CMPK1
Basic information
Region (hg38): 1:47333790-47394866
Previous symbols: [ "CMPK" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMPK1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in CMPK1
This is a list of pathogenic ClinVar variants found in the CMPK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-47334072-G-T | not specified | Uncertain significance (Dec 17, 2021) | ||
| 1-47373075-T-C | not specified | Uncertain significance (Jul 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CMPK1 | protein_coding | protein_coding | ENST00000371873 | 6 | 45043 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.848 | 0.152 | 123814 | 0 | 1 | 123815 | 0.00000404 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 52 | 109 | 0.479 | 0.00000506 | 1486 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000167 | 0.000167 |
dbNSFP
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}.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Lactose Synthesis;Gemcitabine Action Pathway;Lamivudine Metabolism Pathway;Gemcitabine Metabolism Pathway;Pyrimidine metabolism;UTP and CTP <i>de novo</i> biosynthesis;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism;Pyrimidine metabolism;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;CMP phosphorylation;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.200
Intolerance Scores
- loftool
- 0.342
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.95
Haploinsufficiency Scores
- pHI
- 0.203
- hipred
- N
- hipred_score
- 0.437
- ghis
- 0.416
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.250
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cmpk1
- Phenotype
Gene ontology
- Biological process
- nucleoside diphosphate phosphorylation;'de novo' pyrimidine nucleobase biosynthetic process;UMP biosynthetic process;nucleoside triphosphate biosynthetic process;pyrimidine ribonucleotide biosynthetic process;nucleobase-containing small molecule interconversion;nucleoside monophosphate phosphorylation
- Cellular component
- nucleus;nucleolus;cytoplasm;cytosol;extracellular exosome
- Molecular function
- cytidylate kinase activity;nucleoside diphosphate kinase activity;uridine kinase activity;ATP binding;uridylate kinase activity;nucleoside monophosphate kinase activity