RBFOX3 (RNA binding fox-1 homolog 3)

Gene

• Entrez ID: 146713
• Gene name: RNA binding fox-1 homolog 3
• Gene symbol: RBFOX3
• Synonyms (NCBI Gene): FOX-3, FOX3, HRNBP3, NEUN
• Chromosome: 17
• Chromosome location: 17q25.3
• Summary: This gene encodes a member of the RNA-binding FOX protein family which is involved in the regulation of alternative splicing of pre-mRNA. The protein has an N-terminal proline-rich region, an RNA recognition motif (RRM) domain, and a C-terminal alanine-ri

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs972548690	G>A,T	Pathogenic, likely-benign	Stop gained, synonymous variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1294322	hsa-miR-129-5p	CLIP-seq
MIRT1294323	hsa-miR-2115	CLIP-seq
MIRT1294324	hsa-miR-4742-3p	CLIP-seq
MIRT1294325	hsa-miR-516a-3p	CLIP-seq
MIRT1552979	hsa-miR-1307	CLIP-seq
MIRT1552980	hsa-miR-1469	CLIP-seq
MIRT1294325	hsa-miR-516a-3p	CLIP-seq
MIRT2087540	hsa-miR-3689d	CLIP-seq
MIRT1294325	hsa-miR-516a-3p	CLIP-seq
MIRT1552979	hsa-miR-1307	CLIP-seq
MIRT1552980	hsa-miR-1469	CLIP-seq
MIRT2312368	hsa-miR-4292	CLIP-seq
MIRT2457850	hsa-miR-3127-3p	CLIP-seq
MIRT2457851	hsa-miR-361-3p	CLIP-seq
MIRT2457852	hsa-miR-4286	CLIP-seq
MIRT2457850	hsa-miR-3127-3p	CLIP-seq
MIRT2608799	hsa-miR-3185	CLIP-seq
MIRT2457851	hsa-miR-361-3p	CLIP-seq
MIRT2608800	hsa-miR-4709-3p	CLIP-seq
MIRT2608799	hsa-miR-3185	CLIP-seq
MIRT2608800	hsa-miR-4709-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000381	Process	Regulation of alternative mRNA splicing, via spliceosome	IBA
GO:0000381	Process	Regulation of alternative mRNA splicing, via spliceosome	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IEA
GO:0003729	Function	MRNA binding	IBA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0007399	Process	Nervous system development	IBA
GO:0007399	Process	Nervous system development	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0043484	Process	Regulation of RNA splicing	IEA

Other IDs

• MIM: 616999
• HGNC: 27097
• e!Ensembl: ENSG00000167281

Protein

• UniProt ID: A6NFN3
• Protein name: RNA binding protein fox-1 homolog 3 (Fox-1 homolog C) (Neuronal nuclei antigen) (NeuN antigen)
• Protein function: Pre-mRNA alternative splicing regulator. Regulates alternative splicing of RBFOX2 to enhance the production of mRNA species that are targeted for nonsense-mediated decay (NMD).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00076	RRM_1	101 → 169	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain
  PF12414	Fox-1_C	208 → 297	Calcitonin gene-related peptide regulator C terminal	Family

• Sequence:

  MAQPYPPAQYPPPPQNGIPAEYAPPPPHPTQDYSGQTPVPTEHGMTLYTPAQTHPEQPGS
  EASTQPIAGTQTVPQTDEAAQTDSQPLHPSDPTEKQQPKRLHVSNIPFRFRDPDLRQMFG
  QFGKILDVEIIFNERGSKGFGFVTFETSSDADRAREKLNGTIVEGRKIEVNNATARVMTN
  KKTGNPYTNGWKLNPVVGAVYGPEFYAVTGFPYPTTGTAVAYRGAHLRGRGRAVYNTFRA
  APPPPPIPTYGAVVYQDGFYGAEIYGGYAAYRYAQPAAAAAAYSDSYGRVYAAADPYHHT
  IGPAATYSIGTM

• Sequence length: 312

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Self-limited epilepsy with centrotemporal spikes	Pathogenic	rs972548690	RCV000656060

