Submission Details

FOXP3 was first reported in relation to immune dysregulation-polyendocrinopathy-enteropathy-X-linked syndrome (IPEX) in 2000 and 2001 (Chatila et al. 2000 PMID: 11120765, Wildin et al. 2001 PMID: 11137992, and Bennett et al. 2001 PMID: 11137993). IPEX is characterized in babies assigned male at birth by systemic autoimmunity, typically beginning in the first year of life. Presentation is most commonly the clinical triad of watery diarrhea (from autoimmune enteropathy), endocrinopathy (most commonly insulin- deficient autoimmune diabetes mellitus), and eczematous dermatitis. Prenatal phenotypes include hydrops, echogenic bowel, cutaneous lesions, fetal growth restriction, and polyhydramnios. At least 140 unique variants including missense, in-frame indel, nonsense, frameshift variants have been reported in humans. Loss of function or haploinsufficiency is the molecular mechanism of IPEX syndrome. Pathogenic alterations can affect mRNA stability, protein function, and intracellular localization. The FOXP3 protein is a transcription factor that regulates the expression of hundreds of targets and is necessary for proper development of T regulatory cells (Tregs), a population of cells responsible for tolerance of self-antigens.

In summary, FOXP3 is definitively associated with X-linked immune dysregulation-polyendocrinopathy-enteropathy-X-linked syndrome (IPEX). Evidence supporting this gene-disease relationship includes case-level data, segregation data, mouse models, and experimental data. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was reviewed and approved by the ClinGen Prenatal GCEP on October 10, 2023 (SOP Version 9).

Monogenic Diabetes Gene Curation Expert Panel (MDEP) Ammendment:

Since timing of the different clinical manifestations of IPEX is variable, diabetes may be all or part of the initial presentation (PMID: 36600150, 29193502, 25187107, 18931102). FOXP3 is therefore appropriate to include on clinical panels when testing infants for monogenic diabetes, as this condition can be a cause of neonatal diabetes especially in infants assigned male at birth. Molecular diagnosis of a disease-causing FOXP3 variant when diabetes is the first feature and other problems are not yet apparent has several important clinical ramifications: A) affected infants should be closely monitored for other clinical manifestations, especially diarrhea/enteropathy, B) appropriate expertise for the possibility of stem-cell transplant should be sought as early as possible to initiate workup (such as finding matched donor etc.) as there will be a high likelihood for the eventual development of other IPEX features, often within weeks or months. Prolonged delay will likely be associated with clinical deterioration and lower chance of survival even when stem cell transplant is undertaken (PMID: 31322807). If a P/LP FOXP3 variant is found in a patient having other manifestations of IPEX but does not yet have diabetes, glucose monitoring is advised, based on the high likelihood of an eventual diabetes diagnosis. If a P/LP FOXP3 variant is found in the context of prenatal loss (as described above), the mother’s subsequent pregnancies are at risk either for prenatal loss or IPEX and therefore possible neonatal diabetes. While one study showed possible association of specific IPEX domains with specific disease manifestations (PMID: 36867340), there is no clear genotype/phenotype correlation. Therefore, the specific variant does not affect medical recommendations including diabetes screening.

Treg cell-specific demethylated region (TSDR) measurement may help to elucídate the pathogenicity of VUS found in FOXP3 (PMID:36600150).

Primary Immune Regulatory Disorders (PIRD) GCEP Ammendment:

-FOXP3 is primarily expressed in CD4+ regulatory T-cells that exert suppressor function (PMID: 20429413) of effector T cells via NFAT and NFKB. FOXP3 can be transiently expressed on activated human T cells but does not have a suppressor function in this cell subset (Kmieciak M et al, 2009, doi:10.1186/1479-5876-7-89; Allan S et al, 2007, doi:10.1093/intimm/dxm014; Wang J e tal, 2007, doi.org/10.1002/eji.200636929). FOXP3 also acts as a transcription activator for several genes, including CD25, CTLA4, GITR, and folate receptor 4 (PMID: 20429413). Native FOXP3+ cells suppress early immune response in lymphoid tissues and memory. Differences of FOXP3 expression and function have been implicated in autoimmunity and autoimmune diseases in addition to IPEX (PMID: 37085947). Single nucleotide polymorphisms (SNPs) of FOXP3 are also related to autoimmune disorders and allergies, primarily via variants that impact expression levels of FOXP3 and modify its function such as its role in Treg cells (PMID: 25982578). Notably, the strengths of the association between FOXP3 and these diseases are not assessed as part of this curation.

FOXP3 is a well-documented cause of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX; OMIM: 304930) as outlined above (PMID: 11120765; PMID: 11137992; PMID: 11137993; Bacchetta R et al, 2023, https://doi.org/10.1016/j.jaci.2023.11.021, Borna S, 2023, DOI: 10.1111/imr.13289). Symptoms beyond the triad of watery diarrhea, endocrinopathy, and eczematous dermatitis have also been described. Individuals with IPEX often present with additional autoimmune issues such as autoimmune hepatitis, cytopenia, splenomegaly, arthritis, lymphadenopathy, alopecia, and lung disease related to immune dysregulation (PMID: 23060872; 21629128; 25712815; 25911531; 17712989; 24270390; 26918796; 24916357). Suggestive findings of IPEX include eosinophilia, elevated IgE, decreased Tregs, and anemia, neutropenia, and/or thrombocytopenia. Additionally, cases of late onset or mild presentations (including variable expressivity) of IPEX have also been described (PMID: 29312905; 29193502). Females with FOXP3 variants are unaffected carriers.

Diagnosis of IPEX can be challenging due to the clinical heterogeneity and immunological studies that include quantitation of regulatory T cells (Tregs) via CD4+25highCD127low expression or FOXP3 expression on this subset is not always informative as Treg numbers are often normal in IPEX and complete loss of FOXP3 is quite rare (Gambineri E et al, 2008, doi.org/10.1016/j.jaci.2008.09.027; Zemmour D et al, 2021, doi.org/10.1038/s41590-021-00910-8). Treg suppressor function assays are affected by immunosuppression treatment, and generally, difficult to execute and interpret (Barzaghi F et al, 2021, 10.3389/fped.2021.612760). Demethylation of Treg-specific CpG islands within the conserved non-coding sequences of the FOXP3 gene, known as Treg-specific demethylated región (TSDR) is a specific epigentic marker of Tregs, required for stable FOXP3 expression. Assessment of TSDR demethylation offers an epigenetic approach to identify genuine Tegs from other T cells that are methlyated at TSDR, and can be used to quantify Tregs (Narula M et al, 2023, doi.org/10.1016/j.jaci.2022.09.013).

Hematopoietic cell transplantation (HCT) is a potential curative therapy for IPEX, though not necessarily for the insulin-deficient autoimmune diabetes if it has already developed. There are efforts toward developing gene therapy for IPEX though this is not clinically available at present (Borna S et al, 2022, 10.1002/eji.202149210).