Phase II Detox – NATs

N-acetyltransferase is a phase II detoxification enzyme that helps to metabolize aromatic amines, drugs, cigarette smoke, and carcinogens. Basically, it makes specific toxins more water soluble so that they can be excreted through a process called acetylation.

There are several common genetic variants that can classify a person as a slow, intermediate, or rapid acetylator. Although the rapid acetylator is considered to be the ancestral type and is the most common type in Asian and African populations, Caucasian people are actually slightly more likely to be intermediate or slow acetylators.[ref]

Historically, N-acetyltransferase was first recognized in the 1950’s to play a role in the metabolism of tuberculosis drug. A significant percentage of people were found to be poor acetylators resulting in significant side effects of the tuberculosis drug, isoniazid.

Genetic variants involved:

NAT1 metabolizes p-aminobenzoic acid (PABA) and p-aminosalicylic acid (PAS).[ref] PABA used to be commonly found in sunscreens, and PAS is used as an antibiotic for tuberculosis. It also breaks down components of cigarette smoke and heterocyclic aromatic amines, which forms when meats and seafood are grilled at high temperatures.

There have been studies linking NAT1 genetic variants to an increased risk of bladder, colon, breast, lung, prostate, and pancreatic cancers. [ref]

Smoking is even more risky for those with NAT1 slow acetylator variants. NAT1 slow and intermediate acetylators had been shown to have a significantly higher risk for esophageal cancer and lung cancer in smokers.[ref]

It has recently been found that NAT1 slow acetylators have more DNA adducts formed with heterocyclic aromatic amines (carcinogens from meat being cooked at high temps). [ref]  Another study also found red meat consumption for slow and intermediate acetylators to be linked to esophageal cancer. [ref]

NAT1 is also involved in folate metabolism and folate may be a co-enzyme for NAT1 hydrolysis of acetyl-Coenzyme A [ref].  Rs15561 -AA (below) has been associated with cleft lip (especially if the mother smokes) and spina bifida. Note that it is the baby’s genotype, not the mother’s, that is being studied, so this is another really good reason not to smoke. [ref] Both of those conditions are linked to folate metabolism and the methylation cycle.

Check your 23andMe results for rs4986782:

  • AA: NAT1*14B, slow acetylator [ref]
  • AG: slow acetylator,
  • GG: normal


Check your 23andMe results for rs15561:

  • AA: reduced function [ref]
  • AC: reduced function
  • CC: normal


Check your 23andMe results for rs6586714:

  • AA: lower risk of colon cancer from cooked meat carcinogens (protective) [ref]
  • AG: lower risk of colon cancer from a cooked meat carcinogens
  • GG: wildtype/common

There are several other SNPs that are not included in 23andMe data so the above SNPs are not the complete picture for NAT1.

NAT2 also catalyzes the acetylation of a couple of types of carcinogens (aromatic and heterocyclic amines) which include tobacco smoke, well-cooked meat, and exhaust fumes. NAT2 is found mainly in the liver, in contrast with NAT1, which is found throughout the body. NAT2 has been studied extensively and is thought to play a role in the risk for several types of cancers.

NAT2 polymorphisms also create rapid, intermediate, and slow acetylators. Slow acetylators don’t clear out toxins as well and are at a somewhat higher risk for bladder, lung, breast, and esophageal cancers. Rapid acetylators can actually make some toxins more reactive and may be at a slightly higher risk for colon cancer.

There is an online tool from the University of Albany to determine your NAT2 phenotype.  You will need to look up your data for six different SNPs.   It asks you to put in your NAT2 alleles for the following:

NAT2 rs1208 – A, has also been found to be involved in increased insulin resistance, although, to me, the effect looked pretty small.  [ref]

NAT is also being studied in relation to bacteria which can produce it, and their relationship to drug metabolism.


If you need another reason not to smoke, being a slow or intermediate acetylator is a really good reason to never pick up a cigarette.

Slow acetylators may want to cut back on fried meats to limit the intake of heterocyclic aromatic amines.

Further reading:

Arylamine N-acetyltransferases: from drug metabolism and pharmacogenetics to drug discovery

Detox Genes – NQO1

This is part of an ongoing series on the genes involved in detoxification.

NAD(P)H:quinone oxidoreductase 1 (abbreviated as NQO1) uses NADH or NADPH to reduce quinones to hydroquinones.   NQO1 is involved in breaking down exogenous (outside) toxins such as benzene and some chemotherapy drugs.  Benzene, a carcinogen, is found  in gasoline fumes, laundry detergent, furniture wax, industrial uses, pesticides, and smoke.

