UTP11
protein-codingUTP11 small subunit processome component, the group of SSU processome
Gene summary
Enables RNA binding activity. Involved in nervous system development; positive regulation of apoptotic process; and ribosomal small subunit biogenesis. Located in cytoplasm; nucleolus; and obsolete extracellular space. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jun 2026]
- UTP11L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UTP11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016037.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 9 | 9 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 13 | 0 | 0 | 13 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057121.2 | 8 | MANE Select | |
| Ensembl | ENSP00000362105.4 | 8 | MANE Select | |
| Ensembl | ENSP00000560338.1 | 6 | Standard | |
| Ensembl | ENSP00000560338.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| utp11l | Danio rerio | Structure: anatomical system Quality: quality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- rRNA processing
- Metabolism of RNA
- rRNA modification in the nucleus and cytosol
- rRNA processing in the nucleus and cytosol
Biological Process
- rRNA processing
- nervous system development
- positive regulation of apoptotic process
Molecular Function
- RNA binding
- protein binding
Cellular Component
- extracellular space
- nucleoplasm
- nucleolus
- cytoplasm
- small-subunit processome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373014
- Coding exons
- 8
- Length
- 15567
- Individuals with no LoFs
- 125703
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 45
- Defined
- 125748
- p
- 0.000179
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.421 | 129 | 143 | 0.901 | 0.00000827 | 1663 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00023 | 0.00022 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in nucleolar processing of pre-18S ribosomal RNA. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.4
Essentials
- Essential (gene trap)
- E