Vitamin and Minerals Report

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Using this report:
The information provided below is for educational purposes. It shows research study results for genotypes and then your genotype as well. Please don’t take this as carved-in-stone medical advice. It is simply information you can use, along with common sense, in making decisions on food choices and supplemental vitamins.

Genetic variants in one gene may interact or contradict a variant in another gene, so predicting vitamin or mineral levels based on one SNP alone may be inaccurate for you, depending on other genes and your diet. Instead, take this as a roadmap of nutrients that you may want to make sure you are getting enough of in your diet.

Version numbers:
In July/August 2017, 23andMe changed the sequencing chip that they use in producing your genotype information. If you have data from after July 2017, you will have results below for SNPs marked v.5 (version 5), while those with data from 2014 to mid-2017 will have data for SNPs marked v.4 (version 4).

Because I know how expensive it can be to chase down the root cause for health issues, these reports are offered on a ‘Pay what you can’ basis.




Vitamin D:
Vitamin D levels have been associated with a variety of chronic conditions, from mood disorders to cancer risk to immunity to bone density. In general, higher vitamin D levels correspond to a lower risk of getting a variety of chronic diseases.

GC Gene:
The vitamin D binding protein is coded for by the GC gene, and polymorphisms in the gene affect the total serum levels of 25(OH)D. Many of the polymorphisms in the GC gene vary in different ethnic groups, and this is thought to be a big part of the difference in vitamin D levels among populations.

SNP Possible Variants Your Genotype
rs2282679 (v.4, v.5) TT: Normal vitamin D levels
GT: Somewhat lower total serum vitamin D levels
GG: Lower serum vitamin D levels
rs7041 (v.4, v.5) CC: Normal Vitamin D levels
AC: Somewhat Lower Vitamin D https://www.ncbi.nlm.nih.gov/pubmed/29196501
AA: Lower Vitamin D levels
rs1155563 (v.4, v.5) TT: normal
CT: somewhat lower vitamin D levels
CC: significantly lower vitamin D levels
rs12512631 (v4 only) TT: normal
CT: normal
CC: increased vitamin D (both 25 and 1,25) levels

VDR Gene:
After vitamin D (from sunlight, food or supplements) has gone through the conversion steps, the active form of vitamin D, calcitriol, can act on cells through the vitamin D receptor (VDR) which is a transcription factor that turns a gene on or off. Vitamin D receptors control a variety of different functions including the activity of the immune system, skin, pancreas and bone tissue. There have been many, many studies on the VDR gene variants with most studies showing conflicting results. The VDR variants below are listed as ‘normal’ if they are found in the majority of the population. This is for informational purposes. Pubmed.gov is a great place to search for specific reports on the health concerns that have been researched about these variants. Note that there are many popular websites online with reports on the VDR gene that are basing their + or – information on just a few older studies.

SNP Possible Variants Your Genotype
rs1544410 VDR BsmI (v.4, v.5) CC: normal
CT: carrier of one BsmI variant
TT: carrier of two BsmI variants, risk of lower bone mineral density
rs2228570 (v.4) VDR FokI AA: normal
AG: carrier of one FokI variant
GG: carrier of two FokI variants
rs731236 (v.4,v.5) VDR TaqI AA: normal
AG: carrier of one TaqI variant
GG: carrier of two TaqI variants

CYP2R1 Gene:
CYP2R1 is the gene that codes for the enzyme that converts cholecalciferol into calcifediol in the liver. A fairly common genetic variant is associated with decreased vitamin D levels.

SNP Possible Variants Your Genotype
rs2060793 (v.4, v.5) AA: lower vitamin D levels
AG: normal vitamin D levels
GG: higher vitamin D levels
rs1562902 (v.4, v.5) TT: higher vitamin D levels
CT: normal vitamin D levels
CC: normal vitamin D levels

CYP27B1 Gene:
The second step in the conversion to the active form of vitamin D involves CYP27B1 as a catalyst for the conversion of calcifediol to calcitriol. While there are several common polymorphisms in CYP27B1 that have been studied in regards to vitamin D related conditions, none of them have been definitively shown to have an effect. A couple of rare mutations (listed below) of CYP27B1 do affect the conversion to the active form of vitamin D, and these mutations are linked to rickets, a disease caused by the lack of vitamin D in childhood.

