FOXN1

Chr 17q11.2

forkhead box N1

Aliases:: FKHL20
MANE:: ENST00000579795.6

OMIM: 600838 ↗NCBI: 8456 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

FOXN1 · O15353

v62025-08-01

Predicted Aligned Error matrix for FOXN1 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

53.8/ 100

Low

648 residues

Confidence breakdown

Very high(≥ 90)16%
Confident(70–90)2%
Low(50–70)20%
Very low(< 50)62%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

COVID-19 research
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
DDG2P
BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Fetal anomalies
BIALLELIC, autosomal or pseudoautosomal
Intellectual disability
BIALLELIC, autosomal or pseudoautosomal
Familial cicatricial alopecia
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

T-cell immunodeficiency, congenital alopecia, and nail dystrophy
0.81
T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant
0.76
Alymphoid cystic thymic dysgenesis
0.64
Thymic aplasia
0.56
Nezelof syndrome
0.55
severe combined immunodeficiency
0.49
T-B+ severe combined immunodeficiency
0.46
T-B- severe combined immunodeficiency
0.46
autism
0.26
disorder of pharynx
0.21

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Forkhead box protein N1

Transcriptional regulator which regulates the development, differentiation, and function of thymic epithelial cells (TECs) both in the prenatal and postnatal thymus. Acts as a master regulator of the TECs lineage development and is required from the onset of differentiation in progenitor TECs in the developing fetus to the final differentiation steps through which TECs mature to acquire their full functionality. Regulates, either directly or indirectly the expression of a variety of genes that mediate diverse aspects of thymus development and function, including MHC Class II, DLL4, CCL25, CTSL, CD40 and PAX1. Regulates the differentiation of the immature TECs into functional cortical TECs (cTECs) and medullary TECs (mTECs). Essential for maintenance of mTECs population in the postnatal thymus. Involved in the morphogenesis and maintenance of the three-dimensional thymic microstructure which is necessary for a fully functional thymus. Plays an important role in the maintenance of hematopoiesis and particularly T lineage progenitors within the bone marrow niche with age. Essential for the vascularization of the thymus anlage. Promotes the terminal differentiation of epithelial cells in the epidermis and hair follicles, partly by negatively regulating the activity of protein kinase C (By similarity). Plays a crucial role in the early prenatal stages of T-cell ontogeny (PubMed:21507891)