The FTO gene is nick-named the ‘fatso gene’ because of its association with obesity. (Please don’t think that I’m fat-shaming  a gene here – hopefully I didn’t hurt the FTO gene’s feelings :-)

The FTO gene was identified about ten years ago in a genome-wide association study which looked at over 35,000 people to determine genes involved in obesity.  But identifying the gene didn’t explain why it was so widely linked to higher BMI as well as ADHD, depression, and dementia.

Early studies concluded that those with increased BMI and FTO variants also tended to have an increased energy intake with an association with elevated fat consumption.[ref]  In 2013, a study found that those with variants in the FTO gene are expressing more FTO, which was thought to alter ghrelin mRNA causing higher ghrelin (the ‘hunger hormone’) levels.[ref]  Some studies found that FTO deficient mice suffer from growth retardation and have both reduced lean mass and fat mass,[ref] but not all studies come agree.[ref]

Most recently, a 2015 study published in the New England Journal of Medicine points to FTO polymorphisms disrupting ARID5B which leads to increase IRX3 and IRX5.  These two genes are involved in turning fat cells into white fat that stores lipids instead of brown fat which is involved in thermogenesis.  Most of the current research is pointing to the variants in the FTO gene region really being associated with increased IRX3 levels.

Quick recap: FTO genetic variants increase its levels, possibly leading to more ghrelin, aka the hunger hormone.

FTO Genetic Variants

There are actually five FTO variants that are well researched and referenced in many studies: rs9939609, rs1421085, rs1121980, rs1121980, and rs17817449.  These are all in a block of DNA that is usually inherited together, so I’ve only listed the first one below to check for on 23andMe or AncestryDNA data. (i.e. if you have a variant for one, you almost always have the variant in all of them).

The research on these FTO variants shows that those carrying the variant form are more likely to have a higher BMI and be at a risk for obesity.  This doesn’t mean that everyone with the variant will be obese, just that when you look at large groups of people, averaging together those with the variant shows that they tend to have higher BMI’s than those without.

Check your 23andMe results for 23andMe results for rs9939609 (v4, v5)

  • AA: higher risk of obesity, increased BMI
  • AT: increased risk of obesity, BMI
  • TT: normal

Studies on this genetic variant show:

  • one study found a low-fat, low-calorie diet worked better for those carrying the risk variant [ref]
  • in children, the risk variant affected childhood weight gain more for those with low vitamin D levels.  [ref] [ref]
  • The variant prevents the binding of repressor protein ARID5B, therefore leading to increased FTO activity.  ARID5B represses IRX3 and IRX5, which leads to more white fat tissue instead of heat-producing brown fat.  [ref]
  • Carriers of the risk variant had 2.5x greater risk of obesity with high carb intake compared to those with the normal FTO version[ref]
  • in one study, the risk variant is linked to higher BMI only with a high saturated fat intake. [ref]


Other FTO variants:

rs1558902 (A is the minor allele, fairly common in Caucasians)

  • Carriers of the risk allele had a greater reduction in weight, body composition, and fat distribution in response to a high-protein diet, whereas an opposite genetic effect was observed on changes in fat distribution in response to a low-protein diet. [ref]

rs3751812 (T is the minor allele )

  • Associated with higher BMI, lower HDL, higher LDL [ref]



Diet: There seems to be a small link between higher protein / lower fat diets working better for weight loss with FTO genetic variants.

Vitamin D:  Can increasing your vitamin D levels help with weight loss?  A higher BMI leads to a lower vitamin D status, but not vice-versa, according to one study.[ref]  But the studies on childhood obesity and FTO seem to tell a different story.  Vitamin D levels in childhood may make a difference in weight gain, and children with higher vitamin D levels along with FTO variants were less likely to have increased weight than those with lower vitamin D levels. [ref]

Supplements: Angelica Sinensis, also known as Dong Quai,  has been shown in mouse studies to ameliorate obesity in a mouse model of FTO variants. This is a traditional Chinese herbal supplement available in stores and online.

Artificial sweeteners: For men with the obesity causing FTO variant, artificial sweetener consumption increased the weight gain. The study didn’t define which artificial sweeteners, just that the more they were consumed, the greater the weight gain.[ref]

Back to IRX3 and IRX5…

Studies point to FTO variants increasing IRX3.  After the initial study that was published in the New England Journal of Medicine in 2014, an MIT article sums up the new research as follows:

“Follow-up experiments showed that IRX3 and IRX5 act as master controllers of a process known as thermogenesis, whereby adipocytes dissipate energy as heat, instead of storing it as fat. Thermogenesis can be triggered by exercise, diet, or exposure to cold, and occurs both in mitochondria-rich brown adipocytes that are developmentally related to muscle, and in beige adipocytes that are instead related to energy-storing white adipocytes.”[ref]

That article goes on to say “Similarly, repression of IRX3 in mouse adipocytes led to dramatic changes in whole-body energy balance, resulting in a reduction of body weight and all major fat stores, and complete resistance to a high-fat diet.”

