FOXN1 (forkhead box N1)

Gene

• Entrez ID: 8456
• Gene name: Forkhead box N1
• Gene symbol: FOXN1
• Synonyms: FKHL20, RONU, TIDAND, TLIND, WHN
• Chromosome: 17
• Chromosome location: 17q11.2
• 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 gene

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription regulatory region sequence-specific DNA binding	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
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:0002360	Process	T cell lineage commitment	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0006952	Process	Defense response	TAS	7969402
GO:0008544	Process	Epidermis development	TAS	10767081
GO:0009887	Process	Animal organ morphogenesis	TAS	7969402
GO:0030216	Process	Keratinocyte differentiation	IEA
GO:0030858	Process	Positive regulation of epithelial cell differentiation	IDA	24383669
GO:0035878	Process	Nail development	IEA
GO:0043029	Process	T cell homeostasis	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048514	Process	Blood vessel morphogenesis	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

Other IDs

• MIM: 600838
• HGNC: 12765
• e!Ensembl: 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

• Sequence:

  MVSLPPPQSDVTLPGPTRLEGERQGDLMQAPGLPGSPAPQSKHAGFSCSSFVSDGPPERT
  PSLPPHSPRIASPGPEQVQGHCPAGPGPGPFRLSPSDKYPGFGFEEAAASSPGRFLKGSH
  APFHPYKRPFHEDVFPEAETTLALKGHSFKTPGPLEAFEEIPVDVAEAEAFLPGFSAEAW
  CNGLPYPSQEHGPQVLGSEVKVKPPVLESGAGMFCYQPPLQHMYCSSQPPFHQYSPGGGS
  YPIPYLGSSHYQYQRMAPQASTDGHQPLFPKPIYSYSILIFMALKNSKTGSLPVSEIYNF
  MTEHFPYFKTAPDGWKNSVRHNLSLNKCFEKVENKSGSSSRKGCLWALNPAKIDKMQEEL
  QKWKRKDPIAVRKSMAKPEELDSLIGDKREKLGSPLLGCPPPGLSGSGPIRPLAPPAGLS
  PPLHSLHPAPGPIPGKNPLQDLLMGHTPSCYGQTYLHLSPGLAPPGPPQPLFPQPDGHLE
  LRAQPGTPQDSPLPAHTPPSHSAKLLAEPSPARTMHDTLLPDGDLGTDLDAINPSLTDFD
  FQGNLWEQLKDDSLALDPLVLVTSSPTSSSMPPPQPPPHCFPPGPCLTETGSGAGDLAAP
  GSGGSGALGDLHLTTLYSAFMELEPTPPTAPAGPSVYLSPSSKPVALA