NQO1 is also involved in cellular defense against oxidative stress, reduction of CoQ, and reduction of vitamin K.  In the reduction (chemistry meaning, think redox reaction) of Vitamin K, NQO1 is mostly involved in turning K3 into the form that is active in blood clotting and bone building[ref].

Two polymorphisms have been identified.  NQO1*2 leads to a deficiency in the enzyme, while NQO1*3 has reduced a enzyme activity which may depend on the substance.   Absence of NQO1 has recently been studied (in mice) and found to lead to gut impermeability and inflammation (leaky gut) [ref].

Check your 23andMe results for rs1131341:

  • AG: NQO1*3, decreased enzyme function depending on substance
  • GG: normal


Check your 23andMe results for rs1800566:

  • AA: NQO1*2, higher cancer risk from benzene, no NQO1 [ref]
  • AG: NQO1*1/*2, somewhat higher cancer risk from benzene, intermediate enzyme function
  • GG: normal

Researchers have found that the NQO1 enzyme can be induced by green tea extract and broccoli sprouts [ref] as well as resveratrol[ref].

From a 2002 paper in the American Journal of Clinical Nutrition:

The polymorphism results in reduced amounts of the NQO1 protein, possibly as the result of to an accelerated degradation via the ubiquitin pathway. The mutant expressed in E. coli has between 2% and 4% of the activity of the wild-type enzyme (186). The cause of both of these observations is likely to be an aberrant binding of FAD by the mutant enzyme. The Pro187→Ser mutation disturbs the structure of the central parallel β-sheet (192), resulting in a reduction in binding affinity for the FAD cofactor (193). Others found that NQO1 activity can be measured only in the presence of increased concentrations of FAD, confirming that the impairment of activity in the Pro187→Ser enzyme is due to lowered FAD affinity (Ivonne Rietjens, unpublished observations, 2001).

These data suggest that individuals with the NQO1 polymorphism might benefit from high-dose riboflavin treatment by reductions in cancer risk. Further studies should be done to verify or reject this theory.

It looks like there have been several more studies done in the past few years regarding FAD and NQO1 [ref] [ref].

More to read:

NAD(P)H:quinone acceptor oxidoreductase 1 (NQO1), a multifunctional antioxidant enzyme and exceptionally versatile cytoprotector  – this is a very thorough overview from 2011

Association of HMOX1 and NQO1 Polymorphisms with Metabolic Syndrome Components

Induction of the phase II detoxification enzyme NQO1 in hepatocarcinoma cells by lignans from the fruit of Schisandra chinensis through nuclear accumulation of Nrf2.

NAD(P)H:quinone oxidoreductase (NQO1) polymorphism, exposure to benzene, and predisposition to disease: A HuGE review


Phase II detox – GSTs

This is part of an ongoing series on the genes involved in detoxification.

Another phase II detox reaction occurs with the glutathione S-transferases enzymes, which has eight classes identified: alpha, kappa, mu, omega, pi, sigma, theta, and zeta.  The classes are abbreviated with their first letter (i.e. GSTMA for alpha).  These phase II enzymes add a glutathione to toxins in order to detoxify them.  GSTs are found in the liver, intestines, and several other places in the body and are responsible for detoxifying a large number of pesticides, herbicides, carcinogens, and chemotherapy drugs.

Once a toxic substance has been conjugated with glutathione via the GST specific enzyme, it can be excreted from the body via bile or urine.  Glutathione is considered the master antioxidant for the body.  Here is a nice article on ways to boost your glutathione level with food.

There are several fairly common polymorphisms that can decrease the function of your GSTs.  But, once again, environmental factors also play a huge role in your detox system.  So if you have non-functioning genes for a specific enzyme, your body has alternate ways to detox most substances and you can naturally boost those routes through nutrition.  One way of inducing GSTs is thought to be through cruciferous vegetable consumption.  [ref]

There have been quite a few studies done on the GST polymorphisms.  So if you find that you have one of these common polymorphisms, you may want to read up on some of the studies in PubMed.  Some studies are contradictory, and some seem to be specific to gender or ethnicity.

