rs4654748 — NBPF3

Tag SNP in the NBPF3/ALPL locus on chromosome 1 — the strongest common genetic determinant of circulating vitamin B6 (PLP) levels, acting through alkaline phosphatase-mediated catabolism

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NBPF3/ALPL — The Genetic Throttle on Vitamin B6 Levels

Vitamin B6 is not a single molecule but a family of related compounds — pyridoxine, pyridoxal, pyridoxamine, and their phosphorylated forms — that your body continuously interconverts. The active coenzyme form is pyridoxal 5'-phosphate (PLP)11 pyridoxal 5'-phosphate (PLP)
The phosphorylated, active form of vitamin B6 that acts as a coenzyme in over 100 enzymatic reactions, which participates in over 100 enzymatic reactions, from amino acid metabolism and neurotransmitter synthesis to homocysteine clearance and immune function. Despite its importance, circulating PLP levels vary substantially between people eating identical diets. A significant portion of that variation is genetic. The rs4654748 variant, located in an intron of the NBPF3 gene on chromosome 1 and in tight linkage disequilibrium with the nearby ALPL22 ALPL
Alkaline phosphatase, liver type — a cell-surface enzyme that hydrolyzes phosphorylated substrates including PLP, controlling how much circulating B6 is available to tissues gene, is the single strongest common genetic predictor of circulating PLP levels identified by genome-wide association studies. It does not break a gene — it fine-tunes an enzyme that degrades B6, shifting your steady-state PLP level up or down depending on how many C alleles you carry.

The Mechanism

Tissue-nonspecific alkaline phosphatase (TNSALP), encoded by ALPL, is a cell-surface enzyme expressed in liver, bone, kidney, and intestine. One of its natural substrates is circulating PLP: TNSALP dephosphorylates PLP to pyridoxal, which crosses cell membranes more easily, then cells rephosphorylate it back to PLP for use as a coenzyme. This cycle effectively controls how much PLP remains in circulation at any given time. The C allele at rs4654748 is associated with a more active or more highly expressed form of the enzyme at this locus. When alkaline phosphatase activity was included in regression models33 When alkaline phosphatase activity was included in regression models
Tanaka T et al. Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine. Am J Hum Genet, 2009, the association of rs4654748 with plasma B6 disappeared — confirming that ALP activity is the mediating mechanism. C allele carriers have faster PLP catabolism, leading to lower steady-state circulating PLP, even with identical dietary B6 intake.

The Evidence

The founding study by Tanaka et al. 200944 Tanaka et al. 2009
Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations. Am J Hum Genet, 2009 conducted a genome-wide association analysis in three Italian cohorts (InCHIANTI, SardiNIA, BLSA; N = 2,930), identifying rs4654748 as the top locus (p = 1.21 × 10⁻⁸), with replication in an independent cohort of 687 participants (p = 2.08 × 10⁻¹¹). The meta-analysis yielded p = 8.3 × 10⁻¹⁸ and an effect of 1.45 ng/mL lower vitamin B6 per copy of the C allele — an additive, dose-dependent effect. A subsequent meta-analysis of 4,763 participants across three genome-wide scans55 4,763 participants across three genome-wide scans
Hazra A et al. Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. Hum Mol Genet, 2009 confirmed the chromosome 1p36 locus association with plasma PLP (p = 1.40 × 10⁻¹⁵ for the locus), placing it among the most robustly replicated nutrition-metabolism GWAS findings. A candidate gene study in 2,345 healthy Irish adults66 candidate gene study in 2,345 healthy Irish adults
Carter TC et al. Common variants at putative regulatory sites of ALPL influence circulating PLP. J Nutr, 2015 identified 17 ALPL SNPs associated with plasma PLP at genome-wide significance, with rs4654748 (MAF 0.48) among the top hits (p = 4.61 × 10⁻⁸). The locus also influences B6 vitamer ratios in cerebrospinal fluid77 B6 vitamer ratios in cerebrospinal fluid
Loohuis LM et al. The alkaline phosphatase (ALPL) locus is associated with B6 vitamer levels in CSF and plasma. Genes, 2018, not just plasma, confirming that peripheral B6 metabolism affects the brain's B6 supply and making the locus relevant to neurological as well as metabolic outcomes.

