GENE REFERENCE / HGNC:28880

MAGT1

magnesium transporter 1

protein-coding geneXq21.1Gene information

What does this gene do?

The MAGT1 gene provides instructions for making a protein called a magnesium transporter, which moves charged atoms (ions) of magnesium (Mg²⁺) into certain immune system cells called T cells. T cells recognize foreign invaders, such as viruses, bacteria, and fungi, and are then turned on (activated) to attack these invaders in order to prevent infection and illness. Specifically, the magnesium transporter produced from the MAGT1 gene is active in CD8+ T cells, which are especially important in controlling viral infections such as the Epstein-Barr virus (EBV). These cells normally take in magnesium when they detect a foreign invader, and the magnesium is involved in activating the T cell's response.

Researchers suggest that magnesium transport may also be involved in the production of another type of T cell called helper T cells (CD4+ T cells) in a gland called the thymus. CD4+ T cells direct and assist the functions of the immune system by influencing the activities of other immune system cells.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2014-06.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasiaMONDO:0010455 · Evaluated 2025-11-18	X-linked	DefinitivePrimary Immune Regulatory Disorders Gene Curation Expert Panel
X-linked intellectual disabilityMONDO:0100284 · Evaluated 2023-02-01	X-linked	DisputedIntellectual Disability and Autism Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 529
Submissions for variants in or overlapping this gene: 653
Submissions explicitly reporting this gene: 457
Alleles reported pathogenic / likely pathogenic: 53
VariationIDs with uncertain significance: 195
VariationIDs with conflicting classifications: 16

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about MAGT1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 53 alleles in MAGT1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in MAGT1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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