NAMPT

nicotinamide phosphoribosyltransferase

Basic information

Region (hg38): 7:106248297-106285966

Previous symbols: [ "PBEF1" ]

Links

ENSG00000105835 ∙ NCBI:10135 ∙ OMIM:608764 ∙ HGNC:30092 ∙ Uniprot:P43490 ∙ 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 NAMPT gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

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

Variants in NAMPT

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

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

Position	Type	Phenotype	Significance	ClinVar
7-106251135-T-G		not specified	Uncertain significance (Jul 06, 2021)
7-106251201-A-G			Benign (Dec 31, 2019)
7-106253042-T-C		not specified	Uncertain significance (Dec 09, 2023)
7-106261675-A-G			Benign (Dec 31, 2019)
7-106261678-A-G			Benign (Dec 31, 2019)
7-106261699-C-A		not specified	Likely benign (Feb 22, 2023)
7-106263448-G-C		not specified	Likely benign (Dec 22, 2023)
7-106263496-T-C		not specified	Uncertain significance (Aug 23, 2021)
7-106263559-G-T		not specified	Uncertain significance (Oct 26, 2022)
7-106268500-G-C		not specified	Uncertain significance (Jan 17, 2024)
7-106274983-T-C		not specified	Uncertain significance (Dec 08, 2023)
7-106277036-A-G			Benign (Jul 31, 2018)
7-106277142-T-C		not specified	Uncertain significance (Aug 20, 2023)
7-106284863-C-G		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAMPT	protein_coding	protein_coding	ENST00000222553	11	38042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0209	125731	0	8	125739	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	116	247	0.469	0.0000113	3213
Missense in Polyphen		15	81.883	0.18319		1044
Synonymous	0.723	81	89.7	0.903	0.00000447	904
Loss of Function	4.08	3	25.1	0.120	0.00000114	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the condensation of nicotinamide with 5- phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, an intermediate in the biosynthesis of NAD. It is the rate limiting component in the mammalian NAD biosynthesis pathway. The secreted form behaves both as a cytokine with immunomodulating properties and an adipokine with anti-diabetic properties, it has no enzymatic activity, partly because of lack of activation by ATP, which has a low level in extracellular space and plasma. Plays a role in the modulation of circadian clock function. NAMPT-dependent oscillatory production of NAD regulates oscillation of clock target gene expression by releasing the core clock component: CLOCK-ARNTL/BMAL1 heterodimer from NAD-dependent SIRT1-mediated suppression (By similarity). {ECO:0000250|UniProtKB:Q99KQ4, ECO:0000269|PubMed:24130902}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;Adipogenesis;BMAL1-CLOCK,NPAS2 activates circadian gene expression;NAD metabolism, sirtuins and aging;NAD+ metabolism;NAD+ biosynthetic pathways;Caloric restriction and aging;Circadian Clock;BMAL1:CLOCK,NPAS2 activates circadian gene expression;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;NAD salvage (Consensus)

Recessive Scores

• pRec: 0.231

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.785
• hipred: Y
• hipred_score: 0.507
• ghis: 0.606

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nampt
• Phenotype: immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); hematopoietic system phenotype; embryo phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: microglial cell activation;signal transduction;cell-cell signaling;female pregnancy;aging;circadian rhythm;positive regulation of cell population proliferation;insulin receptor signaling pathway;regulation of signaling receptor activity;negative regulation of autophagy;response to organic cyclic compound;regulation of lung blood pressure;circadian regulation of gene expression;NAD biosynthesis via nicotinamide riboside salvage pathway;positive regulation of transcription by RNA polymerase II;positive regulation of smooth muscle cell proliferation;positive regulation of nitric-oxide synthase biosynthetic process;adipose tissue development;neuron death;cellular response to ionizing radiation;cellular response to oxygen-glucose deprivation;cellular response to amyloid-beta;response to D-galactose;negative regulation of cellular senescence
• Cellular component: cytosol;plasma membrane;nuclear speck;cell junction;extracellular exosome
• Molecular function: nicotinate-nucleotide diphosphorylase (carboxylating) activity;cytokine activity;protein binding;drug binding;identical protein binding;protein homodimerization activity;nicotinamide phosphoribosyltransferase activity