UCKL1
protein-codinguridine-cytidine kinase 1 like 1, the group of MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is a uridine kinase. Uridine kinases catalyze the phosphorylation of uridine to uridine monophosphate. This protein has been shown to bind to Epstein-Barr nuclear antigen 3 as well as natural killer lytic-associated molecule. Ubiquitination of this protein is enhanced by the presence of natural killer lytic-associated molecule. In addition, protein levels decrease in the presence of natural killer lytic-associated molecule, suggesting that association with natural killer lytic-associated molecule results in ubiquitination and subsequent degradation of this protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
- URKL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.6 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 UCKL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017859.4. 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 | 68 | 2 | 70 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 69 | 2 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060329.2 | 15 | MANE Select | |
| Ensembl | ENSP00000346155.6 | 15 | MANE Select | |
| RefSeq | NP_001180308.1 | 15 | Standard | |
| RefSeq | NP_001340404.1 | 15 | 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)
- Pyrimidine Metabolism
- UMP Synthase Deiciency (Orotic Aciduria)
- MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)
Biological Process
- viral process
- phosphorylation
- pyrimidine nucleoside salvage
- UMP salvage
- CTP salvage
Molecular Function
- uridine kinase activity
- protein binding
- ATP binding
- kinase activity
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000354216
- Coding exons
- 15
- Length
- 16584
- Individuals with no LoFs
- 125535
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 125601
- p
- 0.000263
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 242 | 367 | 0.659 | 0.0000253 | 3544 |
| Missense (PolyPhen) | 82 | 144.89 | 0.56594 | 1325 | ||
| Synonymous | -1.28 | 182 | 161 | 1.13 | 0.0000124 | 1098 |
| Loss of Function | 0.288 | 23 | 24.5 | 0.937 | 0.00000113 | 293 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00060 | 0.00049 | rare |
| Latino/Admixed American | 0.00056 | 0.00055 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00023 | 0.00021 | rare |
| South Asian | 0.00029 | 0.00026 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May contribute to UTP accumulation needed for blast transformation and proliferation. {ECO:0000269|PubMed:12199906}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.140
- RVIS EVS
- -1.4
- RVIS percentile EVS
- 4.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.936
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |