SIRT1
protein-codingsirtuin 1, the group of Sirtuins|eNoSC complex
Gene summary
This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity. The protein encoded by this gene is included in class I of the sirtuin family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015967
Submitter: ClinGen
Heterozygous variants in the Sirtuin-1 (*SIRT1*) gene were first reported in association with monogenic type 1 diabetes (T1D) in humans in 2013 by Biason-Lauber et al. (PMID: 23473037). The SIRT p.L107P was observed in a family to segregate in an autosomal dominant manner with T1D/autoimmune diabetes and inflammatory bowel disease (IBD). SIRT1’s role in neuronal survival, oxidative stress, and mitochondrial function (PMID: 40120944) suggest its variants could contribute to neurodegenerative diseases, but such associations have not been reported in humans. Per the criteria outlined by the ClinGen Lumping and Splitting Working Group, we found only a single disease entity, T1D, asserted in relation to *SIRT1*, and no lumping or splitting was required. Evidence supporting this gene-disease relationship includes case-level data and experimental data. So far, only one missense variant, p.L107P, has been reported in association with T1D in a large family (PMID: 23473037) that underwent genome-wide linkage analysis followed by targeted and candidate gene sequencing (0.5 points). The published LOD score was 2.4 but was based on 5 instances of segregation of the variant with autoimmune disease (4 with T1D and 1 with ulcerative colitis) and 16 segregations of the reference allele with no autoimmune disease. There were 3 non-proband segregations of the variant with T1D, which was insufficient for calculating a LOD score based on the ClinGen SOP; therefore, 0 points were awarded for segregation. Family members without the variant in the reported family were healthy, with normal insulin secretion and action, except for two individuals who displayed features typical of type 2 diabetes and no autoimmunity. Thus, the genetic evidence reached a total of only 0.5 points. The proposed disease mechanism is reduced anti-inflammatory function of sirtuin-1 based on increased cytokine expression in insulin-producing MIN6 cells transfected with the p.L107P variant compared with wildtype (0.5 points), bringing the total experimental evidence score to 0.5. The combined total score for genetic and experimental evidence is 1.0. In summary, there is limited evidence supporting the relationship between *SIRT1* and autosomal dominant T1D/autoimmune disease, primarily T1D. More evidence is needed to firmly establish this gene-disease relationship; the total score (1.0) falls within the limited range. The lack of genetic evidence outside a single publication remains a major limitation. This classification was approved by the ClinGen Monogenic Diabetes Expert Panel on March 26, 2025 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0007179
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SIRT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012238.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 35 | 3 | 40 | ||
| missense | 120 | 9 | 3 | 132 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 125 | 44 | 6 | 175 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036370.2 | 9 | MANE Select | |
| Ensembl | ENSP00000212015.6 | 9 | MANE Select | |
| RefSeq | NP_001135970.1 | 6 | Standard | |
| RefSeq | NP_001300978.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sirt1 | Danio rerio | Structure: trunk vasculature Quality: spatial pattern abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Longevity regulating pathway - multiple species - Homo sapiens (human)
- FoxO signaling pathway - Homo sapiens (human)
- AMPK signaling pathway - Homo sapiens (human)
- Glucagon signaling pathway - Homo sapiens (human)
- Longevity regulating pathway - Homo sapiens (human)
Biological Process
- single strand break repair
- negative regulation of transcription by RNA polymerase II
- chromatin silencing at rDNA
- pyrimidine dimer repair by nucleotide-excision repair
- DNA synthesis involved in DNA repair
Molecular Function
