ADK

adenosine kinase

Basic information

Region (hg38): 10:74151202-74709963

Links

ENSG00000156110 ∙ NCBI:132 ∙ OMIM:102750 ∙ HGNC:257 ∙ Uniprot:P55263 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• adenosine kinase deficiency (Strong), mode of inheritance: AR
• adenosine kinase deficiency (Supportive), mode of inheritance: AR
• adenosine kinase deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypermethioninemia due to adenosine kinase deficiency	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Biochemical; Cardiovascular; Gastrointestinal; Neurologic	21963049

ClinVar

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

• not provided (1 variants)
• Adenosine kinase deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADK 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	17	2	20
missense	1	1	37		1	40
nonsense		1				1
start loss						0
frameshift	1	2				3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	8	3	13
non coding			13	20	11	44
Total	2	4	52	37	14

Variants in ADK

This is a list of pathogenic ClinVar variants found in the ADK region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-74151299-G-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
10-74151312-A-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
10-74151518-C-A			Benign (May 08, 2021)
10-74176475-G-A		Adenosine kinase deficiency	Likely benign (Jan 13, 2018)
10-74176613-A-T		Adenosine kinase deficiency	Uncertain significance (Jan 13, 2018)
10-74176631-G-A		Adenosine kinase deficiency	Uncertain significance (Jan 12, 2018)
10-74176658-T-C		Adenosine kinase deficiency	Likely benign (Jan 13, 2018)
10-74176681-G-C		Adenosine kinase deficiency	Uncertain significance (Jan 13, 2018)
10-74176755-G-T		Adenosine kinase deficiency	Uncertain significance (Jan 13, 2018)
10-74176797-G-T		Adenosine kinase deficiency	Uncertain significance (Jan 12, 2018)
10-74176798-T-C		Adenosine kinase deficiency	Uncertain significance (Jan 13, 2018)
10-74176853-C-T		Adenosine kinase deficiency	Benign (May 08, 2021)
10-74176879-T-A		Adenosine kinase deficiency	Uncertain significance (Sep 19, 2022)
10-74176904-G-A			Likely benign (Dec 29, 2022)
10-74176906-C-T			Likely benign (Aug 09, 2022)
10-74200688-A-T			Benign (May 10, 2021)
10-74200754-GT-G			Benign (Dec 12, 2022)
10-74200769-A-T		Adenosine kinase deficiency	Uncertain significance (May 03, 2020)
10-74200776-C-G			Likely benign (Jan 28, 2023)
10-74200783-A-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
10-74200787-G-A		Adenosine kinase deficiency	Pathogenic (Oct 07, 2011)
10-74200791-T-C			Likely benign (Jul 23, 2022)
10-74200858-T-C			Likely benign (Oct 05, 2023)
10-74224522-C-T			Likely benign (Dec 02, 2021)
10-74224532-A-T			Likely benign (Aug 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADK	protein_coding	protein_coding	ENST00000286621	11	558102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000313	0.988	125720	0	20	125740	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	129	187	0.690	0.00000878	2404
Missense in Polyphen		28	61.495	0.45532		768
Synonymous	0.800	56	64.2	0.873	0.00000313	654
Loss of Function	2.23	9	19.7	0.457	9.14e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. Serves as a potential regulator of concentrations of extracellular adenosine and intracellular adenine nucleotides.
• Pathway: Purine metabolism - Homo sapiens (human);Abacavir Pathway, Pharmacokinetics/Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Thioguanine Action Pathway;Mercaptopurine Metabolism Pathway;Metabolism of nucleotides;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;adenine and adenosine salvage II (Consensus)

Recessive Scores

• pRec: 0.686

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.613
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.532

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Adk
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: purine ribonucleoside salvage;dATP biosynthetic process;ribonucleoside monophosphate biosynthetic process;phosphorylation;purine-containing compound salvage;AMP salvage
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: RNA binding;adenosine kinase activity;ATP binding;metal ion binding