TK1

thymidine kinase 1, the group of Deoxyribonucleoside kinases

Basic information

Region (hg38): 17:78174090-78187233

Links

ENSG00000167900 ∙ NCBI:7083 ∙ OMIM:188300 ∙ HGNC:11830 ∙ Uniprot:P04183 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TK1 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

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	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	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)
17-78182647-C-T		not specified	Uncertain significance (May 26, 2023)
17-78182674-A-G		not specified	Uncertain significance (Feb 10, 2023)
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)
17-78186972-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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