- RNA polymerase II distal enhancer sequence-specific DNA binding
- p53 binding
- transcription corepressor activity
- NAD+ ADP-ribosyltransferase activity
- histone deacetylase activity
Cellular Component
- nuclear chromatin
- nucleus
- nuclear envelope
- nuclear inner membrane
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000212015
- Coding exons
- 9
- Length
- 33721
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.79 | 243 | 336 | 0.724 | 0.0000161 | 4861 |
| Missense (PolyPhen) | 63 | 127.11 | 0.49564 | 1635 | ||
| Synonymous | -0.978 | 130 | 117 | 1.12 | 0.00000574 | 1466 |
| Loss of Function | 3.47 | 7 | 26.1 | 0.268 | 0.00000133 | 378 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.000062 | 0.000053 | rare |
| South Asian | 0.00020 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: NAD-dependent protein deacetylase that links transcriptional regulation directly to intracellular energetics and participates in the coordination of several separated cellular functions such as cell cycle, response to DNA damage, metobolism, apoptosis and autophagy. Can modulate chromatin function through deacetylation of histones and can promote alterations in the methylation of histones and DNA, leading to transcriptional repression. Deacetylates a broad range of transcription factors and coregulators, thereby regulating target gene expression positively and negatively. Serves as a sensor of the cytosolic ratio of NAD(+)/NADH which is altered by glucose deprivation and metabolic changes associated with caloric restriction. Is essential in skeletal muscle cell differentiation and in response to low nutrients mediates the inhibitory effect on skeletal myoblast differentiation which also involves 5'-AMP-activated protein kinase (AMPK) and nicotinamide phosphoribosyltransferase (NAMPT). Component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone-modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at 'Lys-9' (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus. Deacetylates 'Lys-266' of SUV39H1, leading to its activation. Inhibits skeletal muscle differentiation by deacetylating PCAF and MYOD1. Deacetylates H2A and 'Lys-26' of HIST1H1E. Deacetylates 'Lys-16' of histone H4 (in vitro). Involved in NR0B2/SHP corepression function through chromatin remodeling: Recruited to LRH1 target gene promoters by NR0B2/SHP thereby stimulating histone H3 and H4 deacetylation leading to transcriptional repression. Proposed to contribute to genomic integrity via positive regulation of telomere length; however, reports on localization to pericentromeric heterochromatin are conflicting. Proposed to play a role in constitutive heterochromatin (CH) formation and/or maintenance through regulation of the available pool of nuclear SUV39H1. Upon oxidative/metabolic stress decreases SUV39H1 degradation by inhibiting SUV39H1 polyubiquitination by MDM2. This increase in SUV39H1 levels enhances SUV39H1 turnover in CH, which in turn seems to accelerate renewal of the heterochromatin which correlates with greater genomic integrity during stress response. Deacetylates 'Lys-382' of p53/TP53 and impairs its ability to induce transcription-dependent proapoptotic program and modulate cell senescence. Deacetylates TAF1B and thereby represses rDNA transcription by the RNA polymerase I. Deacetylates MYC, promotes the association of MYC with MAX and decreases MYC stability leading to compromised transformational capability. Deacetylates FOXO3 in response to oxidative stress thereby increasing its ability to induce cell cycle arrest and resistance to oxidative stress but inhibiting FOXO3-mediated induction of apoptosis transcriptional activity; also leading to FOXO3 ubiquitination and protesomal degradation. Appears to have a similar effect on MLLT7/FOXO4 in regulation of transcriptional activity and apoptosis. Deacetylates DNMT1; thereby impairs DNMT1 methyltransferase-independent transcription repressor activity, modulates DNMT1 cell cycle regulatory function and DNMT1-mediated gene silencing. Deacetylates RELA/NF-kappa-B p65 thereby inhibiting its transactivating potential and augments apoptosis in response to