UTP25
protein-codingUTP25 small subunit processome component, the group of SSU processome
Gene summary
Enables RNA binding activity. Involved in several processes, including protein catabolic process; protein destabilization; and protein localization to nucleolus. Located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]
- C1orf107
- DIEXF
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.6 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 UTP25 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014388.7. 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 | 4 | 4 | ||||
| missense | 110 | 2 | 112 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 115 | 2 | 0 | 117 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055203.4 | 12 | MANE Select | |
| Ensembl | ENSP00000419005.1 | 12 | MANE Select | |
| Ensembl | ENSP00000407345.1 | 3 | Standard | |
| Ensembl | ENSP00000522928.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| utp25 | Danio rerio | Structure: gut epithelium Quality: morphology abnormal |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000491415
- Coding exons
- 12
- Length
- 29559
- Individuals with no LoFs
- 125679
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 69
- Defined
- 125748
- p
- 0.000274
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.575 | 376 | 409 | 0.920 | 0.0000216 | 5022 |
| Missense (PolyPhen) | 90 | 118.43 | 0.75997 | 1374 | ||
| Synonymous | 0.247 | 156 | 160 | 0.975 | 0.00000884 | 1406 |
| Loss of Function | 3.06 | 16 | 35.7 | 0.448 | 0.00000183 | 423 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00052 | 0.00052 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00031 | 0.00031 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates the p53 pathway to control the expansion growth of digestive organs. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.231
Intolerance Scores
- RVIS EVS
- 1.03
- RVIS percentile EVS
- 91.07
Essentials
- Essential (gene trap)
- E