rs121434290 — SLC39A4 SLC39A4 p.Asn106Lys

Pathogenic missense variant in the ZIP4 intestinal zinc transporter; homozygosity causes acrodermatitis enteropathica, a rare but fully treatable zinc malabsorption disorder

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SLC39A4 and the Zinc Gateway — When the Intestine Cannot Absorb Zinc

Your body cannot make zinc — every atom of it must come through your intestine. ZIP411 ZIP4
Zinc/Iron-regulated transporter-like Protein 4, encoded by SLC39A4, is the dominant apical zinc importer in duodenal and jejunal enterocytes, the protein encoded by SLC39A4, sits at the brush border of the small intestine and acts as the primary gateway for dietary zinc absorption. When both copies of SLC39A4 carry loss-of-function variants, zinc simply cannot get in — and the resulting deficiency is profound and life-threatening without treatment.

This SNP, rs121434290, captures a missense change at codon 106 that replaces asparagine with lysine (p.Asn106Lys). The variant was first reported in a compound heterozygous French family22 compound heterozygous French family
Küry S et al. Identification of SLC39A4, a gene involved in acrodermatitis enteropathica. Nat Genet, 2002, where one chromosome carried this missense change and the other carried an approximately 2-kb upstream deletion that abolished gene expression. The compound heterozygosity was sufficient to cause full acrodermatitis enteropathica (AE)33 acrodermatitis enteropathica (AE)
A rare autosomal recessive disorder of zinc malabsorption presenting with the classic triad of periorificial and acral dermatitis, chronic diarrhea, and alopecia; incidence ~1 in 500,000 newborns globally.

The Mechanism

ZIP4 is a transmembrane zinc transporter with eight predicted membrane-spanning domains and an extracellular amino-terminal domain that is essential for function. Asparagine 106 lies within this extracellular domain44 extracellular domain
The N-terminal ectodomain of ZIP4 folds into a petal-like structure that binds zinc and facilitates its delivery to the transmembrane channel. Under zinc-replete conditions, this domain is proteolytically shed as a regulatory response; under zinc-deficient conditions, the full-length protein is stabilized to maximize uptake and contributes to the folded structure required for zinc capture and channel opening. The Asn106Lys substitution disrupts normal ectodomain function — a 2009 molecular study55 2009 molecular study
Mao X et al. Novel proteolytic processing of the ectodomain of the zinc transporter ZIP4 (SLC39A4) during zinc deficiency is inhibited by acrodermatitis enteropathica mutations. J Biol Chem, 2009 demonstrated that several AE-causing missense mutations, including variants at conserved positions in this domain, block the regulated proteolytic cleavage that normally fine-tunes ZIP4 surface expression in response to dietary zinc availability.

When both ZIP4 alleles are non-functional, zinc absorption in the duodenum and proximal jejunum falls to near zero. Zinc is required as a cofactor for over 300 enzymes and 2,000 transcription factors; its loss disrupts epithelial integrity, T-cell function, wound healing, and cell division. Serum zinc drops below 7 μmol/L (normal 9.8-16.8 μmol/L), and alkaline phosphatase — a zinc-dependent enzyme — is a reliable early marker of deficiency.

The Evidence

SLC39A4 was identified simultaneously by two groups in 2002: Küry et al. in Nature Genetics and Wang et al. in the American Journal of Human Genetics, reporting mutations in eight and five AE families respectively. Since then, a 2009 systematic update66 2009 systematic update
Schmitt S et al. An update on mutations of the SLC39A4 gene in acrodermatitis enteropathica. Hum Mutat, 2009 catalogued over 31 distinct mutations spread across the entire gene — missense, nonsense, frameshift, splice-site, and large deletions — with no clear genotype-phenotype correlation between specific mutation type and clinical severity. The N106K missense variant (this SNP) is one of the founding pathogenic variants described in that initial discovery.

Carrier parents of AE children are uniformly asymptomatic for zinc deficiency under normal dietary conditions. Mouse studies suggest heterozygous Zip4 animals are approximately 10 times more sensitive to zinc deficiency during pregnancy than wild-type littermates (Dufner-Beattie et al. Human Mol Genet, 200777 Dufner-Beattie et al. Human Mol Genet, 2007), but this has not been translated into clinically actionable guidance for human carriers at normal dietary zinc intake.