TNF-alpha. Deacetylates HIF1A, KAT5/TIP60, RB1 and HIC1. Deacetylates FOXO1 resulting in its nuclear retention and enhancement of its transcriptional activity leading to increased gluconeogenesis in liver. Inhibits E2F1 transcriptional activity and apoptotic function, possibly by deacetylation. Involved in HES1- and HEY2-mediated transcriptional repression. In cooperation with MYCN seems to be involved in transcriptional repression of DUSP6/MAPK3 leading to MYCN stabilization by phosphorylation at 'Ser-62'. Deacetylates MEF2D. Required for antagonist-mediated transcription suppression of AR-dependent genes which may be linked to local deacetylation of histone H3. Represses HNF1A- mediated transcription. Required for the repression of ESRRG by CREBZF. Modulates AP-1 transcription factor activity. Deacetylates NR1H3 AND NR1H2 and deacetylation of NR1H3 at 'Lys-434' positively regulates transcription of NR1H3:RXR target genes, promotes NR1H3 proteosomal degradation and results in cholesterol efflux; a promoter clearing mechanism after reach round of transcription is proposed. Involved in lipid metabolism. Implicated in regulation of adipogenesis and fat mobilization in white adipocytes by repression of PPARG which probably involves association with NCOR1 and SMRT/NCOR2. Deacetylates ACSS2 leading to its activation, and HMGCS1. Involved in liver and muscle metabolism. Through deacteylation and activation of PPARGC1A is required to activate fatty acid oxidation in skeletel muscle under low-glucose conditions and is involved in glucose homeostasis. Involved in regulation of PPARA and fatty acid beta-oxidation in liver. Involved in positive regulation of insulin secretion in pancreatic beta cells in response to glucose; the function seems to imply transcriptional repression of UCP2. Proposed to deacetylate IRS2 thereby facilitating its insulin-induced tyrosine phosphorylation. Deacetylates SREBF1 isoform SREBP-1C thereby decreasing its stability and transactivation in lipogenic gene expression. Involved in DNA damage response by repressing genes which are involved in DNA repair, such as XPC and TP73, deacetylating XRCC6/Ku70, and faciliting recruitment of additional factors to sites of damaged DNA, such as SIRT1-deacetylated NBN can recruit ATM to initiate DNA repair and SIRT1-deacetylated XPA interacts with RPA2. Also involved in DNA repair of DNA double-strand breaks by homologous recombination and specifically single-strand annealing independently of XRCC6/Ku70 and NBN. Transcriptional suppression of XPC probably involves an E2F4:RBL2 suppressor complex and protein kinase B (AKT) signaling. Transcriptional suppression of TP73 probably involves E2F4 and PCAF. Deacetylates WRN thereby regulating its helicase and exonuclease activities and regulates WRN nuclear translocation in response to DNA damage. Deacetylates APEX1 at 'Lys-6' and 'Lys-7' and stimulates cellular AP endonuclease activity by promoting the association of APEX1 to XRCC1. Increases p53/TP53-mediated transcription-independent apoptosis by blocking nuclear translocation of cytoplasmic p53/TP53 and probably redirecting it to mitochondria. Deacetylates XRCC6/Ku70 at 'Lys-539' and 'Lys-542' causing it to sequester BAX away from mitochondria thereby inhibiting stress-induced apoptosis. Is involved in autophagy, presumably by deacetylating ATG5, ATG7 and MAP1LC3B/ATG8. Deacetylates AKT1 which leads to enhanced binding of AKT1 and PDK1 to PIP3 and promotes their activation. Proposed to play role in regulation of STK11/LBK1- dependent AMPK signaling pathways implicated in cellular senescence which seems to involve the regulation of the acetylation status of STK11/LBK1. Can deacetylate STK11/LBK1 and thereby increase its activity, cytoplasmic localization and association with STRAD; however, the relevance of such activity in normal cells is unclear. In endothelial cells is shown to inhibit STK11/LBK1 activity and to promote its degradation. Deacetylates SMAD7 at 'Lys-64' and 'Lys-70' thereby promoting its degradation. Deacetylates CIITA and augments its MHC class II transactivation and contributes to its stability. Deacteylates