CMPK1
protein-codingcytidine/uridine monophosphate kinase 1
Gene summary
This gene encodes one of the enzymes required for cellular nucleic acid biosynthesis. This enzyme catalyzes the transfer of a phosphate group from ATP to CMP, UMP, or dCMP, to form the corresponding diphosphate nucleotide. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Feb 2012]
- CMPK
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~61.1 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 CMPK1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016308.3. 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| 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_057392.1 | 6 | MANE Select | |
| Ensembl | ENSP00000360939.5 | 6 | MANE Select | |
| RefSeq | NP_001129612.1 | 5 | Standard | |
| RefSeq | NP_001353064.1 | 6 | 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)
- Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics
- Gemcitabine Pathway, Pharmacodynamics
- GLUT-1 deficiency syndrome
Biological Process
- nucleoside diphosphate phosphorylation
- 'de novo' pyrimidine nucleobase biosynthetic process
- UMP biosynthetic process
- nucleoside triphosphate biosynthetic process
- pyrimidine ribonucleotide biosynthetic process
Molecular Function
- cytidylate kinase activity
- nucleoside diphosphate kinase activity
- uridine kinase activity
- ATP binding
- uridylate kinase activity
Cellular Component
- nucleus
- nucleolus
- cytoplasm
- cytosol
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371873
- Coding exons
- 6
- Length
- 45043
- Individuals with no LoFs
- 123814
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 123815
- p
- 0.00000404
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 52 | 109 | 0.479 | 0.00000506 | 1486 |
| Missense (PolyPhen) | 9 | 30.887 | 0.29138 | 396 | ||
| Synonymous | 0.970 | 31 | 38.7 | 0.802 | 0.00000177 | 406 |
| Loss of Function | 2.73 | 1 | 10.6 | 0.0947 | 5.43e-7 | 141 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. Also displays broad nucleoside diphosphate kinase activity. {ECO:0000255|HAMAP-Rule:MF_03172, ECO:0000269|PubMed:10462544, ECO:0000269|PubMed:11912132, ECO:0000269|PubMed:23416111}.;
Recessive Scores
- pRec
- 0.200
Intolerance Scores
- LoFtool
- 0.342
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 74.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.250
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |