Are your cavities caused by genetics?

Genetics and Cavities: Check your 23 and Me data

Friends accuse me of thinking that everything is genetic. Well – there is some truth to that accusation!  To be honest, though, there are a lot of things that have genetic connections that really surprise me. I had always assumed that my cavities were due to bad dental hygiene and bad dietary choices such as gummy bears. But the fact that I tend to only brush for one minute instead of two may not be as big a factor as my genetic variants linked to cavities.  (Yes, I know that I could always brush better, eat better, etc… I’m not completely eschewing personal responsibility – just pointing out some science. And I don’t eat gummy bears all that often.)

Note: The genetic variants listed below are mainly found in the 23andMe v4 and AncestryDNA data. The newer 23andMe data (v5) doesn’t cover most of these… no idea why. 

Dental Caries

I like the term dental caries better than ‘cavity’ –  sounds fancier and less like a big hole in the tooth. No matter how you refer to it, though, a cavity consists of a damaged area of the tooth enamel that turns into a hole full of decay.

Everyone knows that sugar causes cavities. The party line from dentists is that sugar feeds the bacteria on your teeth which then produce acid that eats away at the enamel.

So all you need is some sugar, bacteria, and failure to brush for two minutes, twice a day.

But wait… There are a lot of people who eat sugar, don’t brush well, and who don’t have a mouth full of cavities.  What is going on?

It turns out that genetics plays a larger role here than you would think. It is estimated by researchers that the ‘heritability’ or genetic component of dental caries is about 50%. [ref]

There are two ways that researchers can dig into how genes impact a disease or trait. They can either start with an idea of which gene should be involved and then check to see if genetic variants in the gene change the risk of the disease/trait. OR – researchers can take the genetic data from a large population and combine it with the data on who has a particular disease/trait to see which genetic variants are related to the disease risk.

Generally, the genetic variants associated with an increased risk of cavities fall into two categories: genes that affect the oral microbiome and genes that affect the formation of the tooth enamel.

Some genetic research points to how the microbiome interacts with foods. For example, a research study found that kids who carry a GALK2 variant along with Streptococcus mutans, a bacteria that increases the risk of cavities, are at a much greater risk of cavities. The GALK2 gene codes for an enzyme that phosphorylates galactose at high concentrations. The genetic variant causes low concentrations of GALK2, and thus higher amounts of galactose are available in the mouth for the S. mutans to munch on.  Galactose is a simple sugar that is found in higher amounts in dairy products.  So perhaps the combo of dairy intake, S. mutans bacteria, and low galactose causes cavities for some of us.

Genetic Variants Linked to Cavities

DEFB1 gene: codes for an oral antimicrobial peptide

Check your genetic data for rs11362 (23andMe v4; AncestryDNA):

  • C/C: increased risk of cavities[ref]
  • C/T: normal risk of cavities
  • T/T: typical

Check your genetic data for rs1799946 (23andMe v4; AncestryDNA):

  • T/T: increased risk of cavities [ref]
  • C/T: normal risk of cavities
  • C/C: typical

IL32 gene: codes for an immune system response to bacteria

Check your genetic data for rs4786370 (23andMe v4, v5; AncestryDNA):

  • CC: much more likely to carry the bacteria that causes cavities (S. mutans)[ref]
  • C/T: more likely to carry the bacteria that causes cavities
  • T/T: typical

GALK2 gene: galactose metabolizing enzyme, galactose is a sugar found in dairy

Check your genetic data for rs11635005 (23andMe v4; AncestryDNA):

  • T/T: carrying S. mutans bacteria doesn’t increase risk of cavities
  • C/T: carrying S. mutans bacteria doesn’t increase the risk of cavities
  • C/C: Carrying S. mutans significantly increases the risk of cavities, lower GALK2 enzyme activity[ref]

AMELX gene: codes for amelogenin which is involved in the formation of tooth enamel

Check your genetic data for rs946252 (23andMe v4):

  • T/T: increased risk of cavities[ref]
  • C/T: increased risk of cavities
  • C/C: typical

AQP6 gene: aquaporin 6, important in the generation of saliva and tears

Check your genetic data for rs1996315 (23andMe v4; AncestryDNA):

