AK5

protein-coding

adenylate kinase 5, the group of Adenylate kinases

Gene summary

This gene encodes a member of the adenylate kinase family, which is involved in regulating the adenine nucleotide composition within a cell by catalyzing the reversible transfer of phosphate groups among adenine nucleotides. This member is related to the UMP/CMP kinase of several species. It is located in the cytosol and expressed exclusively in brain. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_174858.3

Inheritance

—

ClinVar variants

U:71B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr1:77,282,019-77,559,966

External References & Databases

Ensembl (ENSG00000154027)

Transcript & Mutation Effects

hg38 • Region Span ~277.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AK5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174858.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			68 clinvar	1 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	3	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174858.3	RefSeq	NP_777283.1	14	MANE Select
ENST00000354567.7	Ensembl	ENSP00000346577.2	14	MANE Select
NM_012093.4	RefSeq	NP_036225.2	13	Standard
ENST00000344720.10	Ensembl	ENSP00000341430.5	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Purine metabolism - Homo sapiens (human)
Thiamine metabolism - Homo sapiens (human)
adenosine ribonucleotides <i>de novo</i> biosynthesis
Metabolism of nucleotides
purine deoxyribonucleosides salvage

Biological Process

nucleoside diphosphate phosphorylation
ADP biosynthetic process
dADP biosynthetic process
nucleoside triphosphate biosynthetic process
pyrimidine ribonucleotide biosynthetic process

Molecular Function

adenylate kinase activity
nucleoside diphosphate kinase activity
ATP binding
nucleoside kinase activity

Cellular Component

microtubule organizing center
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354567
Coding exons: 14
Length: 277916
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125747
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.15	207	314	0.659	0.0000173	3691
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.253
RVIS EVS: -0.8
RVIS percentile EVS: 12.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.355

Gene Damage Prediction

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