SNP Possible Variants Your Genotype
rs28934607 (v.4, v.5) AA: pathogenic for Vitamin D related rickets
AG: carrier for rickets variant
GG: normal
rs28934605 (v.4, v.5) TT: pathogenic for Vitamin D related rickets
CT: carrier for rickets variant
CC: normal
rs28934604 (v.4, v.5) TT: pathogenic for Vitamin D related rickets
CT: carrier for rickets variant
CC: normal
Lifehacks:

Sunshine on your skin is the natural (best) way to get vitamin D. Food sources of vitamin D include seafood and mushrooms. Supplemental vitamin D3 is also available.

References:

CG gene:
SNPedia.com rs2282679
Vitamin D-related genes, serum vitamin D concentrations and prostate cancer risk
Genome-wide association study of circulating vitamin D levels
A systematic review of the association between common single nucleotide polymorphisms and 25-hydroxyvitamin D concentrations.
 Vitamin D binding protein rs7041 genotype alters vitamin D metabolism in pregnant women.
 Genetic and environmental predictors of serum 25-hydroxyvitamin D concentrations among middle-aged and elderly Chinese in Singapore.
Vitamin D-related genes, serum vitamin D concentrations and prostate cancer risk
Environmental and genetic determinants of vitamin D insufficiency in 12-month-old infants
VDR gene:
A systematic review of the association between common single nucleotide polymorphisms and 25-hydroxyvitamin D concentrations.
Association between circulating vitamin D, the Taq1 vitamin D receptor gene polymorphism and colorectal cancer risk among Jordanians.
Association Between Single Gene Polymorphisms and Bone Biomarkers and Response to Calcium and Vitamin D Supplementation in Young Adults Undergoing Military Training.
Vitamin D receptor BsmI polymorphism and osteoporosis risk: a meta-analysis from 26 studies.
Association of the VDR translation start site polymorphism and fracture risk in older women.
Association of vitamin D receptor gene polymorphisms with clinical outcomes of dengue virus infection.
CYP2R1 gene:
Genome-wide association study of circulating vitamin D levels 
Common genetic variants are associated with lower serum 25-hydroxyvitamin D concentrations across the year among children at northern latitudes.
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CYP27B1 gene:
ClinVar NM_000785.3(CYP27B1):c.1144C>T (p.Pro382Ser)
Association between Vitamin D Receptor Gene BsmI Polymorphism and Bone Mineral Density in A Population of 146 Iranian Women.


Vitamin C:
SLC23A1 and SLC23A2 are the genes that code for vitamin C transporters. Variants of these genes affect the plasma levels of vitamin C. All of these variants are very common; some are associated with higher plasma vitamin C concentrations and some with lower concentrations.

SNP Possible Variants Your Genotype
rs6133175 (v.4) GG: higher plasma vitamin C (on avg. 24% higher)
AG: normal vitamin C levels
AA: normal vitamin C levels
rs6053005 (v.5) TT: higher plasma vitamin C (on avg. 24% higher)
CT: normal vitamin C levels
CC: normal vitamin C levels
rs33972313 (v.5) TT: decreased vitamin C levels
CT: decreased vitamin C levels
CC: normal vitamin C levels
Lifehacks:

Good food sources of vitamin C include citrus fruits and colorful veggies.

References:

Vitamin C transporter gene (SLC23A1 and SLC23A2) polymorphisms, plasma vitamin C levels, and gastric cancer risk in the EPIC cohort
Genetically high plasma vitamin C, intake of fruit and vegetables, and risk of ischemic heart disease and all-cause mortality: a Mendelian randomization study.
Polymorphisms in the sodium-dependent ascorbate transporter gene SLC23A1 are associated with susceptibility to Crohn disease.


Vitamin E:
Vitamin E is a fat soluble vitamin that acts as an antioxidant in the body. It is found in nature in eight different forms: four tocopherol and four tocotrienols.
GSTP1 gene:
A 2012 study published in the American Journal of Clinical Nutrition showed that men supplementing with 75 IU of alpha-tocopherol (the common synthetic form of Vitamin E in supplements), had either increased or decreased inflammation, depending on GSTP1 genotype.