GSTA1 has a common polymorphism that significantly reduces its function.  When looking at research studies, GSTA1*A is the functioning enzyme, and GSTA1*B is the reduced function version.  A couple of studies show that with GSTA1*B there is a higher risk for colon cancer with high cruciferous vegetable intake, especially broccoli [ref], [ref].  Before you stop eating broccoli all together, weigh this against cancers that are prevented by it.  GSTA1*B with higher cruciferous veggie consumption were found to have more protection against breast cancer.[ref]  GSTA1*B is also associated with a higher risk of asthma and allergies. [ref]

Check your 23andMe results for rs3957357:

  • AA: GSTA1*B, low/ non-functioning enzyme
  • AG: GSTA1*A/*B
  • GG: GSTA1*A


GSTM1 has a very common (about half of some populations) mutation that is associated with little or no GSTM1 expression.  It can be found in 23andMe data through looking at rs366631 which is a SNP that has been correlated with a deletion in GSTM1.  [ref]  There are over 2500 PubMed entries for ‘GSTM1 polymorphism’, and it has been studied in reference to many different types of cancer, glaucoma, and diabetes. There is a higher risk of some cancers with non-functioning GSTM1 gene, but the association is modified for some by diet and environment.  This seems to be a mutation that should encourage people to eat healthy and not smoke!

Check your 23andMe results for rs366631:

  • AA: GSTM1, low/ non-functioning enzyme
  • AG: GSTM1 functioning
  • GG: GSTM1 functioning


GSTP1 is another GST gene with very common polymorphisms.  It is involved in estrogen metabolism, and in a 2009 US study, the polymorphism (GG) was found to reduce the risk of breast cancer in post-menopausal women vs. AA [ref]. Conversely, women with GSTP1 GG were found to have a higher risk of breast cancer in a 2008 Chinese study.  Those with the lowest intake of cruciferous vegetables with GG were found to have the highest risk of breast cancer.  [ref]  The difference between the two studies may be ethnicity or pre- vs. post-menopausal women.

A 2012 study on men taking Vitamin E (alpha-tocopherol) supplements found that those with GSTP1 AA and AG had higher levels of inflammation (measured IL-6), while those with GG had decreased IL-6 levels. It is an interesting study that is worth reading.  Note though that there were only 160 participates, male only.[ref]

A study in rats in 2015 found that carnosic acid (found in rosemary) up-regulates the GSTP enzyme.  [ref] And a study in mice found that GSTP-null mice had less weight gain on a high fat diet. [ref] Another study in mice showed less acetaminophen toxicity in GSTP-null. [ref]

Check your 23andMe results for rs1695:

  • AA: normal
  • AG: somewhat reduced GSTP1 activity
  • GG: somewhat reduced GSTP1 activity [ref]


GSTT1 is another GST with deletion or null activity being fairly common — ~20% of Caucasians and 80% of Asians.  GSTT1 null has been implicated in increased risk of several diseases: MS [ref], kidney disease from exposure to organochlorine pesticides [ref],  esophageal cancer [ref], lymphoma due to polycyclic aromatic hydrocarbons [ref], and many more.

There is no SNP that defines GSTT1 null vs present, as far as I can find.  The Genetic Genie detox report does include it.  If you go to your raw data on 23andMe and search for the GSTT1 gene, a lot of ‘no call’s should indicate GSTT1 null.


Nrf2 Pathway: Increasing the body’s ability to get rid of toxins

This is part of an ongoing series on the genes involved in detoxification.

The Nrf2 signaling pathway regulates the expression of antioxidants and phase II detoxification enzymes. I think of it as flipping the switch to call up the phase II enzymes to take out the trash produced in phase I detox.

The phase II enzymes then further break down the metabolites from phase I detoxification, making them into something that can be excreted by the body.  Specifically, the Nrf2 signaling pathway is involved in GSTs, NQO1, UGTs, and SULTs.


Genetic Variants:

Variants in the NFE2L2 (Nrf2 pathway) gene are fairly common, with some variants increasing Nrf2 pathway signaling and some diminishing it. Some of these are being studied in relation to cancer prognosis, lung volume in smokers, and Parkinson’s disease.

