Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8456
Gene name Gene Name - the full gene name approved by the HGNC.	Forkhead box N1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	FOXN1
Synonyms (NCBI Gene) Gene synonyms aliases	FKHL20, RONU, TIDAND, TLIND, WHN
Chromosome Chromosome number	17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	17q11.2
Summary Summary of gene provided in NCBI Entrez Gene.	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 gene

Show/Hide all(20)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34814444	T>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, downstream transcript variant, coding sequence variant, intron variant, missense variant
rs104894562	C>T	Pathogenic	Stop gained, coding sequence variant
rs797046135	C>T	Likely-pathogenic	Genic upstream transcript variant, missense variant, upstream transcript variant, coding sequence variant, intron variant
rs886043619	TGTCCGCCCCCTGGGCTGTCCGGCTCAGGCC>-	Likely-pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1064793129	CCCCCTGGGCTGTCCG>-	Likely-pathogenic, pathogenic, uncertain-significance	Frameshift variant, coding sequence variant, intron variant
rs1064795660	GT>AG	Likely-pathogenic	Splice donor variant
rs1064796115	G>-	Pathogenic, uncertain-significance	Frameshift variant, coding sequence variant
rs1288977950	C>T	Pathogenic	Missense variant, coding sequence variant
rs1438890364	C>G,T	Pathogenic	Stop gained, intron variant, missense variant, coding sequence variant
rs1555609768	G>T	Likely-pathogenic	Splice donor variant
rs1567886959	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1567887558	GGGCC>CCA	Pathogenic	Frameshift variant, coding sequence variant, intron variant, 3 prime UTR variant
rs1597552140	A>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, genic upstream transcript variant, upstream transcript variant
rs1597558200	->TA	Pathogenic	Frameshift variant, coding sequence variant
rs1597566356	->ACCC	Pathogenic	Frameshift variant, coding sequence variant
rs1597566413	C>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs1597566699	->A	Pathogenic	Frameshift variant, coding sequence variant
rs1597566726	GAAGAGGAAAGATCC>-	Pathogenic	Coding sequence variant, inframe indel
rs1597567985	TCCTGGACCC>-	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1597568117	C>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant

Show/Hide all(14)

miRTarBase ID	miRNA	Experiments	Reference
MIRT438125	hsa-miR-18b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438125	hsa-miR-18b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438123	hsa-miR-518b	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438123	hsa-miR-518b	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438125	hsa-miR-18b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438125	hsa-miR-18b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438123	hsa-miR-518b	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT438123	hsa-miR-518b	Flow, Luciferase reporter assay, qRT-PCR, Western blot	24383669
MIRT1997211	hsa-miR-1306	CLIP-seq
MIRT1997212	hsa-miR-3189-5p	CLIP-seq
MIRT1997213	hsa-miR-3677-5p	CLIP-seq
MIRT1997214	hsa-miR-4460	CLIP-seq
MIRT1997215	hsa-miR-4727-3p	CLIP-seq
MIRT1997216	hsa-miR-4758-3p	CLIP-seq

Show/Hide all(38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001942	Process	Hair follicle development	IEA
GO:0002260	Process	Lymphocyte homeostasis	IEA
GO:0002360	Process	T cell lineage commitment	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	10767081
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	TAS	10767081
GO:0006952	Process	Defense response	TAS	7969402
GO:0008544	Process	Epidermis development	IEA
GO:0008544	Process	Epidermis development	TAS	10767081
GO:0009887	Process	Animal organ morphogenesis	TAS	7969402
GO:0010468	Process	Regulation of gene expression	IEA
GO:0030097	Process	Hemopoiesis	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030216	Process	Keratinocyte differentiation	IEA
GO:0030216	Process	Keratinocyte differentiation	IEA
GO:0030858	Process	Positive regulation of epithelial cell differentiation	IDA	24383669
GO:0033081	Process	Regulation of T cell differentiation in thymus	IEA
GO:0035878	Process	Nail development	IEA
GO:0043029	Process	T cell homeostasis	IEA
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048514	Process	Blood vessel morphogenesis	IEA
GO:0048538	Process	Thymus development	IEA
GO:0048538	Process	Thymus development	IEA
GO:0051798	Process	Positive regulation of hair follicle development	IEA
GO:0097535	Process	Lymphoid lineage cell migration into thymus	IEA
GO:0097536	Process	Thymus epithelium morphogenesis	IEA
GO:1902232	Process	Regulation of positive thymic T cell selection	IEA

