Molecular genetic analysis of primary lactose and hereditary fructose intolerances

Abdominal cramps, nausea, bloating, and diarrhea are often symptoms observed in patients with gastrointestinal (GI) issues. Even though such complaints are common, they are difficult to diagnose accurately.1 Most patients with such symptoms are frequently misdiagnosed, such as with irritable bowel syndrome (IBS).1 However, such issues could be also due to genetic deficiencies in digestive enzymes, as seen in primary lactose intolerance or hereditary fructose intolerance. Lactose and fructose are two types of sugar that are naturally occurring in milk and fruit, respectively. Both lactose and fructose comprise a significant amount of daily intake, and the human body can sometimes metabolize and digest them. However, many individuals are intolerant to these sugars, exhibiting signs and symptoms that lead to poor health and well-being. It is imperative to analyze the causes of these enzyme deficits to aid in differential diagnosis and appropriate treatment, resulting in efficient management of these conditions.

Lactose intolerance

Primary lactose intolerance is the most common form throughout the world.2 Primary lactose intolerance arises from an inherited defect of lactase, an intestinal enzyme responsible for breaking lactose into glucose and galactose.2 Primary lactose intolerance is common among mammals due to a decrease in lactase activity upon weaning.2 This usually occurs after the age of 2, with symptoms being most prominent in adulthood.2 In lactose intolerant individuals, undigested lactose is fermented in the ileum and large intestine, producing byproducts that cause nausea, diarrhea, and abdominal pain.2 Other secondary symptoms, such as chronic tiredness, fatigue, and depression, have been attributed to vitamin deficiencies.2

In addition to the primary genetic form, there is also a secondary acquired form of lactose intolerance. This form develops as a result of damage to the small intestine, which may lead to a decrease in lactase production.3 Although the symptoms of both primary and secondary lactose intolerance may be similar, accurate diagnosis is essential for appropriate treatment and management regimens. Improper management of lactose intolerance may predispose individuals to reduced bone health, fragility fractures and osteoporosis.4

Fructose intolerance

Fructose is a simple ketonic monosaccharide found in certain foods including fruits, vegetables, and honey. The inability to digest fructose is referred to as fructose intolerance. GI manifestations of fructose intolerance include nausea, bloating, vomiting, sweating, abdominal pain, and growth retardation.5 Fructose intolerance results from either a genetic deficiency in a key enzyme in the fructose metabolism pathway or is more commonly due to a defect in fructose absorption by the intestine.6,7

Fructose malabsorption is caused by a deficit in the transport of fructose into absorptive intestinal cells called enterocytes.8 While the exact molecular mechanism for fructose malabsorption is not known, it is believed to involve the main fructose transporter GLUT5.8 Further, studies have shown a link between fructose malabsorption and IBS, and have demonstrated that patients with IBS benefit from a fructose-restricted diet.9

Hereditary fructose intolerance (HFI) is a rare metabolic disorder caused by specific mutations of the aldolase B enzyme.10 Aldolase B is responsible for the breakdown of fructose-1 phosphate (F-1-P) into dihydroxyacetone phosphate, and glyceraldehyde. Aldolase deficiency results in the buildup of toxic F-1-P in the body and subsequent gastrointestinal symptoms. In addition to gastrointestinal disorders, fructose ingestion by patients with HFI may lead to severe hypoglycemia.10 Early diagnosis of HFI is critical to avoid permanent damage to the liver, kidney, and small intestine.


