TK1
thymidine kinase 1, the group of Deoxyribonucleoside kinases
Basic information
Region (hg38): 17:78174091-78187233
Links
Phenotypes
GenCC
Source:
No genCC data.
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 TK1 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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 1 |
Variants in TK1
This is a list of pathogenic ClinVar variants found in the TK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-78174769-G-A | not specified | Uncertain significance (Dec 04, 2021) | ||
| 17-78174847-C-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 17-78174868-C-A | Uncertain significance (-) | |||
| 17-78174870-G-A | Benign (Jul 05, 2018) | |||
| 17-78174887-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 17-78174908-G-A | not specified | Uncertain significance (Mar 22, 2022) | ||
| 17-78174940-A-G | not specified | Uncertain significance (Jul 14, 2022) | ||
| 17-78175064-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 17-78175073-T-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 17-78175101-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 17-78175111-G-A | not specified | Uncertain significance (Jun 07, 2024) | ||
| 17-78175114-G-A | not specified | Uncertain significance (Mar 26, 2024) | ||
| 17-78182647-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 17-78182674-A-G | not specified | Uncertain significance (Feb 10, 2023) | ||
| 17-78185056-G-A | not specified | Uncertain significance (May 24, 2024) | ||
| 17-78185124-T-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 17-78185132-C-G | not specified | Uncertain significance (Jul 20, 2021) | ||
| 17-78186961-C-T | not specified | Uncertain significance (Nov 20, 2023) | ||
| 17-78186970-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 17-78186972-G-A | not specified | Uncertain significance (Jul 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TK1 | protein_coding | protein_coding | ENST00000301634 | 7 | 13155 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.137 | 0.845 | 125596 | 0 | 9 | 125605 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.31 | 101 | 146 | 0.694 | 0.00000927 | 1499 |
| Missense in Polyphen | 24 | 52.197 | 0.4598 | 513 | ||
| Synonymous | 0.645 | 54 | 60.4 | 0.894 | 0.00000419 | 459 |
| Loss of Function | 2.04 | 3 | 9.92 | 0.302 | 4.19e-7 | 125 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000233 | 0.000214 |
| Ashkenazi Jewish | 0.000100 | 0.0000993 |
| East Asian | 0.0000668 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000280 | 0.0000264 |
| Middle Eastern | 0.0000668 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Fluoropyrimidine Activity;Mitotic G1-G1-S phases;Pyrimidine metabolism;Metabolism of nucleotides;Metabolism;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;Mitotic G1-G1/S phases;Pyrimidine salvage;Nucleotide salvage;superpathway of pyrimidine deoxyribonucleoside salvage;Pyrimidine nucleotides nucleosides metabolism;G1/S Transition;pyrimidine deoxyribonucleosides salvage;Cell Cycle;Cell Cycle, Mitotic;Validated targets of C-MYC transcriptional activation;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.444
Intolerance Scores
- loftool
- 0.442
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.741
- hipred
- Y
- hipred_score
- 0.754
- ghis
- 0.656
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tk1
- Phenotype
- endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; digestive/alimentary phenotype; renal/urinary system phenotype;
Gene ontology
- Biological process
- nucleobase-containing compound metabolic process;DNA metabolic process;deoxyribonucleoside monophosphate biosynthetic process;nucleotide biosynthetic process;phosphorylation;pyrimidine nucleoside salvage;thymidine metabolic process;protein homotetramerization;DNA biosynthetic process
- Cellular component
- cytosol
- Molecular function
- thymidine kinase activity;protein binding;ATP binding;zinc ion binding;nucleoside kinase activity;identical protein binding