DCK
Basic information
Region (hg38): 4:70992538-71030914
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 DCK 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 | 1 | |||||
| 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 | 1 | 0 |
Variants in DCK
This is a list of pathogenic ClinVar variants found in the DCK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-70998091-A-G | not specified | Uncertain significance (Aug 17, 2022) | ||
| 4-71023583-T-C | Likely benign (Jul 07, 2018) | |||
| 4-71023617-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 4-71025831-A-C | not specified | Uncertain significance (Jul 30, 2024) | ||
| 4-71029374-T-G | not specified | Uncertain significance (May 02, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DCK | protein_coding | protein_coding | ENST00000286648 | 7 | 38377 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000154 | 0.873 | 125708 | 1 | 39 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 98 | 131 | 0.751 | 0.00000599 | 1721 |
| Missense in Polyphen | 28 | 48.78 | 0.57401 | 619 | ||
| Synonymous | -0.422 | 48 | 44.4 | 1.08 | 0.00000199 | 442 |
| Loss of Function | 1.46 | 10 | 16.4 | 0.610 | 8.82e-7 | 196 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000186 | 0.000182 |
| Ashkenazi Jewish | 0.00220 | 0.00199 |
| East Asian | 0.000288 | 0.000272 |
| Finnish | 0.0000466 | 0.0000462 |
| European (Non-Finnish) | 0.0000628 | 0.0000615 |
| Middle Eastern | 0.000288 | 0.000272 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000351 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents. {ECO:0000269|PubMed:18377927, ECO:0000269|PubMed:20614893}.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;Gemcitabine Action Pathway;Lamivudine Metabolism Pathway;Gemcitabine Metabolism Pathway;Retinoblastoma (RB) in Cancer;Pyrimidine metabolism;Metabolism of nucleotides;purine deoxyribonucleosides salvage;Purine metabolism;Metabolism;Pyrimidine salvage;Nucleotide salvage;Pyrimidine metabolism;superpathway of pyrimidine deoxyribonucleoside salvage;Purine salvage;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleosides salvage
(Consensus)
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- loftool
- 0.263
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.57
Haploinsufficiency Scores
- pHI
- 0.0292
- hipred
- Y
- hipred_score
- 0.504
- ghis
- 0.466
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.160
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dck
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; normal phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- pyrimidine nucleotide metabolic process;deoxyribonucleoside monophosphate biosynthetic process;nucleotide biosynthetic process;phosphorylation;pyrimidine nucleoside salvage;purine-containing compound salvage
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- deoxycytidine kinase activity;ATP binding;drug binding;deoxynucleoside kinase activity;nucleoside kinase activity;protein homodimerization activity