NADK

NAD kinase

Basic information

Region (hg38): 1:1751232-1780457

Links

ENSG00000008130 ∙ NCBI:65220 ∙ OMIM:611616 ∙ HGNC:29831 ∙ Uniprot:O95544 ∙ 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 NADK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NADK 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				5		5
missense			39	1	3	43
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	6	4

Variants in NADK

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

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

Position	Type	Phenotype	Significance	ClinVar
1-1752908-C-CCCT		not specified	Benign (Dec 12, 2023)
1-1752941-T-C		not specified	Uncertain significance (Jul 19, 2023)
1-1752960-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-1752977-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-1753014-G-A		not specified	Uncertain significance (Mar 04, 2024)
1-1753025-G-A		not specified	Uncertain significance (May 16, 2023)
1-1754135-G-A			Likely benign (Aug 01, 2018)
1-1754137-T-G		not specified	Uncertain significance (Jul 06, 2021)
1-1754149-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-1754175-G-A		not specified	Uncertain significance (Aug 20, 2024)
1-1754347-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-1754353-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-1754369-C-T			Likely benign (Apr 01, 2022)
1-1754575-A-G		not specified	Likely benign (Feb 28, 2025)
1-1754638-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-1756298-C-T		not specified	Uncertain significance (Feb 07, 2025)
1-1756508-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-1756523-T-C		not specified	Uncertain significance (Dec 23, 2024)
1-1756560-T-C		not specified	Uncertain significance (Aug 14, 2024)
1-1756620-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-1756643-G-A		not specified	Uncertain significance (May 20, 2024)
1-1756656-T-A		not specified	Uncertain significance (Jan 23, 2024)
1-1757120-G-A		not specified	Uncertain significance (Aug 05, 2023)
1-1757121-G-C		not specified	Uncertain significance (Aug 11, 2022)
1-1757129-C-T		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NADK	protein_coding	protein_coding	ENST00000344463	13	29226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-10	0.755	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	277	380	0.729	0.0000245	3787
Missense in Polyphen		39	90.208	0.43234		820
Synonymous	0.126	167	169	0.988	0.0000127	1196
Loss of Function	1.58	20	29.2	0.684	0.00000156	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000436	0.000435
South Asian	0.0000662	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;NAD+ metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;NAD phosphorylation and dephosphorylation (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.501
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.446
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nadk

Gene ontology

• Biological process: NADP biosynthetic process;phosphorylation;NAD metabolic process;positive regulation of insulin secretion involved in cellular response to glucose stimulus;ATP metabolic process
• Cellular component: cytosol
• Molecular function: NAD+ kinase activity;protein binding;ATP binding;metal ion binding