RBFOX1

RNA binding fox-1 homolog 1, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 16:5239802-7713340

Links

ENSG00000078328 ∙ NCBI:54715 ∙ OMIM:605104 ∙ HGNC:18222 ∙ Uniprot:Q9NWB1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AD
• autism susceptibility 1 (Limited), mode of inheritance: Unknown
• neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBFOX1 gene.

• Idiopathic_generalized_epilepsy (474 variants)
• Inborn_genetic_diseases (77 variants)
• not_provided (42 variants)
• RBFOX1-related_disorder (19 variants)
• Self-limited_epilepsy_with_centrotemporal_spikes (4 variants)
• not_specified (4 variants)
• Neurodevelopmental_disorder (1 variants)
• Intellectual_disability,_autosomal_dominant_46 (1 variants)
• Intellectual_disability (1 variants)
• Colorectal_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBFOX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018723.4. 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			1	108	8	117
missense		3	199	6	1	209
nonsense			10			10
start loss						0
frameshift	1		5			6
splice donor/acceptor (+/-2bp)			4			4
Total	1	3	219	114	9

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBFOX1	protein_coding	protein_coding	ENST00000311745	13	1694246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125725	0	8	125733	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.196	271	280	0.967	0.0000185	2661
Missense in Polyphen		98	107.7	0.90995		1063
Synonymous	-3.41	175	126	1.39	0.0000101	858
Loss of Function	4.12	4	27.2	0.147	0.00000159	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000442	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis. {ECO:0000269|PubMed:16537540}.
• Pathway: MECP2 and Associated Rett Syndrome (Consensus)

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: 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

Zebrafish Information Network

• Gene name: rbfox1
• Affected structure: atrium
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;nervous system development;RNA splicing;RNA transport
• Cellular component: nucleus;cytoplasm;trans-Golgi network
• Molecular function: RNA binding;mRNA binding;protein binding;protein C-terminus binding