Warning Signs You're Lacking Crucial Nutrients

Kate BartonJul 07, 2022

Through studies testing how genes affect nutrient status, it's become apparent that even those who eat a healthy diet complete with all the vitamins and minerals may still develop nutrient deficiencies.

The problem lies not in what is eaten but how the body metabolizes it. For every given nutrient, there exists genetic abnormalities that can result in altered metabolism of that nutrient.


The utilization of B vitamins in the body can be affected by genetic variances.

Vitamin B-12, an essential nutrient in energy production and nervous system function, is no exception. In a study reviewing SNPs (single nucleotide polymorphisms, or genetic variances) in B-12 metabolism, 59 different polymorphisms were identified [7].

In addition, a twin study showed the heritability of B-12 status was about 60%, further proving a strong genetic component influences how each body uses this B vitamin [7].


Though there are many genetic variations that impact vitamin B-12 absorption, one of the common SNPs is with transcobalamin 1.

The transcobalamin 1 (TCN1) gene on chromosome 11 codes for the vitamin B12 binding protein, transcobalamin I (known as TCI or haptocorrin) [7]. TCI helps B-12 enter the cells via receptor-mediated endocytosis. Multiple studies have found alterations in this gene affects the amount of B-12 in circulation.

Signs of B vitamin deficiency

Signs of vitamin B-12 deficiency are weakness or tiredness, a swollen tongue, hair loss, brittle nails, nerve issues like numbness or tingling, cracked lips, vision loss, and changes in behavior/cognitive issues [8].

Vitamin A

Vitamin A is important for healthy vision, immune system functioning, reproduction, development, and repairing tissue.

Vitamin A is present in the blood in different forms (mainly retinol and provitamin A carotenoids). The amount of it in circulation is affected by several factors: dietary intake, absorption efficiency, efficiency of provitamin A carotenoid conversion to vitamin A, tissue uptake, and more [11].

Most of the factors listed above are influenced by genetic variations in genes involved in vitamin A metabolism. Several studies have found SNPs associated with blood concentrations of retinol, beta-carotene, and β-carotene bioavailability [11].

One of the impairments associated with a certain SNP is converting beta-carotene into vitamin A. Beta-carotene is a precursor to vitamin A and is converted by the liver.


The main enzyme involved in this conversation is BCMO1. It's been observed that the conversion from beta-carotene into vitamin A is highly variable, with differences as much as 45% observed in healthy people [12].

This means when comparing two people, both in good health, one may require almost double the amount of vitamin A than the other.

Difference in food source

Another factor that may contribute to the wide absorption range of vitamin A is consuming plant sources versus animal sources.

Plant foods "high in vitamin A", like kale, orange vegetables, and orange fruits are actually high in beta-carotene, which can later be converted to vitamin A. However, this conversion rate ranges from 5% to 65% in humans [12].

Preformed vitamin A however has much higher absorbancy rates and is only found in animal products like eggs, dairy, and meat. Some researchers hypothesize the increasing prevalence of vitamin A deficiency in the United States may be due to the popularity of plant foods versus animal foods.

Signs of vitamin A deficiency

Signs you may have a nutrient deficiency of vitamin A are dry skin, dry eyes, a weakened immune system, night blindness (usually observed in children), stunted growth, muscle weakness, or slow wound healing.

Almonds in the shape of a K

Vitamin K

Vitamin K serves an important role in wound healing, blood clot formation, and bone health.

The active form of vitamin K is a co-factor in reactions that control blood coagulation and bone metabolism. This vitamin K dependent reaction is controlled by the gamma glutamyl carboxylase (GGCX) gene, and afterwards vitamin K reverts back to it's inactive form. The inactive form of vitamin K is later converted back to the active form by the enzyme vitamin K epoxide reductase 1 (VKORC1) [1].

Genetic variations of both the GGCX and VKORG1 gene influence the use of vitamin K.

On the VKORG1 gene, there is an allele that upregulates this process, increasing the availability of vitamin K. There is also an allele that downregulates it, making vitamin K less available and the person more susceptible to a nutritional deficiency.

