UTP11

UTP11 small subunit processome component, the group of SSU processome

Basic information

Region (hg38): 1:38009257-38024820

Previous symbols: [ "UTP11L" ]

Links

ENSG00000183520 ∙ NCBI:51118 ∙ OMIM:609440 ∙ HGNC:24329 ∙ Uniprot:Q9Y3A2 ∙ 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 UTP11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP11 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in UTP11

This is a list of pathogenic ClinVar variants found in the UTP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-38018504-C-A		not specified	Uncertain significance (Sep 17, 2021)
1-38019303-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-38023605-T-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP11	protein_coding	protein_coding	ENST00000373014	8	15567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-7	0.561	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.421	129	143	0.901	0.00000827	1663
Missense in Polyphen		42	48.627	0.86372		511
Synonymous	-0.404	53	49.4	1.07	0.00000268	455
Loss of Function	1.01	13	17.6	0.740	9.88e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000231	0.000220
Middle Eastern	0.000165	0.000163
South Asian	0.000263	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.614
• ghis: 0.634

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Utp11

Zebrafish Information Network

• Gene name: utp11l
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: rRNA processing;nervous system development;positive regulation of apoptotic process
• Cellular component: extracellular space;nucleoplasm;nucleolus;cytoplasm;small-subunit processome
• Molecular function: RNA binding;protein binding