MIM	HGNC	e!Ensembl
600838	12765	ENSG00000109101

Protein

UniProt ID

O15353

Protein name

Forkhead box protein N1 (Winged-helix transcription factor nude)

Protein function

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

PDB

5OCN , 6EL8

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00250	Forkhead	270 → 357	Forkhead domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in thymus.

Sequence

MVSLPPPQSDVTLPGPTRLEGERQGDLMQAPGLPGSPAPQSKHAGFSCSSFVSDGPPERT
PSLPPHSPRIASPGPEQVQGHCPAGPGPGPFRLSPSDKYPGFGFEEAAASSPGRFLKGSH
APFHPYKRPFHEDVFPEAETTLALKGHSFKTPGPLEAFEEIPVDVAEAEAFLPGFSAEAW
CNGLPYPSQEHGPQVLGSEVKVKPPVLESGAGMFCYQPPLQHMYCSSQPPFHQYSPGGGS
YPIPYLGSSHYQYQRMAPQASTDGHQPLFPKPIYSYSILIFMALKNSKTGSLPVSEIYNF
MTEHFPYFKTAPDGWKNSVRHNLSLNKCFEKVENKSGSSSRKGCLWALNPAKIDKMQEEL
QKWKRKDPIAVRKSMAKPEELDSLIGDKREKLGSPLLGCPPPGLSGSGPIRPLAPPAGLS
PPLHSLHPAPGPIPGKNPLQDLLMGHTPSCYGQTYLHLSPGLAPPGPPQPLFPQPDGHLE
LRAQPGTPQDSPLPAHTPPSHSAKLLAEPSPARTMHDTLLPDGDLGTDLDAINPSLTDFD
FQGNLWEQLKDDSLALDPLVLVTSSPTSSSMPPPQPPPHCFPPGPCLTETGSGAGDLAAP
GSGGSGALGDLHLTTLYSAFMELEPTPPTAPAGPSVYLSPSSKPVALA

Sequence length

648

Interactions

View interactions

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Lymphoblastic Leukemia	T-cell immunodeficiency, congenital alopecia, and nail dystrophy	rs104894562, rs1597566470, rs2069729948, rs1597566699, rs2070018439, rs1057524466, rs1597567692, rs745708044, rs1064796115, rs1597567985, rs1169577591, rs1064795660, rs1438890364, rs1064793129, rs1288977950 View all (10 more)	N/A
severe combined immunodeficiency disease	Severe combined immunodeficiency disease	rs104894562	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
autism	Autism	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Alopecia universalis	Associate	22590644
Autistic Disorder	Associate	30755392
Carcinoma Hepatocellular	Associate	28662289
Carcinoma Squamous Cell	Stimulate	39628682
Dermatofibrosarcoma	Associate	23614918
Developmental Disabilities	Associate	30755392
Hepatitis B	Associate	28662289
Hereditary renal agenesis	Associate	22590644
Histiocytoma Benign Fibrous	Associate	23614918
Immune System Diseases	Associate	30755392
Keratosis Seborrheic	Associate	28410231
Neoplasm Metastasis	Associate	39628682
Neoplasms	Associate	30755392
Severe Combined Immunodeficiency	Associate	31151968, 33464451, 35303369
Tertiary Lymphoid Structures	Associate	39628682
X Linked Combined Immunodeficiency Diseases	Associate	33464451

FOXN1 (forkhead box N1)