SNP Possible Variants Your Genotype
rs1695 (v.4, v.5) AA: increased inflammation with supplemental alpha-tocopherol
AG: increased inflammation with supplemental alpha-tocopherol
GG: decreased inflammation with supplemental alpha-tocopherol

CYP4F2 gene:
This enzyme is involved in the breakdown or metabolism of vitamin E in the body.  Slower CYP4F2 gene variants will possibly cause higher vitamin E levels in the body. Note that if you carry the genetic variants below, this gene also metabolizes vitamin K and plays a role in Warfarin dosing.

SNP Possible Variants Your Genotype
rs2108622 (v.4, v.5) TT: decreased metabolism of vitamin E -> higher levels
CT:decreased metabolism of vitamin E -> higher levels
CC: normal
Lifehacks:

Check your supplements to see if you are taking one with alpha-tocopherol.  If you are at an increased risk of inflammation from supplementing with higher levels of alpha-tocopherol, you might want to talk with your doctor about the risk vs. benefits.  Note that the study was looking at the synthetic version of vitamin E that is found in common supplements. Food sources of vitamin E have natural, mixed-tocopherols.

References:

Variants in the genes encoding TNF-α, IL-10, and GSTP1 influence the effect of α-tocopherol on inflammatory cell responses in healthy men
Genome-wide association study identifies common variants associated with circulating vitamin E levels


Vitamin A:
Plant sources of vitamin A, such as from carrots or sweet potatoes, are in the form of beta-carotene.  Beta-carotene is then converted by the enzyme β-carotene 15,15′-monooxygenase (BCMO1 gene) into retinol, which is then used by the body in the same way as preformed vitamin A from animal products.

Individual conversion rates of beta-carotene into vitamin A vary widely.  Carrying both of the variants below (having a “T” in your genotype on both SNPs) will decrease conversion of beta-carotene to vitamin A by 69%.

SNP Possible Variants Your Genotype
rs7501331 (v.4 and v.5) CC: normal
CT: decreased beta-carotene conversion by 32%
TT: decreased beta-carotene conversion by 32%
rs12934922 (v.4 and v.5) AA: normal
AT: decreased beta-carotene conversion by 32%
TT: decreased beta-carotene conversion by 32%
Lifehacks:

For those with a decreased conversion of beta-carotene, a diet that includes plenty of vitamin A from sources that provide the retinol form is essential.  Liver (beef, chicken, lamb) is an excellent source, as are egg yolks from pasture-raised chickens. Fermented cod liver oil is also high in vitamin A.

References:

Two common single nucleotide polymorphisms in the gene encoding beta-carotene 15,15′-monoxygenase alter beta-carotene metabolism in female volunteers.


Vitamin B9 (Folate):
MTHFR is a central gene in the methylation cycle; common genetic variants in the coding of this gene affect more than half the population. Specifically, the MTHFR(methylenetetrahydrofolate reductase) gene codes for an enzyme that turns folate (think leafy greens) into the active form, 5-methyltetrahydrofolate, that your body uses. This, along with the active form of vitamin B-12  (methylcobalamin) drives an important portion of the methylation cycle. The methylation pathway is a central biochemical process that impacts all of our cells. Methylation is the adding and removing of a methyl group (CH3) to amino acids, DNA, or other enzymes or proteins. Methylation turns on and off genes, maintaining and repairing your DNA, as well as altering proteins. It is important in the nervous system in the production and breakdown of neurotransmitters.

SNP Possible Variants Your Genotype
rs1801133 (v.4 and v.5) GG: normal
AG: one copy of C677T allele (heterozygous), MTHFR efficiency reduced by 40%
AA: two copies of C677T (homozygous), MTHFR efficiency reduced by 70 – 80%
rs1801131 (v.4 and v.5) TT: normal
GT: one copy of A1298C allele (heterozygous), MTHFR efficiency reduced
GG: two copies of A1298C (homozygous), MTHFR efficiency reduced
Lifehacks:

Folate is found in vegetables and legumes.  If you are a carrier of one of the MTHFR variants above, I suggest reading more about it: MTHFR & Methylation.  There is a lot of information on the internet about MTHFR variants, some of it doom-and-gloom that over-inflates the importance and some that is completely dismissive.  I think the truth lies somewhere in between, and knowing that you have an MTHFR variant is a very good reason to ensure you are getting enough green veggies and/or legumes in a healthy diet.

References:

A candidate genetic risk factor for vascular disease: a common mutation in methylenetetrahydrofolate reductase.
Biological and clinical implications of the MTHFR C677T polymorphism.


Choline:
While not exactly a vitamin, this essential nutrient is also affected by genetic variants. Choline is involved in several critical roles in the body: supporting methylation reactions; formation of acetylcholine, a neurotransmitter and cell-signaling molecule; proper functioning of muscles; and prevention of fatty liver disease.

PEMT gene:
The PEMT pathway is responsible for the body’s production of phosphatidylcholine which is part of the phospholipid bilayer making up the membranes surrounding our cells.  Note that 23andMe does not cover all of the SNPs in PEMT that are relevant to choline levels.

SNP Possible Variants Your Genotype
rs7946 (v.4, v.5) TT: somewhat decreased PEMT enzyme activity
CT: somewhat decreased PEMT enzyme activity
CC: normal choline levels

CHKA gene:
The first step of the CDP-PC pathway.

SNP Possible Variants Your Genotype
rs10791957 (v.4, v.5) AA: lower turnover of methionine to phosphatidylcholine
AC: lower turnover of methionine to phosphatidylcholine
CC: normal gene function

BHMT gene:

SNP Possible Variants Your Genotype
rs3733890 (v.4, v.5) AA: lower conversion of choline to betaine and more conversion of choline to CDP-PC
AG: lower conversion of choline to betaine and more conversion of choline to CDP-PC
GG: normal gene function

MTHFD1 gene:

SNP Possible Variants Your Genotype
rs2236225 (v.4, v.5) AA: more likely to have choline deficiency on a low choline diet (modified by folate intake)
AG: more likely to have choline deficiency on a low choline diet (modified by folate intake)
GG: normal gene function
Lifehacks:

Egg yolks and liver are great sources of choline. If you aren’t getting enough choline from your diet, CDP Choline and Alpha GPC are both good options for supplements.

References:

PEMT:
Genetic Variation in Choline-Metabolizing Enzymes Alters Choline Metabolism in Young Women Consuming Choline Intakes Meeting Current Recommendations
CHKA gene:
Genetic Variation in Choline-Metabolizing Enzymes Alters Choline Metabolism in Young Women Consuming Choline Intakes Meeting Current Recommendations 
Identification of new genetic polymorphisms that alter the dietary requirement for choline and vary in their distribution across ethnic and racial groups
BHMT gene:
Genetic Variation in Choline-Metabolizing Enzymes Alters Choline Metabolism in Young Women Consuming Choline Intakes Meeting Current Recommendations
MTHFD1 gene:
Identification of new genetic polymorphisms that alter the dietary requirement for choline and vary in their distribution across ethnic and racial groups
Genetic variation of folate-mediated one-carbon transfer pathway predicts susceptibility to choline deficiency in humans
CDP-choline: pharmacological and clinical review.


Vitamin B12:

FUT2 gene:
The FUT2 gene encodes the enzyme fucosyltransferase, which plays a role in forming oligosaccharides. Oligosaccharides are part of your blood antigen system.  FUT2 variants that cause you not to secrete your blood type in your mucus and saliva also affect both your intestinal microbiome, your susceptibility to h. pylori, and your B12 levels. Note that while the plasma levels of B12 may be higher in non-secretors, this doesn’t mean that the B12 is being transported into cells and used effectively. This may be information that is relevant for interpreting blood test results.

SNP Possible Variants Your Genotype
rs602662 (v.4 and v.5) AA: higher plasma B12 levels, non-secretor
AG: normal B12 levels
GG: normal/ lower B12 levels
rs492602 (v.4 and v.5) AA: normal/ lower B12 levels
AG: normal  B12 levels
GG: higher plasma B12 levels

TCN1 and TCN2 gene:
This gene is responsible for transport of B12 into the cells.

SNP Possible Variants Your Genotype
rs526934 (v.4 and v.5) AA: normal
AG: lower B12 levels
GG: lower B12 levels
rs1801198 (v.4) CC: normal
CG: normal
GG: lower B12 levels

CUBN gene:
The cubilin protein binds to vitamin B12 and absorbs it in the intestines.

SNP Possible Variants Your Genotype
rs1801222 (v.4) AA: lower B12 levels
AG: lower B12 levels
GG: higher B12 levels
Lifehacks:

Good food sources of vitamin B12 include
Note that for the TCN2 genetic variant, rs1801198, a study found that in elderly people with the GG genotype there is almost a 7-times greater chance of peripheral neuropathy with higher folic acid intake (>800 μg). In general for elderly populations, there is an increased chance of B12 deficiency being masked by higher folate intake.

References:

Common variants of FUT2 are associated with plasma vitamin B12 levels
The transcobalamin (TC) codon 259 genetic polymorphism influences holo-TC concentration in cerebrospinal fluid from patients with Alzheimer disease
Transcobalamin codon 259 polymorphism in HT-29 and Caco-2 cells and in Caucasians: relation to transcobalamin and homocysteine concentration in blood.
An update on vitamin B12-related gene polymorphisms and B12 status  10.1186/s12263-018-0591-9
GWAS identifies population-specific new regulatory variants in FUT6 associated with plasma B12 concentrations in Indians.
B vitamin polymorphisms and behavior: Evidence of associations with neurodevelopment, depression, schizophrenia, bipolar disorder and cognitive decline
Transcobalamin 776C→G polymorphism is associated with peripheral neuropathy in elderly individuals with high folate intake
Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway


Magnesium:

Magnesium is an essential mineral that is a cofactor for over 300 different enzyme systems in the body.  It is estimated that over 80% of people are not meeting the daily recommended intake (320mg/day for women and 420mg/day for men).

TRPM6 gene:
This gene encodes the epithelial Mg2+ channel.

SNP Possible Variants Your Genotype
rs2274924 (v.4) CC: lower magnesium levels
TT: normal
rs3750425 (v.4, v.5) TT: lower magnesium levels
CT: somewhat lower magnesium levels
CC: normal

ATP2B1 gene:
This gene encodes a calcium ion transporter that moves molecules out of the cell.

SNP Possible Variants Your Genotype
rs7965584 (v.5) AA: normal
AG: lower magnesium
GG: lower magnesium

MUC1 gene:
The mucin1 gene codes for a protein involved in the mucin lining of the intestines. It is possible that a thicker mucin layer would slow the absorption of magnesium from the intestines.

SNP Possible Variants Your Genotype
rs4072037 (v.4, v.5) TT: normal
CT: lower magnesium
CC: lower magnesium v5
Lifehacks:

While genetic variants play a role in lower magnesium levels, most people need to first ensure that they are meeting the RDA. Foods high in magnesium include whole grain oats, brown rice, fish, almonds, spinach and swiss chard. There are many forms of supplemental magnesium. Magnesium citrate is often used for constipation and is not usually considered the best form for raising magnesium levels. Magnesium glycinate is often recommended.

References:

Common genetic variants of the ion channel transient receptor potential membrane melastatin 6 and 7 (TRPM6 and TRPM7), magnesium intake, and risk of type 2 diabetes in women.
Genetic loci for serum magnesium among African-Americans and gene-environment interaction at MUC1 and TRPM6 in European-Americans: the Atherosclerosis Risk in Communities (ARIC) study
Genome-Wide Association Studies of Serum Magnesium, Potassium, and Sodium Concentrations Identify Six Loci Influencing Serum Magnesium Levels
Magnesium-permeable TRPM6 polymorphisms in patients with meningomyelocele


Disclaimer: Information given on Genetic Lifehacks is for educational purposes only. Errors are possible. 23andMe does not guarantee the accuracy of using their data for health purposes.