FOXN1 forkhead box N1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FOXN1provided by HGNC
Official Full Name: forkhead box N1provided by HGNC
Primary source: HGNC:HGNC:12765
See related: Ensembl:ENSG00000109101 MIM:600838; AllianceGenome:HGNC:12765
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: WHN; RONU; TLIND; FKHL20; TIDAND
Summary: Mutations in the winged-helix transcription factor gene at the nude locus in mice and rats produce the pleiotropic phenotype of hairlessness and athymia, resulting in a severely compromised immune system. This gene is orthologous to the mouse and rat genes and encodes a similar DNA-binding transcription factor that is thought to regulate keratin gene expression. A mutation in this gene has been correlated with T-cell immunodeficiency, the skin disorder congenital alopecia, and nail dystrophy. Alternative splicing in the 5' UTR of this gene has been observed. [provided by RefSeq, Jul 2008]
Expression: Biased expression in skin (RPKM 9.7) and esophagus (RPKM 2.5) See more
Orthologs: mouse all
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Genomic context

Location:: 17q11.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (28506348..28538900)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (29449365..29481520)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (26833366..26865918)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Comprehensive phenotypic analysis of diverse FOXN1 variants.
Title: Comprehensive phenotypic analysis of diverse FOXN1 variants.
[Effects of FoxN1, p63 and AIRE on the process of age-related thymus involution: An update].
Title: [Effects of FoxN1, p63 and AIRE on the process of age-related thymus involution: An update].
Expression of BMP4 and FOXN1 in orthokeratinized odontogenic cyst compared to odontogenic keratocyst suggests an epidermal phenotype.
Title: Expression of BMP4 and FOXN1 in orthokeratinized odontogenic cyst compared to odontogenic keratocyst suggests an epidermal phenotype.
Expanding the Nude SCID/CID Phenotype Associated with FOXN1 Homozygous, Compound Heterozygous, or Heterozygous Mutations.
Title: Expanding the Nude SCID/CID Phenotype Associated with FOXN1 Homozygous, Compound Heterozygous, or Heterozygous Mutations.
The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity.
Title: The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity.
FOXN1 compound heterozygous mutations cause selective thymic hypoplasia in humans.
Title: FOXN1 compound heterozygous mutations cause selective thymic hypoplasia in humans.
observations establish a FOXN1 gene dosage effect on thymic function and identify FOXN1 haploinsufficiency as an important genetic determinant of T cell lymphopenia at birth.
Title: Heterozygous FOXN1 Variants Cause Low TRECs and Severe T Cell Lymphopenia, Revealing a Crucial Role of FOXN1 in Supporting Early Thymopoiesis.
Here, by engineering a time-delayed feedback system of BMP inhibition in mouse embryos, the authors demonstrate that thymopoiesis irreversibly fails if Foxn1 gene expression does not occur during a defining time span in mid-gestation. They also reveal an epistatic interaction between the extent of BMP signalling and the gene dosage of Foxn1.
Title: Cooperative interaction of BMP signalling and Foxn1 gene dosage determines the size of the functionally active thymic epithelial compartment.
FOXN1 founder Italian mutation identified in an indian newborn with severe combined immunodeficiency.
Title: FOXN1 Italian founder mutation in Indian family: Implications in prenatal diagnosis.
Whole-exome sequencing in a South American cohort links ALDH1A3, FOXN1 and RARB/retinoic acid regulation pathways to autism spectrum disorders.
Title: Whole-Exome Sequencing in a South American Cohort Links ALDH1A3, FOXN1 and Retinoic Acid Regulation Pathways to Autism Spectrum Disorders.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
T-cell immunodeficiency, congenital alopecia, and nail dystrophy MedGen: C1866426 OMIM: 601705 GeneReviews: Not available	Compare labs
T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant MedGen: C5394133 OMIM: 618806 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in T cell homeostasis	IEA Inferred from Electronic Annotation more info
involved_in T cell lineage commitment	IEA Inferred from Electronic Annotation more info
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in defense response	TAS Traceable Author Statement more info	PubMed
involved_in epidermis development	TAS Traceable Author Statement more info	PubMed
involved_in hair follicle development	IEA Inferred from Electronic Annotation more info
involved_in keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in lymphoid lineage cell migration into thymus	IEA Inferred from Electronic Annotation more info
involved_in nail development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of epithelial cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of hair follicle development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of positive thymic T cell selection	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in thymus epithelium morphogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: forkhead box protein N1

Names: Rowett nude; winged-helix nude; winged-helix transcription factor nude

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.