Treatment with oral zinc supplementation (3 mg/kg/day elemental zinc, typically as zinc sulfate) is dramatically effective in homozygous patients, with clinical improvement within days and full symptom resolution within weeks. StatPearls AE review88 StatPearls AE review cites a 100% response rate with adequate zinc replacement; without treatment, the condition is fatal within early childhood.

Practical Actions

For carriers (GT genotype): carrier status has implications for family planning and genetic screening of at-risk relatives, but does not ordinarily require dietary zinc adjustment. Serum zinc monitoring is warranted during pregnancy due to the heightened zinc demands of fetal development.

For homozygous individuals (TT genotype): lifelong oral zinc supplementation is mandatory. Monitoring must include not only plasma zinc but also serum copper — chronic high-dose zinc competitively inhibits copper absorption through shared transport proteins, and copper deficiency can develop silently. Alkaline phosphatase activity is a useful surrogate marker reflecting the zinc status of both bone and intestinal tissue.

Interactions

Because AE is autosomal recessive, a second loss-of-function SLC39A4 variant must be present on the other chromosome for full disease expression. Clinical sequencing of AE patients typically reveals compound heterozygosity for two different mutations — as in the original family where this N106K variant paired with a promoter deletion. This means a person carrying this variant and a different SLC39A4 pathogenic variant in trans would be clinically affected even though neither individual variant is homozygous. Comprehensive SLC39A4 gene sequencing (not just SNP genotyping) is needed for complete clinical evaluation.

Nutrient Interactions

zinc reduced_absorption

Genotype Interpretations

What each possible genotype means for this variant.

GG Non-carrier Normal

No SLC39A4 p.Asn106Lys variant detected

You carry two copies of the normal G allele at this position, meaning you do not carry the p.Asn106Lys pathogenic variant. Your ZIP4 zinc transporter at this site is structurally intact.

This is the genotype for approximately 99.7% of the general population. Acrodermatitis enteropathica caused by this specific variant does not apply to you.

GT Carrier Carrier

Carrier of one SLC39A4 p.Asn106Lys pathogenic allele

Carrier status for autosomal recessive conditions like acrodermatitis enteropathica typically has no direct health consequence for the carrier themselves. Clinical literature consistently documents that parents of AE-affected children — who are obligate carriers — show normal serum zinc levels and no dermatologic or gastrointestinal symptoms.

The main significance of GT status is reproductive: if your partner also carries any SLC39A4 loss-of-function variant, the recurrence risk for your children is 25% for AE (homozygous or compound heterozygous). Carrier testing of the partner and genetic counseling are appropriate.

One caveat from mouse models: heterozygous Zip4 female mice showed dramatically elevated rates of fetal abnormalities when maintained on zinc-restricted diets during pregnancy. While this has not been formally studied in human carriers, ensuring adequate dietary zinc intake during pregnancy is prudent.

TT Homozygous — AE Risk Homozygous

Two copies of the SLC39A4 p.Asn106Lys pathogenic allele — acrodermatitis enteropathica

Acrodermatitis enteropathica (OMIM #201100) is caused by loss of ZIP4 function in the intestinal brush border. Without a functional zinc transporter, circulating zinc falls to critically low levels (below 7 μmol/L vs. the normal 9.8-16.8 μmol/L). The classic clinical triad includes:

  1. Periorificial and acral dermatitis: sharply demarcated, erythematous, scaly plaques around the mouth, nose, eyes, anogenital region, hands, and feet. Secondary bacterial (S. aureus) and fungal (Candida) infections are common.
  2. Chronic diarrhea: often the first systemic feature, may precede skin changes.
  3. Alopecia: affecting scalp, eyebrows, and eyelashes.

Additional features include growth retardation, immune deficiency, mood disturbance, and delayed puberty if untreated. Onset typically occurs in infancy, classically when transitioning from breast milk (which contains a zinc-binding ligand that facilitates absorption) to cow's milk formula or solid foods.

Treatment with oral zinc at 3 mg/kg/day elemental zinc produces complete symptom resolution within days to weeks. Supplementation must continue for life — discontinuation invariably causes relapse. Because high-dose zinc competitively inhibits copper absorption, periodic copper monitoring is mandatory.

Note that many AE patients are compound heterozygous (two different SLC39A4 mutations) rather than homozygous for a single variant. Full SLC39A4 gene sequencing — not just genotyping at this single position — is required for comprehensive clinical evaluation and family counseling.