MECOM/EVI1. Deacetylates PML at 'Lys-487' and this deacetylation promotes PML control of PER2 nuclear localization. During the neurogenic transition, repress selective NOTCH1-target genes through histone deacetylation in a BCL6-dependent manner and leading to neuronal differentiation. Regulates the circadian expression of several core clock genes, including ARNTL/BMAL1, RORC, PER2 and CRY1 and plays a critical role in maintaining a controlled rhythmicity in histone acetylation, thereby contributing to circadian chromatin remodeling. Deacetylates ARNTL/BMAL1 and histones at the circadian gene promoters in order to facilitate repression by inhibitory components of the circadian oscillator. Deacetylates PER2, facilitating its ubiquitination and degradation by the proteosome. Protects cardiomyocytes against palmitate-induced apoptosis (PubMed:11672523, PubMed:12006491, PubMed:14976264, PubMed:14980222, PubMed:15126506, PubMed:15152190, PubMed:15205477, PubMed:15469825, PubMed:15692560, PubMed:16079181, PubMed:16166628, PubMed:16892051, PubMed:16998810, PubMed:17283066, PubMed:17334224, PubMed:17505061, PubMed:17612497, PubMed:17620057, PubMed:17936707, PubMed:18203716, PubMed:18296641, PubMed:18662546, PubMed:18687677, PubMed:19188449, PubMed:19220062, PubMed:19364925, PubMed:19690166, PubMed:19934257, PubMed:20097625, PubMed:20100829, PubMed:20203304, PubMed:20375098, PubMed:20620956, PubMed:20670893, PubMed:20817729, PubMed:21149730, PubMed:21245319, PubMed:21471201, PubMed:21504832, PubMed:21555002, PubMed:21698133, PubMed:21701047, PubMed:21775285, PubMed:21807113, PubMed:21841822, PubMed:21890893, PubMed:21909281, PubMed:21947282, PubMed:22274616). Deacetylates XBP1 isoform 2; deacetylation decreases protein stability of XBP1 isoform 2 and inhibits its transcriptional activity (PubMed:20955178). Involved in the CCAR2- mediated regulation of PCK1 and NR1D1 (PubMed:24415752). Deacetylates CTNB1 at 'Lys-49' (PubMed:24824780). In POMC (pro- opiomelanocortin) neurons, required for leptin-induced activation of PI3K signaling (By similarity). {ECO:0000250|UniProtKB:Q923E4, ECO:0000269|PubMed:11672523, ECO:0000269|PubMed:12006491, ECO:0000269|PubMed:14976264, ECO:0000269|PubMed:14980222, ECO:0000269|PubMed:15126506, ECO:0000269|PubMed:15152190, ECO:0000269|PubMed:15205477, ECO:0000269|PubMed:15469825, ECO:0000269|PubMed:15692560, ECO:0000269|PubMed:16079181, ECO:0000269|PubMed:16166628, ECO:0000269|PubMed:16892051, ECO:0000269|PubMed:16998810, ECO:0000269|PubMed:17283066, ECO:0000269|PubMed:17290224, ECO:0000269|PubMed:17334224, ECO:0000269|PubMed:17505061, ECO:0000269|PubMed:17612497, ECO:0000269|PubMed:17620057, ECO:0000269|PubMed:17936707, ECO:0000269|PubMed:18203716, ECO:0000269|PubMed:18296641, ECO:0000269|PubMed:18662546, ECO:0000269|PubMed:18687677, ECO:0000269|PubMed:19188449, ECO:0000269|PubMed:19220062, ECO:0000269|PubMed:19364925, ECO:0000269|PubMed:19690166, ECO:0000269|PubMed:19934257, ECO:0000269|PubMed:20097625, ECO:0000269|PubMed:20100829, ECO:0000269|PubMed:20203304, ECO:0000269|PubMed:20375098, ECO:0000269|PubMed:20620956, ECO:0000269|PubMed:20670893, ECO:0000269|PubMed:20817729, ECO:0000269|PubMed:20955178, ECO:0000269|PubMed:21149730, ECO:0000269|PubMed:21245319, ECO:0000269|PubMed:21471201, ECO:0000269|PubMed:21504832, ECO:0000269|PubMed:21555002, ECO:0000269|PubMed:21698133, ECO:0000269|PubMed:21701047, ECO:0000269|PubMed:21775285, ECO:0000269|PubMed:21807113, ECO:0000269|PubMed:21841822, ECO:0000269|PubMed:21890893, ECO:0000269|PubMed:21909281, ECO:0000269|PubMed:21947282, ECO:0000269|PubMed:22274616, ECO:0000269|PubMed:24415752, ECO:0000269|PubMed:24824780}.; FUNCTION: (Microbial infection) In case of HIV-1 infection, interacts with and deacetylates the viral Tat protein. The viral Tat protein inhibits SIRT1 deacetylation activity toward RELA/NF- kappa-B p65, thereby potentiates its transcriptional activity and SIRT1 is proposed to contribute to T-cell hyperactivation during infection. {ECO:0000269|PubMed:18329615}.;
Recessive Scores
- pRec
- 0.622
Intolerance Scores
- LoFtool
- 0.571
- RVIS EVS
- 0.2
- RVIS percentile EVS
- 67.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |