RBFOX3

RNA binding fox-1 homolog 3, the group of RNA binding motif containing

Basic information

Region (hg38): 17:79089344-79611051

Links

ENSG00000167281 ∙ NCBI:146713 ∙ OMIM:616999 ∙ HGNC:27097 ∙ Uniprot:A6NFN3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBFOX3 gene.

• Idiopathic generalized epilepsy (245 variants)
• Inborn genetic diseases (13 variants)
• not provided (7 variants)
• not specified (1 variants)
• RBFOX3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBFOX3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	71	4	78
missense			85	3	2	90
nonsense						0
start loss						0
frameshift			1			1
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			8	10	3	21
non coding			2	50	4	56
Total	0	0	94	124	10

Variants in RBFOX3

This is a list of pathogenic ClinVar variants found in the RBFOX3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-79090888-A-G		Idiopathic generalized epilepsy	Uncertain significance (Jan 20, 2023)
17-79090897-A-T		Idiopathic generalized epilepsy	Likely benign (Aug 17, 2023)
17-79094433-C-T		Idiopathic generalized epilepsy	Likely benign (Nov 12, 2022)
17-79094434-G-A		Idiopathic generalized epilepsy	Likely benign (Dec 27, 2023)
17-79094435-G-A		Idiopathic generalized epilepsy	Likely benign (Jun 13, 2022)
17-79094438-C-T		Idiopathic generalized epilepsy	Likely benign (Dec 13, 2023)
17-79094442-G-T		Idiopathic generalized epilepsy	Likely benign (Dec 06, 2022)
17-79094445-C-T		Idiopathic generalized epilepsy	Uncertain significance (Aug 27, 2023)
17-79094460-A-C		Idiopathic generalized epilepsy	Uncertain significance (Jul 15, 2020)
17-79094461-A-G		Idiopathic generalized epilepsy	Uncertain significance (Aug 16, 2022)
17-79094466-G-A		Idiopathic generalized epilepsy	Likely benign (Dec 23, 2023)
17-79094470-G-A		Idiopathic generalized epilepsy	Uncertain significance (Jan 17, 2024)
17-79094472-C-T		Idiopathic generalized epilepsy	Likely benign (Jan 15, 2024)
17-79094473-G-A		Idiopathic generalized epilepsy	Uncertain significance (Jun 21, 2019)
17-79094475-C-T		Idiopathic generalized epilepsy	Likely benign (Oct 18, 2023)
17-79094476-G-A		Idiopathic generalized epilepsy	Uncertain significance (Jan 02, 2023)
17-79094477-C-T		Idiopathic generalized epilepsy	Uncertain significance (Dec 02, 2022)
17-79094484-G-A			Likely benign (Jun 19, 2018)
17-79094499-C-T		Idiopathic generalized epilepsy	Likely benign (Jan 25, 2024)
17-79094500-G-A		Idiopathic generalized epilepsy	Uncertain significance (Feb 04, 2022)
17-79094500-G-C		Idiopathic generalized epilepsy	Uncertain significance (Nov 22, 2022)
17-79094504-C-T		not specified	Uncertain significance (Nov 15, 2021)
17-79094505-G-A		Idiopathic generalized epilepsy	Likely benign (Oct 14, 2022)
17-79094514-G-A		Idiopathic generalized epilepsy	Likely benign (Dec 04, 2021)
17-79094523-G-A		Idiopathic generalized epilepsy	Uncertain significance (Mar 03, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBFOX3	protein_coding	protein_coding	ENST00000415831	10	528124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00215	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	87	163	0.532	0.0000111	1963
Missense in Polyphen		23	69.595	0.33048		770
Synonymous	-0.647	77	70.1	1.10	0.00000559	628
Loss of Function	3.93	0	18.0	0.00	9.93e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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). {ECO:0000250|UniProtKB:Q8BIF2}.

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• ghis: 0.706

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rbfox3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;nervous system development;RNA splicing
• Cellular component: nucleus;cytoplasm;perikaryon
• Molecular function: DNA binding;mRNA binding