rs11950646 — SLC23A1

Intronic variant in the intestinal and renal vitamin C transporter gene (SVCT1) that independently predicts circulating plasma vitamin C levels, with the A allele associated with reduced ascorbate concentrations

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SLC23A1 rs11950646 — An Intronic Switch in Your Vitamin C Transporter

Vitamin C is not made by the human body. Every molecule of ascorbate11 ascorbate
The active, ionized form of ascorbic acid at physiological pH in your bloodstream arrived via active transport: absorbed in the gut by SVCT122 SVCT1
Sodium-dependent Vitamin C Transporter 1 — encoded by SLC23A1 on chromosome 5, expressed on the apical surface of intestinal enterocytes and proximal kidney tubule cells and then conserved by the kidneys, also by SVCT1, before filtered vitamin C can be lost in urine. rs11950646 sits in an intron of SLC23A1 — not in the protein-coding sequence, but in a region that influences how much transporter the gene produces. Carriers of the A allele have measurably lower plasma vitamin C on equivalent diets compared to those carrying the G reference allele.

The Mechanism

Unlike the SLC23A1 missense variant rs33972313 (Val264Met), which alters the SVCT1 protein itself, rs11950646 acts as a regulatory variant. Intronic sequences can harbour splice enhancer or silencer elements, secondary promoters, and binding sites for RNA-binding proteins. The mechanistic detail for this specific site has not been fully characterized in published functional studies, but the association with plasma vitamin C levels is reproducible. The most likely explanation is that the A allele reduces either the efficiency or quantity of functional SVCT1 protein produced from the transcript, subtly impairing both intestinal absorption of dietary vitamin C and renal reabsorption of filtered ascorbate.

The critical importance of SVCT1 for vitamin C homeostasis was established in a Slc23a1 knockout mouse model33 Slc23a1 knockout mouse model
Corpe CP et al. Vitamin C transporter Slc23a1 links renal reabsorption, vitamin C tissue accumulation, and perinatal survival in mice. J Clin Invest, 2010: mice lacking the gene entirely excrete 18 times more ascorbate in urine than controls, nearly eliminating renal conservation capacity, and 45% of offspring die perinatally. rs11950646 represents a far milder perturbation, but its physiological direction is the same — more ascorbate lost, less retained.

The Evidence

The primary evidence comes from the EPIC cohort study by Duell et al. 201344 EPIC cohort study by Duell et al. 2013
Genes & Nutrition — 365 gastric cancer cases and 1,284 controls in the European Prospective Investigation into Cancer and Nutrition; four SLC23A1 and SLC23A2 SNPs independently predicted plasma vitamin C in multivariable regression models. In that study, rs11950646 was one of four genetic predictors of circulating ascorbate, alongside rs33972313 (SLC23A1) and two SLC23A2 variants (rs6053005, rs6133175). The effect operated independently of dietary intake — meaning even people with similar fruit and vegetable consumption showed genotype-driven differences in plasma vitamin C.

Broader context comes from a GWAS of 52,018 European individuals55 GWAS of 52,018 European individuals
Zheng JS et al. Plasma Vitamin C and Type 2 Diabetes: GWAS and Mendelian Randomization in European Populations. Diabetes Care, 2021 that identified 11 genomic regions associated with plasma vitamin C (P < 5×10⁻⁸), with the strongest signal at SLC23A1 — confirming this transporter locus as the dominant genetic determinant of circulating ascorbate in European ancestry populations.

Mendelian randomization studies using SLC23A1 variants as genetic instruments have consistently found that genetically lower vitamin C does not causally drive disease outcomes such as cardiovascular disease, type 2 diabetes, or Alzheimer's disease — suggesting the observational associations between low vitamin C and disease risk are largely due to confounding (people with poor diets tend to have both lower vitamin C and higher disease risk). What the genetic data do confirm is that the SLC23A1 locus reliably and robustly predicts plasma ascorbate concentrations.

Practical Actions

The allele frequency pattern of rs11950646 is striking: the A allele (associated with lower vitamin C) is common in Europeans (~65%) and South Asians (~55%) but uncommon in Africans (~15%) and East Asians (~27%). This means the majority of people of European descent carry at least one copy of the A allele. For AA homozygotes (~36% of Europeans), both copies of the regulatory sequence carry the variant, and plasma ascorbate runs consistently lower relative to GG carriers on the same diet.

