FOXF1 (forkhead box F1)

Gene

• Entrez ID: 2294
• Gene name: Forkhead box F1
• Gene symbol: FOXF1
• Synonyms: ACDMPV, FKHL5, FREAC1
• Chromosome: 16
• Chromosome location: 16q24.1
• Summary: This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in the regulation of pulmonary genes as we

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121909337	T>C	Pathogenic	Terminator codon variant, stop lost
rs397854726	TTT>-,T,TT,TTTT,TTTTTT,TTTTTTTTT,TTTTTTTTTTTT	Conflicting-interpretations-of-pathogenicity, benign	3 prime UTR variant
rs672601295	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs752504125	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs1064796420	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1481006723	C>A,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs1567511932	A>C	Likely-pathogenic	Stop lost, terminator codon variant
rs1597291300	C>A	Pathogenic	Coding sequence variant, missense variant
rs1597291318	T>C	Pathogenic	Coding sequence variant, missense variant
rs1597291380	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1597291554	GCGGCGGC>-	Pathogenic	Coding sequence variant, frameshift variant
rs1597291710	TT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1597291719	C>T	Pathogenic	Coding sequence variant, stop gained
rs1597291722	CCCCCTGT>-	Pathogenic	Coding sequence variant, stop gained
rs1597291767	->TGTCC	Pathogenic	Coding sequence variant, frameshift variant
rs1597292524	TT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1597292620	G>C	Pathogenic	Stop lost, terminator codon variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1001640	hsa-miR-3671	CLIP-seq
MIRT1001641	hsa-miR-3941	CLIP-seq
MIRT1001642	hsa-miR-466	CLIP-seq
MIRT1001643	hsa-miR-4672	CLIP-seq
MIRT1001644	hsa-miR-607	CLIP-seq
MIRT1996809	hsa-miR-4685-5p	CLIP-seq
MIRT1996810	hsa-miR-578	CLIP-seq
MIRT1996811	hsa-miR-581	CLIP-seq
MIRT1996809	hsa-miR-4685-5p	CLIP-seq
MIRT1996810	hsa-miR-578	CLIP-seq
MIRT1996811	hsa-miR-581	CLIP-seq
MIRT2429001	hsa-miR-105	CLIP-seq
MIRT2429002	hsa-miR-1251	CLIP-seq
MIRT2429003	hsa-miR-15a	CLIP-seq
MIRT2429004	hsa-miR-15b	CLIP-seq
MIRT2429005	hsa-miR-16	CLIP-seq
MIRT2429006	hsa-miR-195	CLIP-seq
MIRT2429007	hsa-miR-2052	CLIP-seq
MIRT2429008	hsa-miR-3153	CLIP-seq
MIRT2429009	hsa-miR-3162-5p	CLIP-seq
MIRT2429010	hsa-miR-424	CLIP-seq
MIRT2429011	hsa-miR-4524	CLIP-seq
MIRT2429012	hsa-miR-4719	CLIP-seq
MIRT2429013	hsa-miR-4793-3p	CLIP-seq
MIRT2429014	hsa-miR-497	CLIP-seq
MIRT2429015	hsa-miR-503	CLIP-seq
MIRT2429016	hsa-miR-553	CLIP-seq
MIRT2429017	hsa-miR-646	CLIP-seq
MIRT2429018	hsa-miR-765	CLIP-seq
MIRT2437305	hsa-miR-375	CLIP-seq
MIRT2437306	hsa-miR-382	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
GLI2	Activation	23034409
GLI2	Unknown	19360354