• Sequence length: 648

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Autism	Autistic Disorder	rs121964908, rs121912597, rs2710102, rs7794745, rs142990298, rs62643608, rs181327458, rs797046134, rs869312704, rs1555013332, rs876657679, rs1057518999, rs1057518658, rs771827120, rs1555187899, rs773080572, rs753871454, rs1684130791, rs1684180699, rs1553510219, rs1684182454, rs1559060428, rs1553510677, rs1576352885, rs1574152522, rs1574152672, rs1696658542, rs1751123722, rs1750373491, rs1751075634
Immunodeficiency	Severe T-cell immunodeficiency	rs1565678077, rs121908002, rs1421444086, rs1565688667, rs944235493, rs121918314, rs587776713, rs137852678, rs587776714, rs128620188, rs2147483647, rs1569556522, rs137853331, rs137853332, rs179363866, rs483352928, rs121918659, rs111033580, rs111033581, rs74315290, rs193922740, rs193922741, rs104894199, rs483352927, rs104894286, rs1571865049, rs886041032, rs2069709, rs587776822, rs74315444, rs587776823, rs1315265916, rs104893893, rs104893894, rs121434560, rs387906572, rs587776853, rs104893973, rs587776854, rs587776855, rs587776857, rs104893974, rs121912715, rs1393707607, rs113994136, rs387906593, rs587776870, rs387906763, rs387906913, rs199469663, rs199469662, rs199469664, rs193922640, rs193922641, rs193922645, rs398122890, rs387907316, rs397514710, rs398122383, rs397515453, rs397514332, rs398123058, rs397518423, rs587777075, rs199676861, rs77563738, rs587777337, rs28730670, rs587777389, rs587777390, rs587777413, rs587777414, rs587777415, rs587777416, rs267608260, rs267608261, rs587778405, rs587777446, rs587777562, rs587777564, rs587777565, rs869320745, rs587777709, rs606231305, rs672601318, rs727503779, rs727503780, rs730880296, rs786200953, rs375323253, rs794729666, rs886041037, rs886041038, rs796051887, rs796051888, rs749956849, rs199641706, rs775739391, rs869312886, rs869312857, rs879253731, rs879253732, rs201025290, rs770927552, rs878853275, rs878853276, rs878853277, rs878853278, rs1567506566, rs886037920, rs886037921, rs750610248, rs200044623, rs886043118, rs886060531, rs1057519074, rs1057519075, rs1057518744, rs1057519079, rs1057518745, rs1057518746, rs1057518747, rs782178147, rs55729925, rs1064795762, rs1064794957, rs1085307649, rs745463649, rs773694113, rs1192554889, rs779575307, rs1554051075, rs1554051067, rs1554051033, rs1554067182, rs1555167566, rs1555169270, rs1555908409, rs1555719963, rs1554064929, rs768091235, rs1404084330, rs144104577, rs1553238837, rs1553243550, rs1554020278, rs1554066684, rs762678772, rs570768621, rs1443126481, rs1553721236, rs121434258, rs888230251, rs1759915032, rs1759514836, rs138156467, rs1560914625, rs755373718, rs1561423197, rs1560938296, rs200803157, rs766555082, rs201543770, rs114951157, rs775578531, rs201128237, rs778624945, rs1563340753, rs1561772403, rs1484948342, rs777878144, rs1562364898, rs1561254290, rs1569296295, rs1568815169, rs1568822574, rs1571880832, rs934523851, rs1922072844, rs1266114717, rs137869655, rs869320689, rs1571880941, rs1580875488, rs1581303476, rs1448018291, rs1390410878, rs774803573, rs1591278347, rs1602300615, rs1601340933, rs757598952, rs1181595292, rs1408683294, rs1595843113, rs1595848141, rs779560450, rs1595816926, rs1601861196, rs1601861199, rs756541321, rs1594389703, rs1594390415, rs1581401865, rs1236009877, rs753213766, rs778993919, rs1602878106, rs141698985, rs1264504989, rs1580974401, rs2093571190, rs530286781, rs2086875746, rs2089298923, rs1206185362, rs1581573705, rs1596718225, rs1004337827, rs1573613529, rs1574636674, rs1574657735, rs1574657762, rs1574672718, rs1581573640, rs1553657429, rs200666300, rs1578735747, rs1578771211, rs1578793312, rs1578795536, rs1578809101, rs1578811073, rs1578811245, rs1171694504, rs1578971328, rs140800288, rs374333820, rs1584926133, rs1585040113, rs1584409386, rs1379376784, rs1586940273, rs1587143342, rs748910652, rs1592117677, rs758555433, rs1596712783, rs34019455, rs147766868, rs751386365, rs1600631294, rs1489114116, rs1057520578, rs1603007888, rs1603008329, rs1574450161, rs1578735709, rs1403833564, rs1580262965, rs570910902, rs1589866171, rs1578999313, rs1582635229, rs1582637044, rs1580851910, rs1750760771, rs745453685, rs1249197356, rs201840561, rs1940921909, rs1941410085, rs1941465194, rs1321690789, rs1302362911, rs1730552437, rs2052705192, rs1941856970