Genetic variants that increase Nrf2:

Check your 23andMe results for rs6726395 (v.4):

  • GG:  greater lung volume in smokers [ref], decreased risk of AMD [ref]
  • AG: somewhat greater lung volume in smokers
  • AA: normal


Check your 23andMe results for rs13001694 (v5):

  • GG: reduced risk of all-cause mortality, especially in smokers [study]
  • AG: reduced risk of all-cause mortality, especially in smokers
  • AA: normal

23andMe results for rs1806649 (v4):

  • CC: normal
  • CT: significantly reduced risk of death from COPD
  • TT: significantly reduced risk of death from COPD (70% reduction) [ref]

Genetic variant that reduces Nrf2 expression:

Check your 23andMe results for rs6721961 (v.4):

  • GG: normal
  • TT: significantly diminished Nrf2 expression, increased risk of lung cancer [ref]


Sulforaphane, a natural substance found in broccoli sprouts, Brussels sprouts, cabbage, cauliflower, activates the Nrf2 pathway. [study][study]  Broccoli sprouts are supposed to be one of the best sources of sulforaphane that you can eat. There are also sulforaphane supplements available. Be sure to get one that includes the myrosinase enzyme such as this one from Jarrow.

Green tea, garlic, turmeric, and DHA also activate Nrf2 to some extent.  [study] [study][study]

More to read:

Video explaining Nrf2:

Phase 2 Detoxification – UGTs

This is part of an ongoing series on the genes involved in detoxification.

UDP-glucuronosyltransferase (abbreviated UGT) creates a glucuronidation reaction, which is a big part of Phase II detoxification.  Once a drug, toxin, or other substance is broken down in a Phase I reaction (see the CYP genes), the Phase II reactions further alter the substance so that it can be excreted from the body.

The reaction catalyzed by the UGT enzyme involves the addition of a glucuronic acid moiety to xenobiotics and is the most important pathway for the human body’s elimination of the top 200 drugs. It is also the major pathway for foreign chemical (dietary, environmental, pharmaceutical) removal for most drugs, dietary substances, toxins and endogenous substances.  – Wikipedia

There are quite a few genes involved in glucuronidation, and most are prefixed with UGT.


UGT1A1 is involved in the breakdown of bilirubin, estrogen, and several carcinogens. Gilbert’s Syndrome is associated with this gene and involves bilirubin not being broken down appropriately.  One study in 2009 showed that the levels of UGT1A1 activity can be increased with cruciferous vegetables.  This may be one way that cruciferous veggies are protective against cancer.

Bilirubin, a substance that brings to mind jaundice in babies, is a breakdown product naturally caused in a body as it clears out aged red blood cells.  It is excreted in bile and urine, and gives feces its brown color.

UGT1A1 is also responsible for the breakdown of BPA (in plastics) [ref].

There are a couple of SNPs that are supposed to code for higher bilirubin and lower activity in UGT1A1 known as *28. UGT1A1*28 is significant for those undergoing irinotecan treatment for colon cancer.  I’m unclear right now as to what each SNP means since I’m seeing conflicting information.  You can look at the information on SNPedia for rs34815109 which gives an explanation, and then look at rs34983651 and rs35600288. PharmGKB also lists several articles showing that rs8175347 (not in 23andMe) is associated with UGT1A1*28, as well as rs6742078 (see below).


Check your 23andMe results for rs4148323:

  • AA: UGT1A1*6 – increased bilirubin level, Gilbert’s syndrome in Asian populations
  • AG: Carrier of UGT1A1*6
  • GG: normal


Check your 23andMe results for rs4124874:

  •  GG: UGT1A1*60[ref], reduced activity, increased bilirubin (Caucasian)[ref]
  •  TT: normal


Check your 23andMe results for rs6742078:

  •  TT: increased bilirubin levels, increased gallstone risk (males)[ref]
  •  GG: normal

 UGT1A6 is also involved in transforming bilirubin, hormones, and certain drugs (aspirin, acetaminophen)  into water-soluble metabolites that can then be excreted from the body.  Studies on this gene also look at the polymorphisms in association with benzene poisoning.


Check your 23andMe results for rs887829:

  •  TT: higher serum bilirubin levels, protective against heart disease
  •  CC: normal


Check your 23andMe results for rs17863783:

  •  T-allele: protective against bladder cancer
  • GG: normal


UGT1A9 polymorphisms:   There is not a lot of information was available for this gene, so it is something to come back to in the future.  UGT1A9*3 is thought to be a non-functioning version, but the SNP (rs72551330) isn’t available in 23andMe data.  [ref]

Check your 23andMe results for rs6714486:

  • AA: higher activity [ref] [ref]
  • TT: normal



More to read:
UGT1a1 polymorphisms are important determinants of dietary carcinogen detoxification in the liver (2005)

Regulation of the UGT1a1 Bilirubin-Conjugating Pathway (2006)