The practical consequence is similar to that of other SLC23A1 variants: your body is somewhat less efficient at capturing dietary vitamin C and retaining it through the kidneys. This does not require megadosing — intestinal absorption saturates at high single doses regardless of genotype. It means being consistently attentive to vitamin C intake, targeting food sources across the day (citrus fruits, bell peppers, kiwi, strawberries, broccoli), and potentially using a modest daily supplement (200–500 mg ascorbic acid) to ensure plasma levels stay comfortably above the adequacy threshold of ~28 µmol/L.

Interactions

rs11950646 acts on the same gene and same pathway as rs33972313 (the Val264Met missense variant). If both risk variants are present simultaneously — one altering the regulatory sequence and the other altering the transporter protein itself — the combined effect on vitamin C absorption and retention would be expected to be additive or compounding. Similarly, variants in SLC23A2 (which encodes SVCT2, the tissue-level vitamin C transporter responsible for delivery to the brain, adrenals, and immune cells) may interact with SLC23A1 variants to further reduce tissue-level ascorbate even when plasma levels appear borderline-adequate.

Nutrient Interactions

vitamin C reduced_absorption

Genotype Interpretations

What each possible genotype means for this variant.

GG Reference Transporter Normal

Two reference copies — vitamin C transport at full regulatory capacity

You carry two copies of the G reference allele at this SLC23A1 regulatory site. This is the ancestral allele that is predominant in African populations (~85% frequency) and present in about 35% of people of European descent. Your SVCT1 transporter gene is regulated normally at this intronic site, and your plasma vitamin C levels are determined primarily by your dietary intake rather than any genetic regulatory constraint.

About 16% of people of European ancestry and a higher proportion of African ancestry individuals share this GG genotype. Your vitamin C absorption and renal conservation operate at the reference baseline efficiency.

AG Reduced Regulatory Activity Intermediate

One A allele — mildly reduced transporter gene expression and lower plasma vitamin C

The rs11950646 intronic variant sits in a regulatory region of SLC23A1 that influences the gene's transcriptional or post-transcriptional output. Unlike the Val264Met missense variant (rs33972313), which alters the SVCT1 protein structure directly, this variant likely reduces the amount of functional SVCT1 produced. One A allele means approximately half of your SVCT1 regulatory inputs come from the variant sequence, resulting in partial reduction in absorption and renal reabsorption efficiency. The Duell et al. 2013 EPIC cohort study identified this variant as independently predicting plasma vitamin C after accounting for dietary intake — meaning genotype, not just diet, explains a meaningful portion of individual variation in circulating ascorbate.

AA Lower Transporter Output Reduced

Two A alleles — consistently lower plasma vitamin C from reduced transporter regulation

With two copies of the A allele, both regulatory sequences of the SLC23A1 gene carry the variant. In the additive model consistent with how intronic regulatory variants typically act, the AA genotype produces the maximum reduction in SVCT1 output relative to GG. The EPIC cohort study (Duell et al. 2013) identified rs11950646 as a statistically independent predictor of plasma vitamin C levels in European subjects — independent of dietary intake. This means AA homozygotes have a genetically driven floor below which their plasma ascorbate tends to sit, even with good dietary habits.

The SLC23A1 locus is the dominant genetic predictor of circulating vitamin C in European populations across multiple GWAS and candidate-gene studies. The broader GWAS by Zheng et al. (2021, n=52,018) confirmed SLC23A1 as the strongest signal among 11 genomic regions associated with plasma vitamin C. For AA homozygotes with marginal dietary intake — or those who smoke, have high oxidative stress, or frequently face infection — the genetically lower absorption and renal reabsorption efficiency can push plasma levels toward the lower end of adequacy.

Unlike rs33972313 Val264Met (which alters the SVCT1 protein itself and is rare in Europeans, ~3%), rs11950646 is a common regulatory variant. AA homozygosity does not prevent vitamin C absorption — it reduces the efficiency of the system so that more dietary intake is needed to achieve the same plasma level as a GG individual.