UPP2
protein-codinguridine phosphorylase 2
Gene summary
Enables identical protein binding activity and pyrimidine-nucleoside phosphorylase activity. Involved in pyrimidine nucleoside monophosphate catabolic process; uridine catabolic process; and xenobiotic catabolic process. Acts upstream of or within dCMP catabolic process. Located in type III intermediate filament. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~259.5 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 UPP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173355.4. 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 | 1 | 1 | ||||
| missense | 47 | 6 | 1 | 54 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 48 | 6 | 2 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_775491.1 | 7 | MANE Select | |
| Ensembl | ENSP00000005756.5 | 7 | MANE Select | |
| RefSeq | NP_001128570.1 | 9 | Standard | |
| Ensembl | ENSP00000520425.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pyrimidine metabolism - Homo sapiens (human)
- Drug metabolism - other enzymes - Homo sapiens (human)
- Fluoropyrimidine Pathway, Pharmacokinetics
- Pyrimidine Metabolism
- UMP Synthase Deiciency (Orotic Aciduria)
Biological Process
- nucleoside metabolic process
- nucleotide catabolic process
- pyrimidine nucleoside salvage
- UMP salvage
- uridine metabolic process
Molecular Function
- uridine phosphorylase activity
- protein binding
Cellular Component
- cytosol
- type III intermediate filament
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000605860
- Coding exons
- 9
- Length
- 259453
- Individuals with no LoFs
- 110916
- Homozygous LoFs
- 1095
- Heterozygous LoFs
- 13730
- Defined
- 125741
- p
- 0.0608
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.378 | 193 | 208 | 0.926 | 0.0000109 | 2457 |
| Missense (PolyPhen) | 52 | 60.331 | 0.86192 | 760 | ||
| Synonymous | 0.465 | 70 | 75.1 | 0.932 | 0.00000402 | 723 |
| Loss of Function | 1.85 | 7 | 14.7 | 0.477 | 7.83e-7 | 200 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.27 | 0.26 | notable |
| Latino/Admixed American | 0.030 | 0.029 | notable |
| Ashkenazi Jewish | 0.073 | 0.072 | notable |
| East Asian | 0.13 | 0.13 | notable |
| Finnish | 0.019 | 0.019 | notable |
| European (Non-Finnish) | 0.030 | 0.030 | notable |
| South Asian | 0.11 | 0.11 | notable |
| Other | 0.051 | 0.049 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis. Shows substrate specificity and accept uridine, deoxyuridine, and thymidine as well as the two pyrimidine nucleoside analogs 5-fluorouridine and 5-fluoro-2(')-deoxyuridine as substrates.;
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- LoFtool
- 0.408
- RVIS EVS
- -0.11
- RVIS percentile EVS
- 45.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |