CYP2R1 rs10749479: Vitamin D Metabolism and Your Genetics
The rs10749479 polymorphism is a common non-coding single-nucleotide variant located within or near the CYP2R1 gene on chromosome 11. It is statistically associated with modest differences in hepatic vitamin D 25-hydroxylase expression and baseline circulating serum 25-hydroxyvitamin D concentrations. Because evidence is limited and non-diagnostic, it reflects population-level predispositions rather than clinical vitamin D deficiency.
What each genotype means
Typical vitamin D metabolism
This genotype represents the most common form of the CYP2R1 gene in many populations. Research suggests individuals with this profile typically maintain baseline levels of 25-hydroxyvitamin D, though individual vitamin D status is heavily influenced by diet, sun exposure, and other lifestyle factors.
This is the most common genotype globally, carried by the majority of individuals in most studied populations.
Intermediate vitamin D association
Carrying one copy of the minor allele may be associated with slight variations in how your body processes vitamin D. Studies have explored links between this variant and circulating 25-hydroxyvitamin D concentrations, but the clinical significance remains limited and may vary based on your ancestry.
This genotype is found in a significant portion of the population, with the minor allele frequency reported between 0.38 and 0.42 globally.
Potential vitamin D variation
Individuals with this genotype carry two copies of the minor allele, which has been studied for its association with baseline serum 25-hydroxyvitamin D levels. While some research suggests a correlation with altered enzyme activity, these findings are limited and do not account for the complex environmental factors that determine your actual vitamin D status.
This genotype is less common than the AA or AG profiles, appearing in a smaller subset of the global population.
Understanding the rs10749479 Polymorphism
The single-nucleotide polymorphism rs10749479 is mapped to human chromosome 11 in proximity to the CYP2R1 gene. Rather than altering the amino acid sequence of the resulting enzyme directly, this variant sits in a non-coding genomic region. Variants in such positions typically influence regulatory mechanisms, such as promoter activity, splicing efficiency, or transcription factor binding affinity. In genome-wide association studies and candidate gene screens, rs10749479 is frequently evaluated alongside other prominent CYP2R1 loci to understand inherited variations in vitamin D homeostasis. It is important to emphasize that having one or two copies of a particular allele at rs10749479 is an inherited baseline marker, not a damaging disruption or genetic mutation in the classical sense. Large-scale catalogs of human genetic variation monitor this site to untangle how common variations collectively shape circulating biochemical traits.
The Biological Role of the CYP2R1 Gene
The CYP2R1 gene provides the genetic blueprint for cytochrome P450 family 2 subfamily R member 1, commonly referred to as microsomal vitamin D 25-hydroxylase. This liver enzyme plays an indispensable initial role in the multi-step activation pathway of both cholecalciferol (vitamin D3) and ergocalciferol (vitamin D2). Once synthesized in the skin via sunlight or ingested through dietary sources, unhydroxylated vitamin D travels to hepatic tissue, where CYP2R1 introduces a hydroxyl group at carbon 25. This biochemical conversion generates 25-hydroxyvitamin D [25(OH)D], also known as calcidiol. Because 25(OH)D is the predominant circulating form with a half-life of several weeks, it serves as the standard clinical benchmark for assessing an individual's overall vitamin D status before subsequent renal conversion into bioactive calcitriol.
Current Scientific Evidence and Clinical Strength
Evidence evaluating rs10749479 is categorized as limited, as this specific locus is often co-inherited alongside well-documented functional variants like rs10741657. Population studies and genetic association screens have observed that the minor allele at rs10749479 correlates with subtle, statistically significant differences in baseline circulating serum 25(OH)D concentrations and relative hepatic enzyme activity. However, the effect size attributable solely to rs10749479 is modest. Genome-wide association findings emphasize that blood vitamin D levels are polygenic, shaped by multiple loci across genes including GC (vitamin D binding protein), DHCR7, and CYP24A1. Furthermore, non-genetic determinants—including latitude, seasonal sun exposure, skin pigmentation, dietary intake, and body mass index—consistently exert a stronger overall influence on serum calcidiol than any single common non-coding variant.
Distribution Across Global Populations
The rs10749479 polymorphism is widely distributed throughout worldwide human populations, exhibiting an overall global minor allele frequency ranging between approximately 0.38 and 0.42. Because the alternate allele is present at such substantial frequencies across diverse ancestral groups, including European, African, East Asian, and Admixed American cohorts, it represents normal human variation rather than a rare pathogenic lesion. Linkage disequilibrium architecture across the CYP2R1 region can vary meaningfully between different ancestral backgrounds, meaning the degree of correlation between rs10749479 and nearby functional regulatory sites may differ by genetic heritage. Such population-level differences underline why association findings from one ancestry cohort cannot be directly assumed to produce identical numeric effects in another.
Actionable Steps and Practical Limitations
Understanding your rs10749479 genotype provides educational insight into your inherited baseline biology, but it cannot determine whether you have vitamin D deficiency. Genetic results should never replace standard clinical blood work, nor should they prompt unguided self-treatment with high-dose vitamin D supplements. Excess vitamin D supplementation carries risks, including hypercalcemia and renal complications. If your genetic report indicates an allele associated with lower baseline concentrations, the appropriate action is to discuss your routine lab testing with a qualified healthcare professional. Only a clinical 25-hydroxyvitamin D blood test can measure your true physiological status, and any changes to supplement dosing or therapeutic regimens must be supervised by your clinician or pharmacist.
How common is this variant?
The minor allele for rs10749479 is widespread globally, maintaining an estimated minor allele frequency of approximately 0.38 to 0.42 across diverse continental populations.
Frequently asked questions
Does having the rs10749479 variant mean I am vitamin D deficient?
No. The rs10749479 variant is only statistically associated with slight variations in average baseline vitamin D levels across populations. It does not diagnose deficiency, which depends far more on diet, sun exposure, and lifestyle.
Can this genetic variant show if I need vitamin D supplements?
No, genetic testing cannot establish your need for supplementation. The only reliable way to check your vitamin D status is through a 25-hydroxyvitamin D blood test ordered by a medical professional. Always consult your doctor or pharmacist before beginning high-dose vitamin D supplements.
How does the CYP2R1 gene affect vitamin D in the body?
The CYP2R1 gene encodes the primary liver enzyme responsible for 25-hydroxylation, which transforms circulating vitamin D into 25-hydroxyvitamin D. Variations near this gene can slightly modify enzyme production, altering the speed or efficiency of this initial conversion step.
Is the rs10749479 polymorphism considered a rare genetic disease mutation?
No, rs10749479 is a very common single-nucleotide variant carried by roughly 40% of the world's population. It is regarded as normal human diversity rather than a rare pathogenic mutation causing monogenic disorders like hereditary rickets.
Sources & further reading
Educational information only, last refreshed 9/6/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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This variant is associated with variations in Vitamin D metabolism and circulating levels of 25(OH)D.
This variant in the CYP2R1 gene, which encodes a key vitamin D 25-hydroxylase, is associated with altered serum 25-hydroxyvitamin D concentrations.
Influences hepatic 25-hydroxylation efficiency and circulating 25-hydroxyvitamin D concentrations.
This variant in the CYP2R1 gene is associated with circulating 25-hydroxyvitamin D levels and, in rare cases, pathogenic variants in this gene can cause vitamin D-dependent rickets type 1B.
Affects the body's ability to convert sunlight into active Vitamin D.