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

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
Self-limited epilepsy with centrotemporal spikes	Pathogenic	rs972548690	RCV000656060	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY	—	ClinGen, Disgenet, GenCC ClinGen, Disgenet, GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, ROLANDIC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Idiopathic generalized epilepsy	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MIGRAINE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RBFOX3-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	28598851	Inhibit	★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	Pubtator	29768357	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	27701470		★☆☆☆☆ Found in Text Mining only
Carcinoma Merkel Cell	Merkel cell carcinoma	Pubtator	34974547	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	27432190		★☆☆☆☆ Found in Text Mining only
Cleft Palate	Cleft palate	Pubtator	23512105	Associate	★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	24215932	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	24603971	Associate	★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	29509279, 35232286	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	24039908, 26619789, 27701470		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy Idiopathic Generalized	Epilepsy	Pubtator	24039908	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy Rolandic	Rolandic epilepsy	Pubtator	24039908	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy, Rolandic	Epilepsy	BEFREE	24039908		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy, Rolandic	Epilepsy	CLINVAR_DG	29358611		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioblastoma	Glioblastoma	Pubtator	28418837	Associate	★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington disease	Pubtator	25275533	Associate	★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	26619789, 27701470		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	28839469, 29689552		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	27432190	Inhibit	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	27432190		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29689552		★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	Pubtator	18641877	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	26558787	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28839469		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	25760045		★☆☆☆☆ Found in Text Mining only
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	27701470		★☆☆☆☆ Found in Text Mining only
Secondary malignant neoplasm of colon and/or rectum	Colorectal Neoplasms	GWASCAT_DG	30738427		★☆☆☆☆ Found in Text Mining only