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IMP	8626802
GO:0000978	Function	RNA polymerase II cis-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	IMP	8626802
GO:0001568	Process	Blood vessel development	IMP	19500772
GO:0001570	Process	Vasculogenesis	IEA
GO:0001701	Process	In utero embryonic development	IMP	19500772
GO:0001756	Process	Somitogenesis	IEA
GO:0001763	Process	Morphogenesis of a branching structure	IMP	19500772
GO:0002053	Process	Positive regulation of mesenchymal cell proliferation	IEA
GO:0003197	Process	Endocardial cushion development	IMP	19500772
GO:0003214	Process	Cardiac left ventricle morphogenesis	IMP	19500772
GO:0003677	Function	DNA binding	IDA	9769171
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IC	9769171
GO:0005667	Component	Transcription regulator complex	TAS	9722567
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0007494	Process	Midgut development	IMP	19500772
GO:0007507	Process	Heart development	IMP	19500772
GO:0009887	Process	Animal organ morphogenesis	IBA	21873635
GO:0010811	Process	Positive regulation of cell-substrate adhesion	IEA
GO:0014822	Process	Detection of wounding	IEA
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0030323	Process	Respiratory tube development	IMP	19500772
GO:0030324	Process	Lung development	IMP	19500772
GO:0030335	Process	Positive regulation of cell migration	IEA
GO:0031016	Process	Pancreas development	IMP	19500772
GO:0043305	Process	Negative regulation of mast cell degranulation	IEA
GO:0043565	Function	Sequence-specific DNA binding	ISS	7957066
GO:0045198	Process	Establishment of epithelial cell apical/basal polarity	IEA
GO:0045893	Process	Positive regulation of transcription, DNA-templated	IDA	8626802, 9769171
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	8626802
GO:0048286	Process	Lung alveolus development	IEA
GO:0048371	Process	Lateral mesodermal cell differentiation	IEA
GO:0048557	Process	Embryonic digestive tract morphogenesis	IMP	19500772
GO:0048565	Process	Digestive tract development	IMP	19500772
GO:0048613	Process	Embryonic ectodermal digestive tract morphogenesis	IMP	19500772
GO:0048617	Process	Embryonic foregut morphogenesis	IEA
GO:0050728	Process	Negative regulation of inflammatory response	IEA
GO:0051145	Process	Smooth muscle cell differentiation	IEA
GO:0060426	Process	Lung vasculature development	IMP	19500772
GO:0060438	Process	Trachea development	IMP	19500772
GO:0060441	Process	Epithelial tube branching involved in lung morphogenesis	IEA
GO:0060461	Process	Right lung morphogenesis	IEA
GO:0060463	Process	Lung lobe morphogenesis	IEA
GO:0060841	Process	Venous blood vessel development	IMP	19500772
GO:0061030	Process	Epithelial cell differentiation involved in mammary gland alveolus development	IEA
GO:0071345	Process	Cellular response to cytokine stimulus	IEA
GO:0071407	Process	Cellular response to organic cyclic compound	IEA
GO:0072189	Process	Ureter development	IMP	19500772
GO:0090131	Process	Mesenchyme migration	IEA
GO:0097070	Process	Ductus arteriosus closure	IMP	19500772
GO:0098609	Process	Cell-cell adhesion	IEA

Other IDs

• MIM: 601089
• HGNC: 3809
• e!Ensembl: ENSG00000103241

Protein

• UniProt ID: Q12946
• Protein name: Forkhead box protein F1 (Forkhead-related activator 1) (FREAC-1) (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1)
• Protein function: Probable transcription activator for a number of lung-specific genes.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00250	Forkhead	47 → 133	Forkhead domain	Domain

• Sequence:

  MSSAPEKQQPPHGGGGGGGGGGGAAMDPASSGPSKAKKTNAGIRRPEKPPYSYIALIVMA
  IQSSPTKRLTLSEIYQFLQSRFPFFRGSYQGWKNSVRHNLSLNECFIKLPKGLGRPGKGH
  YWTIDPASEFMFEEGSFRRRPRGFRRKCQALKPMYSMMNGLGFNHLPDTYGFQGSAGGLS
  CPPNSLALEGGLGMMNGHLPGNVDGMALPSHSVPHLPSNGGHSYMGGCGGAAAGEYPHHD
  SSVPASPLLPTGAGGVMEPHAVYSGSAAAWPPSASAALNSGASYIKQQPLSPCNPAANPL
  SGSLSTHSLEQPYLHQNSHNAPAELQGIPRYHSQSPSMCDRKEFVFSFNAMASSSMHSAG
  GGSYYHQQVTYQDIKPCVM