"About 58-64% of Caucasians and Hispanics and 85-92% of Africans carry the C allele", the allele responsible for enhancing vitamin K expression. And 87-94% of Asians carry the T allele, the variation that results in lower vitamin K activity [1].

APOE gene

The APOE gene provides instructions for making a protein called apolipoprotein E [2]. Apolipoprotein E combines with fat molecules to form lipoproteins.

Lipoproteins are responsible for packaging and transporting fats and fat-soluble nutrients throughout the blood stream. Since vitamin K is a fat-soluble nutrient, alterations in this gene can affect vitamin K utilization.

There are (at least) three types of this gene, E2, E3, and E4. Those with E2 and E3 alleles have higher vitamin K levels than those with the E4 allele. The lower vitamin K levels observed with the E4 gene is due to the reduced uptake of vitamin K [1].

A study analyzing bone density of people with the E4 allele found they had lower bone mineral density and lower lumbar spine density compared with control groups [3].

This could be a sign of lowered utilization of fat-soluble nutrients, especially ones important for bone health like vitamin D and vitamin A.

Signs of vitamin K deficiency

Signs of a nutrient deficiency of vitamin K can be significant bleeding, slow blood clotting, poor bone development, bone pain, bleeding gums, osteoporosis, and an increased risk of cardiovascular disease [9].

Foods rich in vitamin K are dark leafy greens, avocado, blueberries, and leafy green vegetables like broccoli.

Image of foods with iron and outline of a body


Iron is a great example of why it's important to undergo genetic testing. Some people inherit genes that lower their body's ability to absorb iron while others have a variation that absorbs too much iron and can lead to iron overload.

Iron overload

Hereditary hemochromatosis causes your body to absorb too much iron from food sources.

Excess iron is stored in the organs, particularly the liver, heart and pancreas. Too much iron can cause organ damage and other adverse effects like diabetes, impotence, and joint pain [4].

HFE gene

The HFE gene is linked to hereditary hemochromatosis. It has two common mutations: C282Y and H63D. You inherit one HFE gene from each of your parents; if you receive two abnormal genes you will likely develop hemochromatosis.

If you only recieve one abnormal gene, you will be a carrier for hemochromatosis and may have children that develop the condition (if your spouse also has an abnormal copy that would get passed on).

Most people aren't aware they have this condition until symptoms appear in the 40s for men or 60s for women. The later onset of symptoms for women is due to iron loss from menstruation.

Treatment for this condition is donating blood 2-3 times a year to decrease iron levels and circulating red blood cells. It's also crucial to avoid iron supplementation and limit consumption of foods rich in iron, like red meat.

Low iron levels

On the other hand, there are several genetic conditions that alter iron content in the body.

Iron refractory iron deficiency anemia

Iron refractory iron deficiency anemia is a hereditary anemia caused by a defect in the TMPRSS6 gene [5]. The gene causes changes in the protein matriptase-2 which is responsible for down-regulating hepcidin, the regulator of iron homeostasis.

It's a unique condition because acquired iron deficiency (from inadequate intake of iron) results in low or undetectable hepcidin levels.

However, in patients with iron refractory anemia, serum hepcidin is abnormally high for the low iron status.

This makes oral supplementation difficult; many patients have no response to supplementation. Identifying the condition as soon as possible can be helpful in formulating an effective treatment plan.


Thalassemia is a genetic condition that occurs when your body is unable to produce enough hemoglobin, the protein that carries oxygen throughout the body [6]. It's an inherited disease caused by mutations in the α- and β-globin gene clusters on chromosome 16 and chromosome 11.

Some cases are mild with common symptoms like fatigue and don't get detected until later on in life. More severe cases have reported symptoms like an enlarged spleen, slowed growth, bone problems, and jaundice.

Since it shares many symptoms with iron deficiency anemia, people may assume they have low iron and turn to a supplement. This may be helpful for some cases, but it could also cause adverse reactions (like iron overload) in others.

It's important to undergo testing to find what type of anemia you have before implementing a supplement.

