AK4

adenylate kinase 4, the group of Adenylate kinases

Basic information

Region (hg38): 1:65147549-65232145

Previous symbols: [ "AK3", "AK3L1" ]

Links

ENSG00000162433 ∙ NCBI:205 ∙ OMIM:103030 ∙ HGNC:363 ∙ Uniprot:P27144 ∙ 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 AK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AK4 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			11	1		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	11	1	0

Variants in AK4

This is a list of pathogenic ClinVar variants found in the AK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-65148478-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-65148483-G-T		not specified	Uncertain significance (Feb 13, 2024)
1-65190729-G-T		not specified	Uncertain significance (Aug 10, 2023)
1-65190731-A-G		not specified	Uncertain significance (Feb 07, 2023)
1-65190776-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-65190781-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-65190806-G-A		not specified	Uncertain significance (Jun 23, 2023)
1-65218768-T-G		not specified	Uncertain significance (Nov 12, 2021)
1-65218861-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-65218864-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-65218913-C-T		not specified	Uncertain significance (May 03, 2023)
1-65224764-G-A		not specified	Likely benign (Nov 27, 2023)
1-65226095-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-65226143-A-G		not specified	Uncertain significance (Mar 20, 2024)
1-65226144-G-T		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AK4	protein_coding	protein_coding	ENST00000395334	5	84597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.134	0.847	125733	0	3	125736	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	89	128	0.694	0.00000757	1451
Missense in Polyphen		20	39.392	0.50772		511
Synonymous	-0.0281	50	49.7	1.01	0.00000316	427
Loss of Function	2.02	3	9.84	0.305	5.02e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000377	0.0000327
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. Efficiently phosphorylates AMP and dAMP using ATP as phosphate donor, but phosphorylates only AMP when using GTP as phosphate donor. Also displays broad nucleoside diphosphate kinase activity. {ECO:0000255|HAMAP-Rule:MF_03170, ECO:0000269|PubMed:19073142, ECO:0000269|PubMed:19766732, ECO:0000269|PubMed:23416111}.
• Pathway: Purine metabolism - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Tenofovir/Adefovir Pathway, Pharmacodynamics;Tenofovir/Adefovir Pathway, Pharmacokinetics;adenosine ribonucleotides <i>de novo</i> biosynthesis;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Purine metabolism;Metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.642
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ak4

Gene ontology

• Biological process: liver development;nucleoside diphosphate phosphorylation;ADP biosynthetic process;brain development;nucleoside triphosphate biosynthetic process;nucleobase-containing small molecule interconversion;response to drug;AMP metabolic process;ATP metabolic process;GTP metabolic process;nucleoside monophosphate phosphorylation
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: adenylate kinase activity;nucleoside diphosphate kinase activity;ATP binding;GTP binding;nucleoside triphosphate adenylate kinase activity;nucleoside monophosphate kinase activity