• Sequence length: 379

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Atrial septal defect	Atrial Septal Defects	rs137852951, rs137852953, rs137852955, rs267607106, rs104893900, rs104893901, rs104893903, rs606231358, rs606231359, rs137852683, rs606231360, rs104893907, rs104894073, rs1585703301, rs104894074, rs267606903, rs121912677, rs387906585, rs387906773, rs72554028, rs587782928, rs587782929, rs587782930, rs587784067, rs1555226315, rs879253754, rs1114167356, rs773922431, rs1554093487, rs1554093433, rs1554093461, rs1561621507, rs1561619801, rs766692577, rs1581108237, rs1581111034, rs1579663872, rs1583066622, rs1456289029, rs1761430125
Bicuspid aortic valve	Bicuspid aortic valve	rs1569484234, rs1569484208
Congenital diaphragmatic hernia	Congenital diaphragmatic hernia	rs121908602, rs121908604, rs864309713, rs780263938, rs756636036, rs775394591	27663689
Gastrointestinal stromal tumor	Gastrointestinal Stromal Tumors, Gastrointestinal Stromal Sarcoma	rs587776653, rs74315368, rs74315369, rs587776793, rs587776794, rs587776795, rs606231209, rs121908589, rs121913685, rs121913680, rs794726675, rs587776804, rs121913517, rs121913234, rs121913512, rs267607032, rs387906780, rs201286421, rs587778661, rs587781270, rs587782243, rs74315370, rs587782703, rs786203457, rs764575966, rs786203251, rs587782604, rs200245469, rs397516836, rs786202732, rs786201161, rs786201063, rs751000085, rs869025568, rs876660642, rs876658713, rs151170408, rs878854632, rs752360961, rs121913235, rs121913521, rs121913513, rs1057519708, rs1057519710, rs121913514, rs1057519713, rs778582853, rs1060503757, rs1060502521, rs1060502543, rs898854295, rs981049067, rs916516745, rs1553887262, rs1057520032, rs1553887960, rs775143272, rs1560395607, rs1560418178, rs751904543, rs1560420761, rs1560417385, rs1560417396, rs1560417427, rs1560417438, rs1560417535, rs1560417642, rs1560417666, rs1560417673, rs1577992594, rs1577995761, rs1578003055, rs1301704156, rs1734957331	27793025
Hirschsprung disease	Hirschsprung Disease	rs104893891, rs76262710, rs75075748, rs75996173, rs79014735, rs77316810, rs75076352, rs76087194, rs76534745, rs76764689, rs76449634, rs78098482, rs79661516, rs104894389, rs769735757, rs267606780, rs1568823467, rs377767412, rs193922699, rs75030001, rs606231342, rs1553540620, rs759944122, rs1057519322, rs1057519323, rs1057519052, rs1588873476, rs1588866040, rs1838178869
Hypertension	Hypertensive disease	rs13306026, rs13333226
Hypertrophic pyloric stenosis	Pyloric Stenosis, Infantile Hypertrophic, 5	rs672601295
Hypoplastic left heart syndrome	Hypoplastic Left Heart Syndrome	rs1554284604, rs1843006535
Patent ductus arteriosus	Patent ductus arteriosus	rs80338911, rs879253870, rs879253871, rs879255278, rs879255279, rs879253872
Pulmonary arterial hypertension	Pulmonary arterial hypertension, Idiopathic pulmonary arterial hypertension	rs121909288, rs137852741, rs137852742, rs137852743, rs137852744, rs137852745, rs137852746, rs137852748, rs137852749, rs137852750, rs137852751, rs137852753, rs863223423, rs863223426, rs863223424, rs863223408, rs869025366, rs876657748, rs886039506, rs886041324, rs1060502576, rs1060502581, rs1060502584, rs1085307149, rs1085307154, rs1085307157, rs1085307163, rs1085307169, rs1085307177, rs1085307180, rs1085307184, rs1085307188, rs1085307191, rs1085307203, rs1085307222, rs1085307223, rs1085307225, rs1085307229, rs1085307234, rs1085307246, rs1085307261, rs1085307267, rs576091247, rs200948870, rs1085307278, rs1085307282, rs1085307285, rs1085307290, rs1085307301, rs1085307306, rs1085307307, rs1085307308, rs1085307315, rs1085307316, rs1553509997, rs1085307324, rs1085307340, rs1085307349, rs1085307352, rs765887545, rs1085307183, rs1555208696, rs1592224412, rs1574415785, rs1574415799, rs1574462520, rs1085307197, rs1574464060, rs749485755, rs1574464121, rs1574464150, rs1574464160, rs1085307214, rs1574485996, rs1574486497, rs1574486566, rs1574488314, rs1574488346, rs1574488353, rs1574488357, rs1574488412, rs1414031345, rs1574488484, rs1574488490, rs863223419, rs1574489046, rs1574494632, rs1574494655, rs1574500018, rs1574505253, rs1574505321, rs371174955, rs1574506729, rs1574506732, rs1574506781, rs1574506790, rs1574506799, rs1574506914, rs1574506976, rs1574507076, rs1574507124, rs1574507215, rs1574507268, rs1574507272, rs1574507276, rs1574507290, rs1574507331, rs398123042, rs374644720, rs1588573831, rs1592222308, rs1592223392, rs756315327, rs1603248167, rs1397811125, rs1603255267, rs1603255327, rs1603255336, rs1603255339, rs754897911, rs1603256095, rs1085307155, rs1085307156, rs1574464226, rs1085307226, rs1574486038, rs1553508321, rs1574488277, rs1574488501, rs1574493841, rs1574499954
Tetralogy of fallot	Tetralogy of Fallot	rs28939668, rs727504412, rs864321649, rs774966208, rs876660981, rs886044220, rs1114167357, rs1569484126, rs1569484164, rs1569484122, rs1569484124, rs1569484042, rs1569484120, rs1569484299, rs1569484301, rs1569484288
Vacterl association	VATER/VACTERL ASSOCIATION	rs752504125, rs869320684, rs776556963	2629409
Ventricular septal defect	Ventricular Septal Defects	rs104894073, rs387906775

