NAMPT
nicotinamide phosphoribosyltransferase
Basic information
Region (hg38): 7:106248298-106285966
Previous symbols: [ "PBEF1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 10 | |||||
| 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 | 8 | 2 | 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) | ||
| 7-106254481-T-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 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:
| 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:
- 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