So the key seems to be to decrease IRX3 and/or IRX5 levels.  There are studies being done on different synthetic/pharmaceutical inhibitors, but so far I’m not finding much about natural foods or supplements that inhibit or decrease these two genes.

One interesting thought and rabbit trail is that according to a doctoral thesis from June 2016:  “Irx3 is stimulated under hypoxic conditions in vitro and mimics the expression pattern of EPAS1 under pro-angiogenic conditions.” The study is in endothelial cells and may not translate to adipose tissue. But if it does translate, then looking at decreasing hypoxia (lack of oxygen) may decrease IRX3.  So where does this lead me?  Breathing correctly as a way to decrease hypoxia.   Yoga and yoga breathing methods have been associated with health for thousands of years.  Tai Chi also involves a breathing component.[ref]

Here is a website on Normal Breathing with information on how many times per minute a person should be breathing. Deep breathing and hyperventilating cause less oxygen in your cells (hypoxia).  There is a chart on their homepage showing how breathing has changed over the last 100 years — and it is shaped a lot like charts for obesity.  (I know – correlation is not causation.)  Another resource to check out is Dr. Ray Peat’s articles on CO2.  The Normal Breathing website says “When we breathe more than the medical norm, we lose CO2 and reduce body oxygenation due to vasoconstriction and the suppressed Bohr effect caused by hypocapnia (CO2 deficiency). Hence, overbreathing leads to reduced cell oxygenation, while slower and easier breathing (with lower respiratory rates) improves cell-oxygen content.”

There are also supplements that claim to ‘oxygenate’ the blood.  CellFood is one such supplement, though I’m not sure if it works for weight loss or not.  The Amazon reviews seem to be mixed, but then everyone is different and what works for one person may not work for another.

As a side note, it is interesting to note where the weight goes in ‘weight loss’.  Turns out the majority of it is expelled as carbon dioxide from the lungs.  [ref]

The other issue involved in IRX3 and IRX5 seems to be brown fat and thermogenesis.  Cold showers and ice baths may be an option for weight loss here.

And finally coming full circle, an inhibitor of IRX5 (in prostate cancer cells) is Vitamin D, specifically the active version,  1,25-Dihydroxyvitamin D3. [ref]

More to read:

Growing up Big Boned: MC4R and Obesity

5 Ways You Can Optimize Your Diet Based on Your Genes


Maria · July 20, 2018 at 1:05 am

Hello and thank you for sharing this very informative post!

I risk to appear stupid by asking this but, here i go..

If disabling the genes IRX3 and IRX5 in mice switched their fat cells to burn the stored energy, is it possible to apply this on a human body? I mean, how far do you think we are from such treatment for potential clients who struggle with these genes? Would it be a prescribed medication under the form of a pill or injection?

Apparently I am not a doctor or have studied the human body in such depth. I just got very curious reading your post and wanted to ask this.

Thank you in advance!


    Debbie Moon · July 21, 2018 at 8:07 pm

    Hi Maria,
    Good question. I think all the news about CRISPR and gene editing makes us think that it is right around the corner. But I don’t think that we will be able to switch off a gene like IRX3/5 any time soon. The gene editing that may be possible fairly soon seems to be in the field of blood cancers like leukemia because blood cells have a high turnover rate.
    There does seem to be research going on as far as being able to manipulate IRX3 for weight loss, but no breakthroughs so far that I know of. There would be lots of money there if the could find a way to turn IRX3 down safely.
    I need to update the FTO article… I was just reading a study the other day linking FTO genetic variants to changes in circadian rhythm gene functions. You may want to check out my article on circadian rhythm, meal timing, and weight loss:
    Thanks for reading and commenting!

dresha · October 10, 2018 at 8:57 am

Hello. Is there a difference between FTO AT variation and FTO TA variation? And what does minor allele mean?

    Debbie Moon · October 11, 2018 at 6:19 pm

    Hi – There is no difference between AT and TA. If you are using 23andMe, they usually report it in alphabetical order (AT), but other genetic test companies may report it as “TA”.
    The minor allele is the allele that is least common in the population. For rs9939609, A is the minor allele because it has a frequency of 35%.
    Thanks for posting your questions! I’ll go back and edit the article to make it more clear.

Weight Loss Genetics – Circadian Rhythm genes | Genetic Lifehacks · October 10, 2016 at 10:53 pm

[…] FTO is another gene associated with obesity.  A 2015 study found that FTO deficient mice had robust circadian locomotor activity rhythms, while “Overexpression of FTO represses the transcriptional activation by CLOCK and BMAL1.”[ref]  Other studies have shown that over-expression of FTO leads to increased body fat.  [ref] […]

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