AK9

adenylate kinase 9, the group of Adenylate kinases

Basic information

Region (hg38): 6:109492854-109691217

Previous symbols: [ "C6orf224", "AKD2", "C6orf199", "AKD1" ]

Links

ENSG00000155085 ∙ NCBI:221264 ∙ OMIM:615358 ∙ HGNC:33814 ∙ Uniprot:Q5TCS8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• postsynaptic congenital myasthenic syndrome (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AK9 gene.

• Inborn genetic diseases (59 variants)
• not provided (20 variants)
• SPERMATOGENIC FAILURE 89 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AK9 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				3	6	9
missense			57	2	4	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding			1	1	1	3
Total	0	0	58	6	11

Variants in AK9

This is a list of pathogenic ClinVar variants found in the AK9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-109493382-G-T		not specified	Uncertain significance (Nov 09, 2022)
6-109493386-C-A		not specified	Uncertain significance (Sep 01, 2021)
6-109493551-C-T		not specified	Uncertain significance (Nov 03, 2022)
6-109494025-C-T		not specified	Uncertain significance (Oct 02, 2023)
6-109495381-G-A		not specified	Uncertain significance (Oct 18, 2021)
6-109497503-A-G			Benign (May 09, 2018)
6-109497859-C-T		not specified	Uncertain significance (Aug 21, 2023)
6-109497896-T-G		not specified	Uncertain significance (Feb 05, 2024)
6-109497932-G-A		not specified	Uncertain significance (Feb 02, 2022)
6-109499129-A-G		not specified	Uncertain significance (Mar 29, 2022)
6-109499186-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-109499194-C-T			Benign (Feb 26, 2018)
6-109499214-A-ATAAC		Spermatogenic failure 89	Pathogenic (Feb 05, 2024)
6-109499227-G-A			Benign (Mar 01, 2023)
6-109499235-C-T		not specified	Uncertain significance (Jun 02, 2023)
6-109506403-C-A			Benign (Oct 09, 2017)
6-109506491-T-C		not specified	Uncertain significance (Dec 17, 2023)
6-109506526-A-G			Benign (Apr 30, 2018)
6-109506531-G-A		not specified	Uncertain significance (Mar 07, 2024)
6-109506743-C-A		not specified	Uncertain significance (Apr 27, 2023)
6-109509278-A-G		not specified	Uncertain significance (Jun 29, 2023)
6-109509299-G-A		not specified	Uncertain significance (Aug 19, 2021)
6-109509377-G-T		not specified	Uncertain significance (Dec 03, 2021)
6-109514253-A-G		not specified	Uncertain significance (Feb 10, 2022)
6-109514370-C-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AK9	protein_coding	protein_coding	ENST00000424296	40	198362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.69e-26	1.00	125607	0	141	125748	0.000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.19	725	911	0.795	0.0000445	12605
Missense in Polyphen		259	308.46	0.83965		4256
Synonymous	2.34	254	306	0.830	0.0000152	3325
Loss of Function	3.71	57	96.3	0.592	0.00000453	1418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00134
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000283	0.000272
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000501	0.000492
Middle Eastern	0.000283	0.000272
South Asian	0.000673	0.000621
Other	0.00102	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in maintaining the homeostasis of cellular nucleotides by catalyzing the interconversion of nucleoside phosphates. Has both nucleoside monophosphate and diphosphate kinase activities. Catalyzes the phosphorylation of AMP, dAMP, CMP and dCMP with ATP as phosphate donor and of CMP with GTP as phosphate donor. Also catalyzes the production of ATP, CTP, GTP, UTP, dATP, dCTP, dGTP and TTP from the corresponding diphosphate substrates with either ATP or GTP as phosphate donor. Shows substrate preference of CDP > UDP > ADP > GDP > TDP. {ECO:0000269|PubMed:23416111}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0711

Intolerance Scores

• rvis_EVS: 1.72
• rvis_percentile_EVS: 96.5

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.195
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ak9

Zebrafish Information Network

• Gene name: ak9
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: dADP phosphorylation;dGDP phosphorylation;AMP phosphorylation;ATP generation from ADP;nucleobase-containing small molecule interconversion;CDP phosphorylation;dAMP phosphorylation;CMP phosphorylation;dCMP phosphorylation;GDP phosphorylation;UDP phosphorylation;dCDP phosphorylation;TDP phosphorylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;nuclear membrane
• Molecular function: nucleoside diphosphate kinase activity;ATP binding;nucleoside kinase activity;nucleoside monophosphate kinase activity