Macrocephaly	Relative macrocephaly	rs786204854, rs764333096, rs1557739557
Severe combined immunodeficiency disease	Severe combined immunodeficiency due to FOXN1 deficiency	rs886037607, rs118203993, rs121908714, rs121908739, rs121908740, rs121908735, rs121908721, rs121908722, rs121908156, rs1564414523, rs1564418254, rs1564446526, rs786205074, rs121908157, rs121908159, rs786200884, rs397515357, rs104894562, rs137852624, rs137852625, rs137852626, rs137852627, rs137852507, rs137852509, rs111033619, rs111033620, rs1569480018, rs111033621, rs137852510, rs587776729, rs111033622, rs111033617, rs111033618, rs121917894, rs121917896, rs2133313409, rs121917897, rs28933392, rs104894282, rs104894283, rs104894285, rs121918570, rs121918572, rs730880318, rs104893674, rs730880319, rs104894453, rs104894454, rs104894451, rs137853206, rs777503956, rs267606645, rs267606648, rs397515390, rs193922346, rs193922347, rs193922348, rs193922349, rs193922350, rs137852508, rs193922640, rs193922641, rs193922643, rs193922645, rs193922361, rs193922364, rs193922464, rs148508754, rs193922574, rs113994174, rs606231246, rs397514671, rs397514686, rs397514755, rs199474679, rs199474685, rs199474686, rs199474681, rs150739647, rs267605358, rs886041036, rs587777335, rs587778405, rs145092287, rs587777562, rs606231256, rs200296680, rs786205456, rs786205517, rs774202259, rs786205615, rs878853261, rs786205890, rs782753385, rs746052951, rs869025224, rs869312857, rs869320660, rs869320659, rs869320658, rs879253742, rs886037924, rs886037925, rs750610248, rs886039394, rs761242509, rs886039387, rs886041043, rs886041044, rs886042051, rs886041333, rs749481781, rs1057517747, rs1057519506, rs1057523762, rs1057521062, rs1057520644, rs761583890, rs751635016, rs55729925, rs1064793248, rs1064793347, rs1064794027, rs781410769, rs1555524788, rs1486760100, rs769633203, rs1556330713, rs1555322558, rs1556330234, rs1556330755, rs1556329779, rs1556330552, rs1556329822, rs1556330286, rs1556331272, rs2146178281, rs376610445, rs757797994, rs775704953, rs1555743321, rs1564995660, rs1564995662, rs1556330249, rs144104577, rs886041796, rs1026474882, rs570768621, rs1556330562, rs1556330568, rs780014431, rs778343059, rs1555844617, rs1567629968, rs1567628757, rs1567629943, rs1567632864, rs1567632829, rs1567626023, rs1559328006, rs1561423197, rs1452483770, rs1568400897, rs1569479913, rs1568404443, rs1569480047, rs1563340753, rs368303189, rs1568431262, rs1568431102, rs1561424886, rs1602289943, rs1241698978, rs1569479994, rs1569480082, rs1602289649, rs1573261820, rs770985198, rs1589050343, rs1340132582, rs1589064324, rs1589070600, rs1213680890, rs149316157, rs1599873591, rs755706305, rs1602288051, rs1602289411, rs1602289183, rs1583513256, rs1589136659, rs1380154594, rs1011307501, rs1599876167, rs1569967422, rs1602289631, rs1573262398, rs760191638, rs1592117677, rs1640406042, rs372597855, rs1839558393, rs1839622622, rs1839957089, rs777008519, rs1233957241, rs2092261618, rs1839255008, rs1677695565, rs936493226, rs1162344514, rs991089005

Unknown
Disease name	Disease term	dbSNP ID	References
Alopecia	Alopecia
Aplasia of the thymus	Congenital absence of thymus
Congenital alopecia totalis	Congenital alopecia totalis
Immunologic deficiency syndromes	Immunologic Deficiency Syndromes
Nail dystrophy	Dystrophia unguium
T-cell immunodeficiency, congenital alopecia and nail dystrophy	T-cell immunodeficiency, congenital alopecia and nail dystrophy		8911612, 15180707, 10206641, 11159512