GENE REFERENCE / HGNC:6106

FOXP3

forkhead box P3

protein-coding geneXp11.23Gene information

What does this gene do?

The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protein. The FOXP3 protein attaches (binds) to specific regions of DNA and helps control the activity of genes that are involved in regulating the immune system. The immune system normally protects the body from foreign invaders, such as bacteria and viruses, by recognizing and attacking these invaders and clearing them from the body.

On the basis of its role in controlling gene activity, the FOXP3 protein is called a transcription factor. This protein is essential for the production and normal function of certain immune cells called regulatory T cells, which play an important role in preventing autoimmunity. Autoimmunity occurs when the body attacks its own tissues and organs by mistake. The FOXP3 protein is found primarily in an immune system gland called the thymus, where these regulatory T cells are produced.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2017-05.

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
immune dysregulation-polyendocrinopathy-enteropathy-X-linked syndromeMONDO:0010580 · Evaluated 2023-10-10	X-linked	DefinitivePrenatal 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: 658
Submissions for variants in or overlapping this gene: 902
Submissions explicitly reporting this gene: 712
Alleles reported pathogenic / likely pathogenic: 63
VariationIDs with uncertain significance: 195
VariationIDs with conflicting classifications: 34

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 FOXP3?

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 63 alleles in FOXP3 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 FOXP3.

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

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