Practical Actions

People with the CC genotype have chronically lower circulating PLP than TT individuals on equivalent diets, by approximately 2.9 ng/mL. This gap widens when dietary B6 intake is marginal. The typical plasma PLP reference range is roughly 20–100 nmol/L (5–25 ng/mL), so a 2.9 ng/mL reduction represents a meaningful downward shift, particularly for people near the lower end of normal. The most direct countermeasure is supplementing with pyridoxal-5-phosphate (P5P)88 pyridoxal-5-phosphate (P5P)
The already-active coenzyme form of B6 that does not require hepatic conversion and is taken up directly by tissues. Unlike pyridoxine (the synthetic form found in most multivitamins), P5P does not need to be converted by the liver and is not subject to competitive inhibition with active B6 at high doses. For CC carriers with documented low plasma PLP, P5P (10–25 mg/day) provides the active form directly, bypassing the catabolism bottleneck at ALPL. Dietary B6 remains important: animal proteins (poultry, fish, beef liver), chickpeas, bananas, and fortified cereals are the richest sources. However, given that the variant affects catabolism rather than absorption, dietary intake targets for CC carriers should be at the upper end of the RDA range (1.7 mg/day for adults over 50; 1.3 mg/day for younger adults), with consideration of supplementation if plasma PLP is confirmed low. Plasma PLP can be measured directly — either as part of a vitamin B6 profile panel or as a standalone test. This is the most useful monitoring option for CC carriers, particularly given B6's role in homocysteine transsulfuration and neurotransmitter synthesis.

Interactions

Vitamin B6 (PLP) is a required cofactor for cystathionine beta-synthase and cystathionine gamma-lyase99 cystathionine beta-synthase and cystathionine gamma-lyase
The two enzymes of the transsulfuration pathway that convert homocysteine to cysteine and glutathione, the transulfuration enzymes that convert homocysteine to cysteine. Chronically lower PLP in CC carriers may reduce the efficiency of homocysteine clearance through this pathway, particularly when the folate-dependent remethylation route (which requires MTHFR) is also impaired. This creates a potential compound interaction with MTHFR C677T (rs1801133) and MTRR A66G (rs1801394): when folate-mediated remethylation is reduced and B6-dependent transsulfuration is also less efficient, homocysteine can accumulate significantly. Individuals carrying CC at rs4654748 together with the homozygous risk genotype at MTHFR C677T (rs1801133) may benefit from supplementation addressing both the B6 and methylfolate pathways simultaneously. This compound interaction is worth monitoring with a serum homocysteine test. PLP is also a cofactor for SHMT1 (rs1979277), the enzyme converting serine to glycine in the folate cycle. Reduced PLP in CC carriers may compound SHMT1 variants that already impair this step.

Nutrient Interactions

vitamin B6 increased_need

Genotype Interpretations

What each possible genotype means for this variant.

TT High B6 Levels Normal

Normal alkaline phosphatase activity — efficient vitamin B6 retention

You have two copies of the T allele, which is associated with lower alkaline phosphatase activity at this locus and the slowest catabolism of circulating vitamin B6. Your plasma PLP levels are predicted to be approximately 2.9 ng/mL higher than CC homozygotes on equivalent dietary intake. This is the genotype associated with the highest steady-state B6 levels in population studies. About 23% of the general population carries this genotype. The C allele is the reference (more common) allele, making TT the minor homozygous genotype.

CT Moderately Reduced B6 Intermediate

One C allele moderately lowers circulating PLP — vitamin B6 intake matters more

With one copy of each allele, your alkaline phosphatase activity at this locus falls between TT (lowest activity, highest PLP) and CC (highest activity, lowest PLP). The additive effect means one C allele confers roughly half the PLP reduction seen in CC homozygotes. The clinical significance of a ~1.45 ng/mL reduction in plasma B6 depends on where your baseline falls. People eating B6-poor diets (low in animal protein, legumes, and whole foods) may sit near the lower end of the reference range, where a 1.45 ng/mL reduction has a proportionally greater impact on PLP-dependent enzyme activity than it would for someone with generous B6 intake. PLP is particularly important as a cofactor for neurotransmitter synthesis (serotonin, dopamine, GABA) and for the transsulfuration pathway enzymes that keep homocysteine in check. Ensuring adequate dietary B6 is especially relevant for CT carriers during periods of metabolic stress.

CC Lower B6 Levels Decreased

Two C alleles significantly lower circulating PLP — active B6 supplementation recommended

The CC genotype produces the full additive effect of two C alleles at rs4654748, driving the highest alkaline phosphatase activity at this locus. The founding GWAS by Tanaka et al. (2009) measured this as 2.9 ng/mL lower plasma B6 for CC vs TT homozygotes — additive because each C allele adds approximately 1.45 ng/mL of reduction. Plasma PLP reference ranges are typically 20–100 nmol/L (approximately 5–25 ng/mL). A 2.9 ng/mL downward shift is meaningful for anyone already at the lower end of normal. Since PLP is a cofactor for over 100 enzymatic reactions — including the aromatic L-amino acid decarboxylase that produces serotonin and dopamine from their amino acid precursors, and the transulfuration enzymes that clear homocysteine — subclinical PLP insufficiency can have broad metabolic consequences even without frank deficiency. The ALPL locus association extends to cerebrospinal fluid B6 vitamer concentrations (Loohuis LM et al. 2018), confirming that this peripheral catabolism bottleneck affects the B6 supply reaching the brain. This is particularly relevant given that neurotransmitter synthesis is one of the most PLP-sensitive enzymatic processes. Mendelian randomization analysis confirms that rs4654748 reliably drives plasma pyridoxal levels, making it a valid basis for targeted supplementation recommendations in CC carriers.