AK3

adenylate kinase 3, the group of Adenylate kinases

Basic information

Region (hg38): 9:4709556-4742043

Previous symbols: [ "AK6", "AK3L1" ]

Links

ENSG00000147853 ∙ NCBI:50808 ∙ OMIM:609290 ∙ HGNC:17376 ∙ Uniprot:Q9UIJ7 ∙ 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 AK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AK3 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						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	0	0

Variants in AK3

This is a list of pathogenic ClinVar variants found in the AK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-4712992-G-A		not specified	Uncertain significance (Mar 31, 2023)
9-4713020-T-C		not specified	Uncertain significance (Nov 07, 2022)
9-4713043-G-C		not specified	Uncertain significance (Feb 05, 2024)
9-4713093-T-G		not specified	Uncertain significance (Dec 05, 2022)
9-4713096-C-G		not specified	Uncertain significance (Dec 27, 2023)
9-4718450-C-G		not specified	Uncertain significance (Mar 26, 2024)
9-4718471-T-G		not specified	Uncertain significance (Nov 22, 2022)
9-4718486-G-A		not specified	Uncertain significance (May 23, 2023)
9-4718500-C-A		not specified	Uncertain significance (Apr 23, 2024)
9-4718500-C-T		not specified	Uncertain significance (Mar 06, 2023)
9-4719139-G-C		not specified	Uncertain significance (Aug 28, 2023)
9-4719149-G-A		not specified	Uncertain significance (Jun 19, 2024)
9-4719150-G-C		not specified	Uncertain significance (Sep 22, 2023)
9-4719153-G-C		not specified	Uncertain significance (Jan 02, 2024)
9-4719155-A-G		not specified	Uncertain significance (Mar 07, 2025)
9-4719172-C-T		not specified	Uncertain significance (Feb 02, 2024)
9-4719197-G-C		not specified	Uncertain significance (Apr 04, 2023)
9-4719209-G-A		not specified	Uncertain significance (Jun 06, 2023)
9-4719214-T-C		not specified	Uncertain significance (Mar 22, 2023)
9-4719221-C-T		not specified	Uncertain significance (Oct 13, 2023)
9-4722526-T-C		not specified	Uncertain significance (Oct 08, 2024)
9-4722554-C-T		not specified	Uncertain significance (May 08, 2023)
9-4722560-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-4722574-T-A		not specified	Uncertain significance (Nov 18, 2022)
9-4722577-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AK3	protein_coding	protein_coding	ENST00000381809	5	30889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000113	0.619	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.97	185	124	1.50	0.00000647	1443
Missense in Polyphen		46	40.86	1.1258		445
Synonymous	-1.55	64	50.1	1.28	0.00000261	465
Loss of Function	0.728	7	9.41	0.744	4.84e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000579	0.000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000112	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in maintaining the homeostasis of cellular nucleotides by catalyzing the interconversion of nucleoside phosphates. Has GTP:AMP phosphotransferase and ITP:AMP phosphotransferase activities. {ECO:0000255|HAMAP-Rule:MF_03169, ECO:0000269|PubMed:11485571}.
• Pathway: Purine metabolism - Homo sapiens (human);Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;adenosine ribonucleotides <i>de novo</i> biosynthesis;Factors involved in megakaryocyte development and platelet production;Purine metabolism;Pyrimidine metabolism;Hemostasis;superpathway of purine nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.739
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.416
• hipred: N
• hipred_score: 0.350
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ak3

Zebrafish Information Network

• Gene name: ak3
• Affected structure: myeloid cell development
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: ADP biosynthetic process;blood coagulation;phosphorylation;AMP metabolic process;GTP metabolic process;ITP metabolic process;UTP metabolic process;nucleoside monophosphate phosphorylation
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: adenylate kinase activity;protein binding;ATP binding;GTP binding;nucleoside triphosphate adenylate kinase activity