RFX3 (regulatory factor X3)

Gene

• Entrez ID: 5991
• Gene name: Regulatory factor X3
• Gene symbol: RFX3
• Synonyms (NCBI Gene): -
• Chromosome: 9
• Chromosome location: 9p24.2
• Summary: This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X4, a

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017663	hsa-miR-335-5p	Microarray	18185580
MIRT019371	hsa-miR-148b-3p	Microarray	17612493
MIRT021982	hsa-miR-128-3p	Microarray	17612493
MIRT043701	hsa-miR-342-3p	CLASH	23622248
MIRT039992	hsa-miR-615-3p	CLASH	23622248
MIRT654271	hsa-miR-1264	HITS-CLIP	23824327
MIRT666595	hsa-miR-222-5p	HITS-CLIP	23824327
MIRT666594	hsa-miR-6828-3p	HITS-CLIP	23824327
MIRT666593	hsa-miR-6071	HITS-CLIP	23824327
MIRT666592	hsa-miR-3977	HITS-CLIP	23824327
MIRT666591	hsa-miR-544a	HITS-CLIP	23824327
MIRT666590	hsa-miR-6738-3p	HITS-CLIP	23824327
MIRT666589	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT654271	hsa-miR-1264	HITS-CLIP	23824327
MIRT441720	hsa-miR-3662	PAR-CLIP	22100165
MIRT441719	hsa-miR-3646	PAR-CLIP	22100165
MIRT441718	hsa-miR-4428	PAR-CLIP	22100165
MIRT441717	hsa-miR-892c-5p	PAR-CLIP	22100165
MIRT441716	hsa-miR-4698	PAR-CLIP	22100165
MIRT654271	hsa-miR-1264	HITS-CLIP	23824327
MIRT666595	hsa-miR-222-5p	HITS-CLIP	23824327
MIRT666594	hsa-miR-6828-3p	HITS-CLIP	23824327
MIRT666593	hsa-miR-6071	HITS-CLIP	23824327
MIRT666592	hsa-miR-3977	HITS-CLIP	23824327
MIRT666591	hsa-miR-544a	HITS-CLIP	23824327
MIRT666590	hsa-miR-6738-3p	HITS-CLIP	23824327
MIRT666589	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT654271	hsa-miR-1264	HITS-CLIP	23824327
MIRT441720	hsa-miR-3662	PAR-CLIP	22100165
MIRT441719	hsa-miR-3646	PAR-CLIP	22100165
MIRT441718	hsa-miR-4428	PAR-CLIP	22100165
MIRT441717	hsa-miR-892c-5p	PAR-CLIP	22100165
MIRT441716	hsa-miR-4698	PAR-CLIP	22100165
MIRT1302407	hsa-miR-1281	CLIP-seq
MIRT1302408	hsa-miR-1976	CLIP-seq
MIRT1302409	hsa-miR-410	CLIP-seq
MIRT1302410	hsa-miR-4640-3p	CLIP-seq
MIRT1302411	hsa-miR-4643	CLIP-seq
MIRT1302412	hsa-miR-466	CLIP-seq
MIRT1302413	hsa-miR-4789-3p	CLIP-seq
MIRT1302414	hsa-miR-511	CLIP-seq
MIRT2089794	hsa-miR-3155	CLIP-seq
MIRT2089795	hsa-miR-3155b	CLIP-seq
MIRT2089796	hsa-miR-4477a	CLIP-seq
MIRT2089797	hsa-miR-484	CLIP-seq
MIRT2089798	hsa-miR-513a-3p	CLIP-seq
MIRT2458088	hsa-miR-129-3p	CLIP-seq
MIRT2458089	hsa-miR-759	CLIP-seq
MIRT2610981	hsa-miR-4709-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	20413507
GO:0000785	Component	Chromatin	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	20148032
GO:0000976	Function	Transcription cis-regulatory region binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA 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:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	TAS	8289803
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	8600444
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	ISS	20413507
GO:0003700	Function	DNA-binding transcription factor activity	NAS	8600444
GO:0005515	Function	Protein binding	IPI	16189514, 20148032, 21516116, 25416956, 29892012, 31515488, 32296183, 33961781
GO:0005576	Component	Extracellular region	IEA
GO:0005634	Component	Nucleus	IC	12411430
GO:0005634	Component	Nucleus	IDA	31429579
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	8289803
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005667	Component	Transcription regulator complex	ISS	20413507
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	ISS
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0031018	Process	Endocrine pancreas development	IEA
GO:0031018	Process	Endocrine pancreas development	ISS
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IDA	12411430
GO:0045893	Process	Positive regulation of DNA-templated transcription	IDA	20148032
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS	20413507
GO:0048469	Process	Cell maturation	IEA
GO:0048469	Process	Cell maturation	ISS	20413507
GO:0050796	Process	Regulation of insulin secretion	IEA
GO:0050796	Process	Regulation of insulin secretion	ISS	20413507
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	ISS	20413507
GO:0060285	Process	Cilium-dependent cell motility	IEA
GO:0060285	Process	Cilium-dependent cell motility	ISS
GO:0060287	Process	Epithelial cilium movement involved in determination of left/right asymmetry	IEA
GO:0060287	Process	Epithelial cilium movement involved in determination of left/right asymmetry	ISS
GO:0072560	Process	Type B pancreatic cell maturation	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:2000078	Process	Positive regulation of type B pancreatic cell development	IEA
GO:2000078	Process	Positive regulation of type B pancreatic cell development	ISS	20413507

