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Lactose intolerance and genetic testing

A genetic test is now available to assist in the diagnosis of lactose intolerance in both children and adults.

Key points

The test only needs to be performed once during a person’s lifetime.

How does the test work?

Testing is now available to detect the genetic variant (LCT-13910C>T) that accounts for close to 100% of lactase persistence in Europeans. Three other genetic variants that have a similar effect and are more common in non-European populations are also detected.

These variants are thought to act as enhancers of the lactase gene that in turn stimulates lactase production.

When one of these variants is found, a diagnosis of primary lactose intolerance can be excluded.

Lactose intolerance can be secondary to other conditions that affect the small bowel, such as gastroenteritis, inflammatory bowel disease and coeliac disease. Genotyping can help to distinguish these causes of intolerance.

What causes lactose intolerance?

Lactose is the major carbohydrate in mammalian milk. Lactose intolerance is caused by deficiency of lactase, the enzyme required for digestion of lactose.

Symptoms include abdominal pain, diarrhoea, nausea, flatulence and/or bloating, following the consumption of lactose-containing foods.

Who is affected by lactose intolerance?

After infancy, approximately 75% of the population lose the ability to digest lactose, due to a deficiency in lactase, referred to as primary lactose intolerance. The remainder of people maintain their tolerance for lactose-containing foods because of genetic variants that enable continued production of lactase, referred to as lactase persistence.

The prevalence of primary lactose intolerance varies significantly with ethnic background. Lactose intolerance is uncommon in populations that consume large amounts of dairy, for example, northern Europeans (as low as 10%), but is frequent in other populations (as high as 100% in Asiatic countries). It is hypothesised that this is the result of selective genetic advantage; populations that have historically been dependent on dairy food sources for nutrition have survived by having genetic variants that allow tolerance for lactose.

Other testing alternatives

Currently, testing for lactose intolerance can also be performed by a hydrogen breath test with lactose load, or by measurement of intestinal lactase enzyme activity in a biopsy obtained during endoscopy.

These tests may give a false-positive result when lactase levels have been affected by a recent viral illness or coeliac disease.

These procedures are also not suitable for testing children younger than seven years old. Genotyping is not affected by intercurrent illness and can be performed non-invasively on patients of all ages.

Genetic testing limitations

Please note that genotyping will not identify very rare genetic variants associated with persisting lactase activity, and therefore the absence of a variant can only be used to support a diagnosis of lactose intolerance along with other clinical and laboratory findings.

Arranging a test

  1. Complete a standard pathology request form to refer the patient for ‘lactase persistence’ or ‘lactose intolerance genetic testing’.
  2. Collect or send the patient to a pathology collection centre for a blood test or buccal swab. No special preparation or booking is necessary.
  3. The result is reported back to the doctor, usually within five business days of the laboratory receiving the patient’s sample.


Medicare does not cover the cost of this test and the patient will receive an invoice for $75.*


*Correct at time of printing. Please to refer to the Sonic Genetics website, www.sonicgenetics.com.au, for current pricing.

General Practice Pathology is a regular column each authored by an Australian expert pathologist on a topic of particular relevance and interest to practising GPs. The authors provide this editorial free of charge as part of an educational initiative developed and coordinated by Sonic Pathology.