Vitamins & Nutrient Absorption

Intronic variant in the intestinal and renal vitamin C transporter gene (SVCT1) associated with susceptibility to Crohn disease through impaired ascorbate transport and heightened intestinal oxidative stress; the C allele (minor in Europeans, major in Africans) confers dose-dependent disease risk

Pathogenic missense variant in sepiapterin reductase that abolishes BH4 biosynthesis, causing dopamine and serotonin deficiency in the brain; homozygosity or compound heterozygosity causes DOPA-responsive dystonia (SPR deficiency, OMIM

Missense variant in the concentrative nucleoside transporter 2 (CNT2) gene that increases intestinal ribavirin absorption, raising serum drug levels and doubling the risk of ribavirin-induced hemolytic anemia during hepatitis C treatment; also modulates purine nucleoside bioavailability in liver and gut

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

Nonsense variant in sepiapterin reductase that abolishes BH4 biosynthesis, causing dopamine and serotonin deficiency in the brain; homozygosity leads to DOPA-responsive dystonia (SPR deficiency, OMIM

Nonsense variant in sepiapterin reductase creating a premature stop codon (p.Lys251Ter) that abolishes BH4 synthesis, causing dopa-responsive dystonia with severe neurotransmitter depletion when inherited biallelically

Intronic variant near ALPL associated with increased alkaline phosphatase activity, lowering circulating PLP (the active form of vitamin B6) — those with two G copies have higher ALPL activity and lower plasma B6 levels

Intergenic variant near SLC30A1 (ZnT1), the primary basolateral zinc exporter in intestinal enterocytes; the A allele is markedly less common in East Asian populations (7.6%) than in European (49.4%) or African (42.7%) populations, suggesting population-specific selective pressure on zinc transport efficiency.

Intronic variant in the SVCT2 vitamin C transporter — G allele associated with lower plasma vitamin C, higher glaucoma risk, and modified cognitive decline risk in APOE4 carriers

Reduces beta-carotene to retinol (vitamin A) conversion efficiency, contributing to the "poor converter" phenotype

African lactase persistence variant — MCM6 enhancer SNP that controls LCT expression in East and southern African populations

Pathogenic missense variant in the riboflavin transporter RFVT2 that abolishes cellular vitamin B2 uptake, causing Brown-Vialetto-Van Laere syndrome type 2; high-dose riboflavin supplementation can dramatically reverse neurological decline when started early.

Transcobalamin II variant affecting cellular delivery of vitamin B12 via holotranscobalamin binding efficiency

Pathogenic missense variant in the ZIP4 intestinal zinc transporter causing hereditary acrodermatitis enteropathica when homozygous; heterozygotes are asymptomatic carriers with near-normal zinc absorption

Common missense variant in the primary intestinal zinc transporter ZIP4; the Val372 allele (C on the plus strand) reduces ZIP4 surface expression and zinc uptake capacity and reached near-fixation in West Africa through positive selection, likely via pathogen-zinc-starvation advantages; the Leu372 form (G allele) is standard in European and Asian populations.

Pathogenic splice acceptor variant in MMAB that abolishes adenosylcobalamin synthesis, causing methylmalonic aciduria cblB type when two loss-of-function alleles are inherited

Intronic variant in PPCDC associated with lower circulating serum zinc levels; the C allele reduces zinc by approximately 0.3 standard deviations and has been used as a genetic instrument in Mendelian randomization studies of zinc and cardiometabolic health.

Synonymous coding variant in TMPRSS6 associated with hepcidin levels and iron status; the G allele tags a haplotype with modestly elevated hepcidin and reduced iron absorption efficiency

Intronic variant in the glutathione reductase gene affecting antioxidant defense; the minor A allele has been associated with poorer recovery after sudden sensorineural hearing loss treated with corticosteroids, consistent with impaired cochlear oxidative stress clearance

Intronic CBS variant that tags the CBS locus in GWAS studies; associated with altered homocysteine metabolism capacity and one-carbon methylation efficiency

Promoter variant that increases SLC28A2/CNT2 transcription via enhanced HNF1 binding, affecting nucleoside analog drug transport in liver and kidney

Missense variant eliminating MMAB adenosylcobalamin synthase activity; the most common pathogenic allele in European cblB methylmalonic acidemia, causing absent enzyme protein and complete block of adenosylcobalamin synthesis

Pathogenic missense variant in the hepatic copper transporter ATP7B that abolishes protein trafficking to the trans-Golgi network; the most common Wilson disease mutation in East Asian populations, accounting for ~29% of pathogenic ATP7B alleles in Chinese patients; homozygotes and compound heterozygotes develop progressive copper accumulation causing liver disease, neurological symptoms, and Kayser-Fleischer rings; heterozygous carriers are asymptomatic but can transmit the disease if their reproductive partner also carries an ATP7B pathogenic variant

Primary intestinal and renal vitamin C transporter — variant reduces ascorbate absorption and reabsorption efficiency

Nonsense variant in MMAB creating a premature stop codon (Q234*) that impairs adenosylcobalamin synthesis; pathogenic for methylmalonic aciduria cblB type in biallelic state; heterozygous carriers are asymptomatic.

Near-gene regulatory variant near FUT6 that reduces fucosyltransferase expression and lowers circulating vitamin B12 — especially common in Indians

A 2-bp frameshift deletion in FMO3 that creates a premature stop codon at position 197, completely abolishing the enzyme's ability to convert trimethylamine (TMA) to odorless TMAO — the primary genetic cause of trimethylaminuria (fish odor syndrome) in East Asian populations.

Missense variant in selenoprotein P that alters selenium transport capacity; the T allele (Thr234) is associated with lower circulating SELENOP levels after selenium intake and elevated risk of adverse outcomes in prostate cancer and retinopathy of prematurity

Rare missense variant near the BTD active site (p.Val89Gly) that likely reduces biotinidase enzyme activity; heterozygous carriers have partial enzyme reduction while biallelic inheritance causes biotinidase deficiency

Rare missense variant in the biotinidase enzyme (p.Pro167Ser); a likely pathogenic allele for biotinidase deficiency. Heterozygous carriers have reduced but usually sufficient biotinidase activity; compound heterozygosity with other BTD pathogenic variants can cause partial or profound deficiency requiring lifelong biotin supplementation.

Pathogenic missense variant in biotinidase that abolishes biotin recycling; heterozygous carriers have partial enzyme reduction while homozygotes and compound heterozygotes develop biotinidase deficiency requiring lifelong biotin supplementation

Pathogenic missense variant in riboflavin transporter RFVT2 (p.Leu123Pro) causing Brown-Vialetto-Van Laere syndrome type 2, a rare autosomal recessive neurodegenerative disorder; high-dose riboflavin supplementation is the primary disease-modifying treatment

Pathogenic 5-bp frameshift deletion in the biotinidase enzyme gene, eliminating the final 41 amino acids of the protein and causing biotinidase deficiency when inherited in biallelic form; heterozygotes are asymptomatic carriers

East African lactase persistence allele — MCM6 enhancer SNP that independently maintains LCT expression in Oromo, Somali, Beja, and related pastoral populations

Regulatory variant 2 kb upstream of TFR2 that modulates hepcidin production and is associated with NAFLD risk, iron loading parameters, and age-related macular degeneration in subgroup analyses

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

Upstream regulatory variant near TCN2 associated with reduced holotranscobalamin levels — the bioactive fraction of circulating vitamin B12 available for cellular uptake

Promoter-proximal upstream variant in TCN2 that increases transcobalamin II protein production, boosting circulating capacity to transport vitamin B12 to cells

Determines secretor status — whether ABO blood group antigens are secreted into bodily fluids, affecting gut microbiome, vitamin B12 levels, and infection susceptibility

Missense variant in the FUT2 fucosyltransferase enzyme that alters haptocorrin glycosylation and is one of the strongest genetic determinants of circulating vitamin B12 levels

Intronic variant in the SVCT2 tissue vitamin C transporter — associated with differences in plasma vitamin C levels in the EPIC cohort

Intronic variant in the tissue vitamin C transporter SVCT2 — GG homozygotes carry ~24% higher plasma vitamin C levels than AA homozygotes

Missense variant in the FTCD enzyme that impairs one-carbon unit transfer from histidine catabolism into the folate pool, reducing arsenic methylation efficiency and increasing toxicity risk

Upstream regulatory variant near BCO1 that reduces beta-carotene to vitamin A conversion efficiency by approximately 59%

Upstream regulatory variant that reduces BCO1 (BCMO1) catalytic activity by ~48%, independently limiting beta-carotene to vitamin A conversion; the top GWAS hit for circulating beta-carotene levels

Intronic variant in the intestinal and renal vitamin C transporter gene (SVCT1) representing an independent haplotype signal at the SLC23A1 locus — the G allele is associated with lower plasma vitamin C concentrations via reduced transporter output distinct from the Val264Met missense variant (rs33972313)

Intronic variant in the intestinal and renal vitamin C transporter gene (SVCT1) associated with modestly lower plasma vitamin C levels and increased risk of aggressive periodontitis; the C allele forms part of the Crohn disease risk haplotype at the SLC23A1 locus

Regulates expression of the alpha-tocopherol transfer protein, the key determinant of circulating vitamin E levels

Intronic FMO3 variant associated with reduced hepatic oxidation of garlic-derived sulfur compounds (S-allylcysteine) and trimethylamine; C allele carriers accumulate higher circulating levels of unprocessed sulfur metabolites

Reduces beta-carotene conversion to vitamin A (retinol) by ~32% per T allele, contributing to "poor converter" status for plant-based vitamin A

Intronic regulatory variant in FUT6 that alters HNF4α binding and fucosyltransferase expression, influencing intestinal fucosylation and circulating vitamin B12 levels — especially relevant in South Asian populations

Intergenic GWAS tag SNP near the BCO1 pathway, associated with circulating beta-carotene and retinol levels independently of the functional BCO1 coding variants

PEMT missense variant (Val95Ile) reducing endogenous phosphatidylcholine synthesis and elevating dietary choline requirements, with strongest impact in premenopausal women and during pregnancy