Other IDs

• MIM: 601337
• HGNC: 9984
• e!Ensembl: ENSG00000080298

Protein

• UniProt ID: P48380
• Protein name: Transcription factor RFX3 (Regulatory factor X 3)
• Protein function: Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for t
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04589	RFX1_trans_act	14 → 138	RFX1 transcription activation region	Family
  PF02257	RFX_DNA_binding	181 → 258	RFX DNA-binding domain	Domain

• Sequence:

  MQTSETGSDTGSTVTLQTSVASQAAVPTQVVQQVPVQQQVQQVQTVQQVQHVYPAQVQYV
  EGSDTVYTNGAIRTTTYPYTETQMYSQNTGGNYFDTQGSSAQVTTVVSSHSMVGTGGIQM
  GVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRASPATIEMAIETLQKSDGLSTHRSSLL
  NSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRR
  LGTRGNSKYHYYGIRVKPDSPLNRLQEDMQYMAMRQQPMQQKQRYKPMQKVDGVADGFTG
  SGQQTGTSVEQTVIAQSQHHQQFLDASRALPEFGEVEISSLPDGTTFEDIKSLQSLYREH
  CEAILDVVVNLQFSLIEKLWQTFWRYSPSTPTDGTTITESSNLSEIESRLPKAKLITLCK
  HESILKWMCNCDHGMYQALVEILIPDVLRPIPSALTQAIRNFAKSLEGWLSNAMNNIPQR
  MIQTKVAAVSAFAQTLRRYTSLNHLAQAARAVLQNTSQINQMLSDLNRVDFANVQEQASW
  VCQCDDNMVQRLETDFKMTLQQQSTLEQWAAWLDNVMMQALKPYEGRPSFPKAARQFLLK
  WSFYSSMVIRDLTLRSAASFGSFHLIRLLYDEYMFYLVEHRVAQATGETPIAVMGEFGDL
  NAVSPGNLDKDEGSEVESEMDEELDDSSEPQAKREKTELSQAFPVGCMQPVLETGVQPSL
  LNPIHSEHIVTSTQTIRQCSATGNTYTAV

• Sequence length: 749

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Developmental disorder	Likely pathogenic	rs2489274630	RCV003127293	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic	rs2131116061	RCV001375031	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RFX3-associated neurodevelopmental disorder	Pathogenic	rs2489070185	RCV002294580	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RFX3-related disorder	Likely pathogenic	rs2489684511	RCV003391393	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Attention deficit hyperactivity disorder	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
ATYPICAL FEMORAL FRACTURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder	Uncertain significance	ClinVar GenCC	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DERMATOLOGIC DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RFX3-related intellectual disability	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKIN DISEASES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKIN DISEASES, GENETIC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	BEFREE	26071364		★☆☆☆☆ Found in Text Mining only
Arsenic Encephalopathy	Arsenic Encephalopathy	CTD_human_DG	16835338		★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	29740017	Associate	★☆☆☆☆ Found in Text Mining only
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	33658631	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	33658631	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ciliopathies	Ciliopathies	BEFREE	19671664		★☆☆☆☆ Found in Text Mining only
Dermatologic disorders	Dermatologic Disorders	CTD_human_DG	16835338		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ependymoma	Ependymoma	BEFREE	16825954		★☆☆☆☆ Found in Text Mining only
Epilepsies Myoclonic	Myoclonic epilepsy	Pubtator	29740017	Associate	★☆☆☆☆ Found in Text Mining only
Gout	Gout	Pubtator	25967671, 29879923	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	29740017	Associate	★☆☆☆☆ Found in Text Mining only
Heart Diseases	Heart disease	Pubtator	29740017	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	33658631	Associate	★☆☆☆☆ Found in Text Mining only
MERRF Syndrome	MERRF Syndrome	BEFREE	29740017		★☆☆☆☆ Found in Text Mining only
MERRF Syndrome	Myoclonic epilepsy with ragged red fibers	Pubtator	29740017	Associate	★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	31237926		★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	29740017		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	29740017		★☆☆☆☆ Found in Text Mining only
Sleep Initiation and Maintenance Disorders	Sleep Disorders	GWASCAT_DG	29520036		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	36045400	Stimulate	★☆☆☆☆ Found in Text Mining only