RBFOX3

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

Basic information

Region (hg38): 17:79089345-79611051

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
• epilepsy (Disputed Evidence), mode of inheritance: AD

ClinVar

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

• Idiopathic_generalized_epilepsy (305 variants)
• not_specified (39 variants)
• RBFOX3-related_disorder (13 variants)
• not_provided (9 variants)
• Self-limited_epilepsy_with_centrotemporal_spikes (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. These statistics are base on transcript: NM_001350451.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	84	3	91
missense			126	6	2	134
nonsense	1		2			3
start loss						0
frameshift			3			3
splice donor/acceptor (+/-2bp)			1			1
Total	1	0	136	90	5

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	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

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

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