

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000544	0.000544
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000272	0.000272
South Asian	0.000384	0.000359
Other	0.00	0.00

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: 0.0988

Intolerance Scores

• loftool: 0.904
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.133
• hipred: Y
• hipred_score: 0.706
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp6

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing
• Cellular component: nucleoplasm;nucleolus;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome