DCK

deoxycytidine kinase, the group of Deoxyribonucleoside kinases

Basic information

Region (hg38): 4:70992537-71030914

Links

ENSG00000156136 ∙ NCBI:1633 ∙ OMIM:125450 ∙ HGNC:2704 ∙ Uniprot:P27707 ∙ 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 DCK gene.

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

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		1
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	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)

GnomAD

Source: gnomAD

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: dbNSFP

• 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