Vitamin B6 (ALPL)
ALPL · rs4654748
The active form of vitamin B6 is pyridoxal-5′-phosphate (PLP), a coenzyme for more than a hundred enzymes. The strongest genetic influence on circulating PLP lies at the ALPL gene of alkaline phosphatase. The markers are useful context when a B6 deficiency is suspected.
The markers
Alkaline phosphatase (ALPL) hydrolyses PLP and thereby governs how much active B6 circulates in the blood. In a genome-wide meta-analysis of one-carbon metabolism the ALPL locus on 1p36 was the strongest hit for plasma PLP (p ≈ 10⁻¹⁵), marked by rs4654748; the effect allele lowers the level (Hazra 2009). The adjacent marker rs1256335 in the NBPF3 gene was replicated in the same region.
What it means
These SNPs are context markers, not a deficiency finding. A low measured B6 value is easier to place against the background of an unfavourable ALPL genotype, but does not replace the measurement. As B6 is closely interwoven with homocysteine and folate metabolism, it is worth looking at B6, folate and B12 together.
Context
The effect on the level is statistically robust but moderate in size. Genome shows the markers as technical evidence within the built-in panel 'Vitamins A–E'; only the measurement, together with symptoms, makes a statement about deficiency or need.
What Genome measures. The genotypes at rs4654748 (near ALPL) and the adjacent rs1256335 (NBPF3).
Related topics
Sources
- 1Hazra et al., 2009 Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. Human Molecular Genetics 18:4677–4687. doi.org/10.1093/hmg/ddp428