A 2017 study estimated that the overall frequency of lactose intolerance was around two-thirds of the world’s population with large variations between countries and regions.11 In the United States, the prevalence rate was 36 percent.11 Higher frequencies of lactase persistence are observed in European populations, due to longstanding traditions of dairy farming and livestock raising.12 On the other hand, more than 90 percent of East Asian groups are lactose intolerant, due to their predominantly non-pastoralist population.12

Due to the rarity of the disease, less is known about HFI. Fructose malabsorption is much more common than HFI, occurring in approximately 40 percent of individuals in the western hemisphere.5 The incidence of HFI is estimated to be 1 in 20,000 to 60,000 individuals each year worldwide.5,13

Genetic polymorphisms

The two most common mutations associated with primary lactose intolerance are 13910C/T and 22018-G/A located at the promoter region of the lactase gene (LCT).14 Symptoms of lactose intolerance are generally seen with homozygous genotypes 13910CC and 22018GG.15,16 On the other hand, humans with heterozygous genotypes 13910C/T and 22018G/A may only express symptoms during GI infections or stress.15,16 Individuals who are considered to be lactase persistent often present with the genotype 13910TT and 22018AA.15,16

In HFI, the most frequent single-point amino-acid mutations associated with HFI are A149P, A174D, N334K, and a deletion variant, del4E4, in the aldolase B gene.17 For a person to exhibit symptoms of HFI, both alleles of the individual’s DNA must contain the mutation.


It is important for physicians to diagnose whether an individual presents with primary or secondary lactose intolerance to rule out Crohn’s disease, celiac disease, and other gastrointestinal disorders.12 This ensures appropriate treatment options are provided to patients with primary lactose intolerance. These individuals must indefinitely adhere to a lactose-free or low-lactose diet or take lactase supplements.

To detect lactose intolerance, intestinal function is challenged by the lactose intolerance test, where a lactose solution is consumed at specific intervals to understand the variability and severity of symptoms.3 Another test is the hydrogen breath test (H2 test), which detects hydrogen in the breath formed as a result of the fermentation of undigested lactose into hydrogen, methane and other short-chain fatty acids.18,19 In addition, a blood glucose test may also be done to determine if lactose can be digested normally. If lactose can be digested, blood glucose levels would rise.19 However, due to invasive and frequent blood draws, this approach is not commonly used. These tests have lower specificity and sensitivity because of external influences, such as GI flora, motility, and internal pH levels. Therefore, the clinical value in guiding clinical decisions for patients with bowel disorder is limited with hydrogen breath tests.20,21

Fructose malabsorption is also similarly diagnosed using a H2 test. The scientific basis for this test is that undigested fructose is fermented in the ilium by intestinal bacteria, producing hydrogen as a by-product. In a H2 test, following ingestion of a defined amount of fructose, the amount of hydrogen in a patient’s exhaled air is measured at various time intervals. An increase in hydrogen above baseline levels is an indication of fructose malabsorption. While a hydrogen breath test is a safe procedure for the diagnosis of fructose malabsorption, this test is not recommended for diagnosing HFI, due to the high risk of triggering symptoms in lactose intolerant individuals, especially a newborn child. A liver biopsy test, which determines aldolase B activity, is a conclusive test for the diagnosis of HFI. However, this is an invasive test, which requires minor surgery. The need to distinguish between fructose malabsorption and HFI is due to differences in the dietary requirements of patients, which are needed to prevent long term organ damage.6

Both lactose intolerance and HFI require a more reliable and accurate test method to support accurate diagnosis of these conditions.

Parallel testing of lactose intolerance and HFI

Molecular genetic testing can aid in confirming or excluding primary lactose intolerance with a high probability. Additionally, it can also assist differentiation between primary and secondary forms and does not pose the risk of triggering symptoms in lactose intolerant individuals. Molecular genetic testing for the diagnosis of fructose intolerance is used for the detection of the HFI-associated mutations A149P, A174D, N334K, and del4E4, in human genomic DNA. Furthermore, molecular testing can be used as a reliable non-invasive supplement test in addition to traditional H2 tests or blood glucose tests.22


A conclusive and specific diagnosis of GI disorders is critical to ensure proper treatment and management of patients. If undiagnosed, the patients can experience long-term organ or bone damage. Molecular genetic testing enables verification or exclusion of primary lactose intolerance or HFI to be the cause of a patient’s GI complaints with high accuracy. The ability to simultaneously test for both lactose and fructose intolerance facilitates a prompt diagnosis, which allows patients to readily adapt their diets to alleviate symptoms.


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