Unknown
Disease name	Disease term	dbSNP ID	References
Alveolar capillary dysplasia	Alveolar capillary dysplasia, Congenital alveolar capillary dysplasia		19500772, 23505205
Annular pancreas	Annular pancreas
Anomalous pulmonary venous return	Anomalous pulmonary vein
Aortic valve sclerosis	Aortic Valve Stenosis
Asplenia	Congenital absence of spleen
Congenital atresia of pulmonary valve	Congenital atresia of pulmonary valve
Posterolateral diaphragmatic hernia	Congenital hernia of foramen of Bochdalek		27663689
Morgagni diaphragmatic hernia	Congenital hernia of foramen of Morgagni		27663689
Congenital malrotation of intestine	Congenital malrotation of intestine
Duodenal atresia	Duodenal atresia
Fetal megacystis	Fetal megacystis
Agenesis of gallbladder	Gallbladder, Agenesis Of
Hydronephrosis	Hydronephrosis
Imperforate anus	Anus, Imperforate
Intestinal volvulus	Intestinal Volvulus
Lung diseases	Lung Diseases, Obstructive		18421012
Mastocytosis	Mastocytosis		18421012
Meckel diverticulum	Meckel Diverticulum
Persistent fetal circulation	Persistent Fetal Circulation Syndrome		27071622, 19500772, 30058937, 27145217, 23505205
Urethral atresia	Urethral atresia