rs4654748 — NBPF3

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.