NAGK

N-acetylglucosamine kinase

Basic information

Region (hg38): 2:71064344-71079808

Links

ENSG00000124357 ∙ NCBI:55577 ∙ OMIM:606828 ∙ HGNC:17174 ∙ Uniprot:Q9UJ70 ∙ 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 NAGK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAGK 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				2		2
missense			37	2		39
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	38	4	0

Variants in NAGK

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

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

Position	Type	Phenotype	Significance	ClinVar
2-71068606-C-G		not specified	Uncertain significance (Jul 06, 2021)
2-71068624-A-G		not specified	Likely benign (Nov 24, 2024)
2-71068657-G-T		not specified	Uncertain significance (Jul 14, 2023)
2-71068688-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-71068697-A-G		not specified	Uncertain significance (Dec 14, 2024)
2-71070578-A-G		not specified	Uncertain significance (May 23, 2023)
2-71070817-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-71070826-C-T		not specified	Uncertain significance (Mar 01, 2024)
2-71071720-C-A		not specified	Uncertain significance (Aug 20, 2024)
2-71071753-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-71071762-A-G		not specified	Uncertain significance (Mar 01, 2024)
2-71071791-G-A		not specified	Uncertain significance (Aug 04, 2021)
2-71071797-G-A		not specified	Uncertain significance (May 17, 2023)
2-71071800-G-A		not specified	Uncertain significance (Dec 16, 2024)
2-71071806-A-G		not specified	Uncertain significance (Jun 04, 2024)
2-71071822-C-T		not specified	Uncertain significance (Mar 01, 2025)
2-71072655-A-T		not specified	Uncertain significance (Mar 18, 2024)
2-71072674-A-G		not specified	Uncertain significance (Jan 22, 2025)
2-71072691-C-G		not specified	Uncertain significance (Jul 16, 2021)
2-71072704-A-G		not specified	Uncertain significance (May 25, 2022)
2-71072728-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-71072743-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-71073493-G-A		not specified	Uncertain significance (Dec 15, 2022)
2-71073533-A-G		not specified	Uncertain significance (Jan 01, 2025)
2-71073539-A-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAGK	protein_coding	protein_coding	ENST00000455662	10	15462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-9	0.370	125689	1	58	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.434	241	223	1.08	0.0000127	2521
Missense in Polyphen		68	64.357	1.0566		732
Synonymous	-0.664	103	94.8	1.09	0.00000616	786
Loss of Function	0.848	15	19.0	0.790	9.79e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000273	0.000264
Middle Eastern	0.000109	0.000109
South Asian	0.000525	0.000523
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts endogenous N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, from lysosomal degradation or nutritional sources into GlcNAc 6-phosphate. Involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway: although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded. Also has ManNAc kinase activity. {ECO:0000269|PubMed:22692205}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;2-Hydroxyglutric Aciduria (D And L Form);Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Salla Disease/Infantile Sialic Acid Storage Disease;Glutamate Metabolism;<i>N</i>-acetylglucosamine degradation II;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.819
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0834
• hipred: N
• hipred_score: 0.170
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nagk
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: N-acetylglucosamine metabolic process;UDP-N-acetylglucosamine biosynthetic process;N-acetylmannosamine metabolic process;N-acetylneuraminate catabolic process;carbohydrate phosphorylation
• Cellular component: cytosol;extracellular exosome
• Molecular function: protein binding;ATP binding;N-acetylglucosamine kinase activity