AK5

adenylate kinase 5, the group of Adenylate kinases

Basic information

Region (hg38): 1:77282019-77559966

Links

ENSG00000154027 ∙ NCBI:26289 ∙ OMIM:608009 ∙ HGNC:365 ∙ Uniprot:Q9Y6K8 ∙ 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 AK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AK5 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	29	2	2

Variants in AK5

This is a list of pathogenic ClinVar variants found in the AK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-77282360-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-77287052-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-77287075-G-T		not specified	Uncertain significance (Nov 09, 2021)
1-77287107-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-77293825-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-77293834-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-77293835-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-77293905-G-A			Likely benign (Mar 01, 2022)
1-77293927-A-G		not specified	Uncertain significance (Feb 06, 2024)
1-77297630-G-A		not specified	Uncertain significance (Jun 06, 2022)
1-77297661-G-A		not specified	Uncertain significance (Feb 11, 2022)
1-77297857-A-A		not specified	Benign (Mar 29, 2016)
1-77340428-A-G		not specified	Uncertain significance (Feb 06, 2023)
1-77340473-G-A		not specified	Uncertain significance (Dec 02, 2021)
1-77340563-A-G		not specified	Uncertain significance (Mar 29, 2022)
1-77410982-T-G		not specified	Uncertain significance (Dec 17, 2023)
1-77411046-A-T		not specified	Uncertain significance (Dec 01, 2022)
1-77417666-T-C		not specified	Uncertain significance (Oct 06, 2021)
1-77417727-C-T		not specified	Benign (Mar 29, 2016)
1-77483318-G-T		not specified	Uncertain significance (Sep 14, 2022)
1-77483327-A-G		not specified	Uncertain significance (Aug 12, 2021)
1-77518641-G-C		not specified	Uncertain significance (Nov 07, 2022)
1-77518707-C-T		not specified	Uncertain significance (Aug 20, 2023)
1-77521829-C-T			Likely benign (Sep 01, 2022)
1-77521833-G-A		not specified	Likely benign (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AK5	protein_coding	protein_coding	ENST00000354567	14	277916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00331	0.997	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	207	314	0.659	0.0000173	3691
Missense in Polyphen		73	136.23	0.53585		1638
Synonymous	-1.43	134	115	1.17	0.00000664	1040
Loss of Function	3.43	10	30.4	0.329	0.00000162	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000589	0.0000589
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000715	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000271	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. Active on AMP and dAMP with ATP as a donor. When GTP is used as phosphate donor, the enzyme phosphorylates AMP, CMP, and to a small extent dCMP. Also displays broad nucleoside diphosphate kinase activity. {ECO:0000269|PubMed:19647735, ECO:0000269|PubMed:23416111}.
• Pathway: Purine metabolism - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);adenosine ribonucleotides <i>de novo</i> biosynthesis;Metabolism of nucleotides;purine deoxyribonucleosides salvage;Interconversion of nucleotide di- and triphosphates;Purine metabolism;Metabolism;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.253
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.290
• hipred: Y
• hipred_score: 0.623
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ak5

Gene ontology

• Biological process: nucleoside diphosphate phosphorylation;ADP biosynthetic process;dADP biosynthetic process;nucleoside triphosphate biosynthetic process;pyrimidine ribonucleotide biosynthetic process;nucleobase-containing small molecule interconversion;ATP metabolic process;nucleoside monophosphate phosphorylation
• Cellular component: microtubule organizing center;cytosol
• Molecular function: adenylate kinase activity;nucleoside diphosphate kinase activity;ATP binding;nucleoside kinase activity