Signs of low iron

Signs of a nutrient deficiency of iron or low red blood cells are extreme fatigue, weakness, pale skin, chest pain, fast heartbeat, shortness of breath, headache or dizziness, cold hands and feet, inflammation or soreness of your tongue, brittle hair and nails, or developing burning mouth syndrome [10].

There are many iron rich foods like spinach, fortified cereals, red meat, fatty fish/seafood, beans, and dark leafy greens. For some, food sources aren't enough and iron supplementation is also needed.


Vitamin and mineral deficiencies have a big impact on your health. Due to genetics, eating a diet rich in every nutrient doesn't avoid deficiencies.

Rootine considers your unique DNA, blood, and lifestyle data when formulating your micronutrient formula. Our DNA Test analyzes 50+ SNPs that are proven to impact nutrient needs due to the influence on nutrient absorption, distribution, metabolism, excretion, and receptor function.

No two people have the same genetic profile, which is why Rootine focuses on understanding how your genetics impact your nutrient requirements to form a science-backed supplement that gives your body everything it needs in one step.


  1. https://www.gbhealthwatch.com/Nutrient-VitaminK-Genes.php
  2. https://medlineplus.gov/genetics/gene/apoe/#resources
  3. Peter, I., Crosier, M. D., Yoshida, M., Booth, S. L., Cupples, L. A., Dawson-Hughes, B., Karasik, D., Kiel, D. P., Ordovas, J. M., & Trikalinos, T. A. (2011, April). Associations of APOE gene polymorphisms with bone mineral density and fracture risk: A meta-analysis. Osteoporosis international. Retrieved June 30, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144470/
  4. Pruthi, S. (2020, December 30). Hemochromatosis. Mayo Clinic. Retrieved June 30, 2022, from https://www.mayoclinic.org/diseases-conditions/hemochromatosis/symptoms-causes/syc-20351443
  5. De Falco, L., Sanchez, M., Silvestri, L., Kannengiesser, C., Muckenthaler, M. U., Iolascon, A., Gouya, L., Camaschella, C., & Beaumont, C. (2013, June). Iron refractory iron deficiency anemia. Haematologica. Retrieved June 30, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669438/
  6. Scott, J. (2010). Hereditary anemia: Types of anemia that can be inherited. EverydayHealth.com. Retrieved June 30, 2022, from https://www.everydayhealth.com/anemia/anemia-and-heredity.aspx
  7. Surendran, S., Adaikalakoteswari, A., Saravanan, P., Shatwaan, I. A., Lovegrove, J. A., & Vimaleswaran, K. S. (2018, February 6). An update on vitamin B12-related gene polymorphisms and B12 status - genes & nutrition. BioMed Central. Retrieved June 30, 2022, from https://genesandnutrition.biomedcentral.com/articles/10.1186/s12263-018-0591-9
  8. Nazario , B. (2021). Vitamin B12 deficiency: Causes, symptoms, and treatment. WebMD. Retrieved June 30, 2022, from https://www.webmd.com/diet/vitamin-b12-deficiency-symptoms-causes
  9. Eden, R., & Coviello , J. (2022). Vitamin K deficiency . National Library of Medicine . Retrieved June 30, 2022, from https://www.ncbi.nlm.nih.gov/books/NBK536983/
  10. Mayo Foundation for Medical Education and Research. (2022, January 4). Iron deficiency anemia. Mayo Clinic. Retrieved June 30, 2022, from https://www.mayoclinic.org/diseases-conditions/iron-deficiency-anemia/symptoms-causes/syc-20355034https://www.mayoclinic.org/diseases-conditions/iron-deficiency-anemia/symptoms-causes/syc-20355034
  11. Borel, P., & Desmarchelier, C. (2017, March 8). Genetic variations associated with vitamin A status and vitamin A bioavailability. National Library of Medicine . Retrieved June 30, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372909/
  12. Leung , W. C. (2009). Two common single nucleotide polymorphisms in ... - Wiley Online Library. The FASEB Journal . Retrieved June 30, 2022, from https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fj.08-121962