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Idiopathic generalized epilepsy	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	rs1208480613, rs2075332971, rs776016743, rs1226535060, rs2074722616, rs1568119836, rs1197865456, rs1204664048, rs2146665255, rs2033670420, rs2076444289, rs2146662664, rs770647329, rs367559413, rs2033680072, rs990728601, rs985551378, rs377709616, rs779066017, rs1226722084, rs530721444, rs754425963, rs925521413, rs1222831726, rs369818738, rs1213853848, rs2146996449, rs776796401, rs551189632, rs992186015, rs746156238, rs1474903517, rs886670631, rs2146564382, rs561710608, rs751793355, rs58352742, rs1351338220, rs80198744, rs368372440, rs11651975, rs1299842245, rs1568139609, rs2146254285, rs2146997386, rs2146999516, rs557599713, rs2146312862, rs1332700365, rs1339077239, rs1440844625, rs990360044, rs1671568075, rs1055293531, rs1037097785, rs2146254444, rs2146211667, rs1403085500, rs775017222, rs372072435, rs1451910541, rs1465377886, rs769052612, rs1568129070, rs2076940658, rs1372121041, rs2146289066, rs1412372562, rs2146313081, rs1010660520, rs1019002644, rs2076947605, rs2075511936, rs2146255373, rs377759206, rs2075546067, rs1196792536, rs780661784, rs940680437, rs957289800, rs758656116, rs1233398072, rs373727615, rs758551578, rs951953480, rs955676022, rs79080598, rs771129435, rs1048996078, rs752716524, rs2146531567, rs761056905, rs998084414, rs1170040285, rs754135050, rs934108895, rs911540420, rs918641407, rs1459023595, rs200580682, rs578218089, rs371537468, rs575797622, rs2033658024, rs749459956, rs780036724, rs1201014995, rs765108817, rs1028999714, rs377444179, rs2146212338, rs2146209619, rs1207044826, rs181329485, rs550827396, rs904015242, rs918046686, rs1272481386, rs901701800, rs1227562251, rs755771324, rs1465690990, rs1430763047, rs2510048344, rs747660044, rs1260150695, rs1406138161, rs1442933151, rs1424681393, rs762990060, rs1005115982, rs2510120143, rs375171072, rs2510554490, rs2510574180, rs968309201, rs2510276012, rs957607666, rs999374552, rs748229870, rs2076942759, rs2033696567, rs552604935, rs565220696, rs2510567398, rs1029382552, rs2146212511, rs2510553994, rs2509972204, rs878854169, rs878854170, rs150282906, rs878854171, rs953830526, rs953699995, rs2076441787, rs1036122764, rs1467252800, rs544051756, rs2074742345, rs1380998131, rs2074723059, rs2510278155, rs1399450037, rs2510278179, rs2510223306, rs1380001327, rs2510559333, rs1389594306, rs1470997327, rs1277972988, rs2510237444, rs2510196130, rs2510117637, rs2510117736, rs1321419714, rs757166078, rs761274622, rs2510223151, rs891632025, rs925722930, rs955408222, rs2075647002, rs1417427470, rs2510119706, rs1157854732, rs2075648974, rs2510196229, rs964392995, rs1214799081, rs1290862566, rs979417860, rs565537117, rs199891032, rs377660420, rs1015038952, rs373093807, rs1294363374, rs542684395, rs375940495, rs375309858, rs376060745, rs1228682560, rs539897924, rs370372079, rs547643968, rs1555694660, rs780865169, rs911641608, rs371067982, rs1167103679, rs1568134061, rs1032718998, rs748110754, rs1003593947, rs1599396290, rs921899416, rs1479403018, rs776142495, rs1340183543, rs1599450000, rs757903881, rs112978510, rs775993784, rs372250322, rs972548690, rs1201055787, rs570994105, rs369398194, rs768508558, rs887758601, rs866943064, rs966632113, rs1599386357, rs1444545956, rs1381383669, rs551476510, rs1456815875, rs566515477, rs748950439, rs1189505871, rs2033713868, rs1311373046, rs368393347, rs1170085775, rs1289325621, rs1298625389, rs2033733857, rs1305432887, rs747394355	RCV001315266 RCV001312990 RCV001327705 RCV001321443 RCV001351896 RCV001350587 RCV001352448 RCV001370601 RCV001370642 RCV001369594 RCV001367037 RCV001404772 RCV001412430 RCV001400991 RCV001399651 RCV001408090 RCV001442647 RCV001426337 RCV001444821 RCV001422799 RCV001438038 RCV001425529 RCV001474081 RCV001456781 RCV001468033 RCV001465691 RCV001453968 RCV001464203 RCV001454124 RCV001488014 RCV001481767 RCV001485053 RCV001504112 RCV001506067 RCV001503461 RCV001491538 RCV001483258 RCV001496172 RCV001520120 RCV001510803 RCV001514695 RCV001520195 RCV002073016 RCV001930194 RCV001974781 RCV001895919 RCV002012845 RCV001950597 RCV001877884 RCV001877887 RCV001933086 RCV001977610 RCV002008464 RCV001889854 RCV002017353 RCV001929775 RCV001929924 RCV001951795 RCV001886430 RCV002006611 RCV002018098 RCV002031116 RCV002036301 RCV001970059 RCV001931638 RCV001972861 RCV002020894 RCV001914043 RCV001986531 RCV002021806 RCV001963656 RCV002024924 RCV002100018 RCV002215532 RCV002149713 RCV002095420 RCV002195260 RCV002123877 RCV002154206 RCV002192386 RCV002080982 RCV002211789 RCV002122318 RCV002181824 RCV002167969 RCV002098243 RCV002102399 RCV002186227 RCV002191585 RCV002213057 RCV002119991 RCV002180241 RCV002095882 RCV002204750 RCV002151502 RCV002082129 RCV002089346 RCV002114353 RCV002073710 RCV002110358 RCV002114764 RCV002113540 RCV002218831 RCV002181080 RCV002195465 RCV002133376 RCV002075963 RCV002206395 RCV002205267 RCV002138236 RCV002182568 RCV002202853 RCV002164621 RCV002132405 RCV002196098 RCV002144847 RCV002098543 RCV002185735 RCV002165400 RCV002137429 RCV002148679 RCV002085873 RCV002097423 RCV002115179 RCV002220272 RCV002109583 RCV002175302 RCV002198383 RCV003053025 RCV003083756 RCV003083784 RCV003089648 RCV003085965 RCV002581915 RCV002607335 RCV002627846 RCV002636615 RCV002606739 RCV003115160 RCV003112658 RCV003110219 RCV002572061 RCV002631643 RCV002657768 RCV002659257 RCV002670827 RCV002736348 RCV002770212 RCV002820453 RCV002842386 RCV002863256 RCV002895419 RCV002957358 RCV002975640 RCV002957999 RCV002985389 RCV002999999 RCV002998926 RCV003008234 RCV003051976 RCV003057148 RCV000228077 RCV000232052 RCV000234265 RCV000233781 RCV005101284 RCV003525644 RCV003525495 RCV003525809 RCV003526698 RCV003526859 RCV003527123 RCV003526947 RCV003527155 RCV003527269 RCV003527454 RCV003527614 RCV003526256 RCV003639040 RCV003639041 RCV003639052 RCV003639436 RCV003639678 RCV003639648 RCV003639724 RCV003640045 RCV003640196 RCV003638141 RCV003638460 RCV003638554 RCV003638449 RCV003638452 RCV003638528 RCV003639140 RCV003639098 RCV003639101 RCV003639072 RCV003639063 RCV003639282 RCV003639236 RCV003639237 RCV003822245 RCV003861936 RCV003861093 RCV003872358 RCV000462716 RCV000477457 RCV000458759 RCV000470915 RCV000467923 RCV000465340 RCV000531221 RCV000545243 RCV000555525 RCV000552791 RCV000542731 RCV000553712 RCV000527850 RCV000634984 RCV000634983 RCV000634997 RCV000634980 RCV000634986 RCV000635003 RCV000634999 RCV000634988 RCV000634968 RCV000703513 RCV000688830 RCV000686802 RCV000700905 RCV000812164 RCV000793890 RCV000807138 RCV000798770 RCV000807716 RCV000803321 RCV000794514 RCV000815012 RCV000811576 RCV000820742 RCV000864049 RCV001481215 RCV001487895 RCV001409013 RCV001470499 RCV002064507 RCV000865639 RCV001461214 RCV001394376 RCV000869522 RCV001438957 RCV000908882 RCV001426989 RCV000937730 RCV001437752 RCV001429706 RCV001042190 RCV001034806 RCV001066274 RCV001064579 RCV001047206 RCV001037806 RCV001040293 RCV001056135 RCV001201663 RCV001211395 RCV001229861 RCV001228520 RCV001235547 RCV001236684 RCV001295472 RCV001309592
RBFOX3-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs779066017, rs368372440, rs150282906, rs974381564, rs79080598, rs375940495, rs370372079, rs780865169, rs112978510, rs530721444, rs747394355	RCV003938731 RCV003948545 RCV003977648 RCV003944019 RCV003925383 RCV003905351 RCV003935775 RCV003928064 RCV003965678 RCV003938291 RCV003393969