  • G/G: typical
  • A/G: decreased risk of cavities
  • A/A: decreased risk of cavities [ref]

WNT10A gene: important in the prenatal development of many tissues, including teeth

Check your genetic data for rs121908120 (AncestryDNA only):

  • T/T: typical
  • A/T: fewer decayed teeth
  • A/A: fewer decayed teeth [ref]

C5orf66 gene:

Check your genetic data for rs1122171 (23andMe v4 only):

  • T/T: an average of 2.4 more cavities [ref]
  • C/T: an average of 1.2 more cavities
  • C/C: typical number of cavities


I’m going to avoid the whole debate on fluoride for tooth decay prevention vs. the negative effects of fluoride…

Killing the bacteria that cause cavities:

Thyme essential oil has been shown to effectively kill S. mutans. [ref][ref]To me, thyme essential oil smells and tastes terrible, so I wouldn’t recommend running out to buy some to swish with. There is a gel formula from PerioSciences that contains Thyme essential oil, and it has a lot of good reviews online. (I haven’t tried it)

Remineralizing Teeth:

Calcium phosphate has been shown in several different studies to help with remineralizing teeth. [ref] Sugar-free gum manufacturers started incorporating calcium into gum to help with remineralization. A study looked at Trident Xtra Care, Orbit Professional, regular Orbit, and regular Extra gums and found that the Trident Xtra Care caused significantly higher enamel remineralization.[ref]  Sounds cool! But Wrigley sued Trident for claiming that it was false advertising. And Trident Xtra Care was discontinued.

A specific type of calcium phosphate known as hydroxyapatite has been used for a number of years in Japan for the remineralization of teeth.  It is now readily available in the US and elsewhere. There are numerous studies showing that nano-hydroxyapatite is effective for remineralizing teeth. [ref][ref]  There are several online options for toothpaste containing nan-hydroxyapatite. You can read the reviews and choose the one that is best for you.

Eat processed cheese??
This was kind of an odd study… [ref]  The study participants were 115 kids age 7-15, living in India. The researchers used cut pieces of permanent molars that had been extracted from other people. The pieces of molar had been demineralized by keeping them in a solution with a pH of 4.8 for a couple of days.  The researchers then created an appliance to go into the kids’ mouths and hold a piece of the molar in there. The kids then wore the appliance while eating (and for an hour afterward) for four different days. Some of the participants had to eat processed cheese slices for three minutes with the appliance in their mouth. Other study participants had to brush with either a calcium phosphate ‘tooth mouse’ or with Colgate toothpaste. The processed cheese slices and the calcium phosphate both worked to remineralize the teeth — and the processed cheese slices were actually just as effective as the remineralization tooth mouse.

Sufficient Vitamin D:
There are quite a few studies that point to low vitamin D levels being a risk factor for cavities, especially in kids. [ref][ref][ref]  Get some sunshine on your skin for a little while every day, if possible.

The obvious:

Brushing your teeth less than 1 time per day increases your risk of getting cavities (but not by nearly as much as I thought it would). [ref]

The World Health Organization (WHO) has a recommendation of eating less than 10% of calories as sugar. But other studies indicate that less than 5% of daily energy intake as sugar may reduce cavities even more. [ref] Studies on kids show that cavity risk increases with daily sugar intake of greater than 10% of calories (including fruit juice). [ref] A different study showed no link between kids’ cavities and fruit juice. But that study does show that kids who had one or more cavities consumed an average of 66 grams of added sugar/day, while the kids with no cavities consumed an average of 58 grams of added sugar/day. [ref]

Keep in mind that sugar itself isn’t causing the cavities, but rather, that sugar is feeding the bacteria which are producing acid. It is the acidic environment that is causing the demineralization that eventually leads to cavities.

More to read:

Here is a good article on remineralizing teeth and healing cavities.

Author Information:   Debbie Moon
Debbie Moon is the founder of Genetic Lifehacks. She holds a Master of Science in Biological Sciences from Clemson University. Debbie is a science communicator who is passionate about explaining evidence-based health information. Her goal with Genetic Lifehacks is to bridge the gap between scientific research and the lay person's ability to utilize that information. To contact Debbie, visit the contact page.