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Understanding SI Gene Variants and Sugar Digestion

The SI gene makes the sucrase-isomaltase enzyme, which helps break down sucrose and some starches in the small intestine. Variations in this gene can reduce enzyme activity and make it harder to digest sugars and certain carbohydrates. When digestion is incomplete, these carbohydrates can reach the colon and be fermented by gut bacteria, producing gas, bloating, pain, and other digestive symptoms often mistaken for FODMAP sensitivity.

How this relates to the FODMAPs diet

The low FODMAPs diet limits short-chain carbohydrates that are poorly absorbed and rapidly fermented. While this approach helps many people with functional gut symptoms, it does not specifically target sucrose or starches that depend on sucrase-isomaltase. If SI activity is reduced, symptoms may persist despite following a low FODMAPs plan. Understanding your SI genotype can help tailor dietary and lifestyle strategies to better manage symptoms.

Common practical strategies for everyone

  • Limit high-sucrose foods: reduce sweetened drinks, candies, desserts, and other added sugars.
  • Monitor starchy choices: favor whole grains and intact starches over refined and highly processed starchy foods.
  • Consider enzyme supplements only with medical guidance: targeted digestive enzyme products exist but should be discussed with a healthcare provider.
  • Eat smaller meals slowly: smaller portions reduce the load on digestive enzymes and lower fermentation in the gut.
  • Manage stress: stress affects gut motility and sensitivity. Relaxation techniques and sleep hygiene support digestion.
  • Keep a food journal: tracking foods, symptoms, timing, and portion sizes helps identify triggers and guides targeted changes.
  • Work with your healthcare team: review symptoms, consider breath testing or other diagnostics if symptoms are persistent or severe.

Genetic Interpretations

Two effect alleles (AA) — Reduced sucrase-isomaltase activity

Having the AA genotype at rs9290264 is linked to lower sucrase-isomaltase enzyme activity. This can reduce the ability to digest sucrose and certain starches in the small intestine. When these sugars are not broken down, they reach the colon where bacteria ferment them and produce symptoms such as gas, bloating, abdominal discomfort, and sometimes diarrhea.

Because a standard low FODMAPs approach does not specifically remove sucrose or all starches that rely on sucrase-isomaltase, symptoms may not fully resolve on that diet alone. A more targeted plan can help reduce digestive burden and improve comfort.

Practical recommendations

  • Aim to limit foods high in added sucrose: sweetened beverages, candies, baked goods, syrups, and many processed snacks.
  • Reduce refined starches that are rapidly digested by sucrase-isomaltase: white bread, many packaged snack foods, and some processed cereals.
  • Prefer whole, minimally processed grains and starches: intact grains, legumes when tolerated, and starchy vegetables in controlled portions.
  • Consider discussion with a clinician about targeted digestive enzyme supplements that contain sucrase activity. Use only under medical supervision.
  • Use smaller, more frequent meals to lower per-meal enzyme demand.
  • Keep a detailed food and symptom diary to identify specific triggers and portion thresholds.
  • If symptoms are frequent or severe, consult your healthcare provider to rule out other causes and to consider diagnostic testing where appropriate.
One effect allele (AC) — Moderately reduced sucrase-isomaltase activity

The AC genotype at rs9290264 is associated with moderately reduced sucrase-isomaltase activity. This may lead to incomplete digestion of sucrose and some starches, increasing the risk of gas, bloating, and discomfort after consuming certain sweet or starchy foods.

Individuals with one effect allele may notice intermittent symptoms that relate to portion sizes and food types. A low FODMAPs diet may help for other fermentable carbohydrates but might not fully address issues caused by reduced sucrase-isomaltase function.

Practical recommendations

  • Moderate intake of added sugars and sweetened beverages. Watch portion sizes for desserts and sugary snacks.
  • Be mindful with refined starchy foods. Swap some refined choices for whole grain or less processed alternatives.
  • Try smaller meals and slower eating to ease enzymatic demand during digestion.
  • Consider keeping a food and symptom journal to identify patterns related to sucrose or starchy meals.
  • Discuss with your healthcare provider whether a trial of enzyme supplementation might be useful.
  • Adopt general gut-friendly habits: hydration, regular physical activity, stress reduction practices, and adequate sleep.
Zero effect alleles (CC) — Typical sucrase-isomaltase activity

The CC genotype at rs9290264 is associated with typical sucrase-isomaltase enzyme activity. With normal enzyme function, digestion of sucrose and many starches is likely efficient in the small intestine. This reduces the likelihood that sucrose or those starches are the primary drivers of gas and bloating.

If digestive symptoms occur, they may be more related to other FODMAP carbohydrates, portion sizes, eating habits, stress, or other gastrointestinal conditions. A standard low FODMAPs diet is more likely to be effective if other fermentable carbohydrates are the cause.

Practical recommendations

  • Maintain balanced sugar and carbohydrate intake. Limit excess added sugars for overall health.
  • Practice mindful eating: slow down, chew thoroughly, and eat regular meals to support optimal digestion.
  • If symptoms appear, use a food journal to identify triggers and consider a low FODMAPs approach under guidance.
  • Continue general digestive health habits: stay active, manage stress, maintain hydration, and get adequate sleep.
  • Consult your healthcare provider for persistent or severe symptoms to evaluate other possible causes and testing options.

Working with your healthcare provider

PlexusDx provides genetic information to help you understand possible predispositions related to sugar and starch digestion. This information is educational and not a diagnosis. Discuss any changes to diet, supplements, or medications with your healthcare provider, especially before starting enzyme supplements or making major dietary shifts. Your provider can help prioritize tests, interpret symptoms in context, and design a personalized plan that considers genetics, medical history, lifestyle, and medications.

Quick checklist

  • Limit added sucrose and watch portions for starchy foods.
  • Prefer whole, less processed carbohydrate sources.
  • Eat smaller meals slowly and mindfully.
  • Keep a detailed food and symptom journal.
  • Talk with your healthcare provider about enzyme supplements and diagnostic testing if needed.
  • Manage stress and support overall gut health with sleep, movement, and hydration.

Disclaimer: PlexusDx does not provide medical advice. The genetic information here is educational only and should not replace consultation with a qualified healthcare professional. Always consult your healthcare provider before making changes to your diet, starting supplements, or pursuing testing or treatment.