Associations from Text Mining
Disease Name	Relationship Type	References
AIDS Associated Nephropathy	Associate	24215932
Alzheimer Disease	Inhibit	28598851
Astrocytoma	Associate	29768357
Carcinoma Merkel Cell	Associate	34974547
Cholesterol pneumonia	Associate	30369316
Cleft Palate	Associate	23512105
Cognition Disorders	Associate	24215932
Developmental Disabilities	Associate	24603971
Down Syndrome	Associate	29509279, 35232286
Epilepsy Idiopathic Generalized	Associate	24039908
Epilepsy Rolandic	Associate	24039908
Frontotemporal Lobar Degeneration	Associate	28877758
Glioblastoma	Associate	28418837
HIV Infections	Associate	24215932
Huntington Disease	Associate	25275533
Lung Neoplasms	Inhibit	27432190
Medulloblastoma	Associate	18641877
Multiple Sclerosis	Associate	26558787
Neoplasms	Associate	15446592, 27432190, 29768357, 35663322, 37240308
Neoplasms Neuroepithelial	Associate	29768357
Nerve Degeneration	Associate	33129359
Neurocytoma	Associate	37088465
Prostatitis	Inhibit	37240308
Speech Disorders	Associate	24603971
Thalamic Diseases	Inhibit	35748636
Warts	Associate	31569353