RBFOX1

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

Basic information

Region (hg38): 16:5239801-7713340

Links

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

Phenotypes

GenCC

Source: genCC

• autism susceptibility 1 (Limited), mode of inheritance: Unknown
• epilepsy (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 (366 variants)
• not provided (26 variants)
• Inborn genetic diseases (25 variants)
• not specified (4 variants)
• RBFOX1-related condition (3 variants)
• Childhood epilepsy with centrotemporal spikes (3 variants)
• Intellectual disability (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.

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			2	89	9	100
missense		2	164	9	3	178
nonsense			10			10
start loss						0
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)			2			2
splice region			14	17	4	35
non coding			6	56	6	68
Total	0	2	189	154	18

Variants in RBFOX1

This is a list of pathogenic ClinVar variants found in the RBFOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-6019890-C-G		not specified	Likely benign (Mar 16, 2020)
16-6316983-TTTC-T			Benign (Nov 30, 2017)
16-6316989-C-T		RBFOX1-related disorder	Likely benign (Apr 15, 2021)
16-6483548-C-A		Idiopathic generalized epilepsy	Benign (May 28, 2019)
16-6654644-C-T		RBFOX1-related disorder	Likely benign (May 21, 2020)
16-7333005-C-G		Idiopathic generalized epilepsy	Uncertain significance (Feb 08, 2022)
16-7333010-G-A		Idiopathic generalized epilepsy	Likely benign (Dec 11, 2023)
16-7333012-C-G		Idiopathic generalized epilepsy • Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 14, 2023)
16-7333019-A-T		Idiopathic generalized epilepsy	Likely benign (Aug 09, 2022)
16-7333023-C-G		Idiopathic generalized epilepsy	Uncertain significance (May 27, 2022)
16-7333025-C-T		Idiopathic generalized epilepsy	Likely benign (Nov 20, 2019)
16-7333026-C-T		Idiopathic generalized epilepsy	Likely benign (Jul 26, 2022)
16-7333033-C-A		Idiopathic generalized epilepsy	Uncertain significance (Apr 24, 2023)
16-7333036-A-G		Idiopathic generalized epilepsy	Uncertain significance (Jul 21, 2022)
16-7333036-A-T		Idiopathic generalized epilepsy	Uncertain significance (Feb 15, 2021)
16-7333037-T-C		Idiopathic generalized epilepsy	Likely benign (Aug 23, 2022)
16-7333039-G-T		Idiopathic generalized epilepsy	Uncertain significance (Oct 13, 2022)
16-7333040-C-T		Idiopathic generalized epilepsy	Likely benign (Jul 14, 2023)
16-7333041-G-A		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
16-7333047-A-G		Idiopathic generalized epilepsy • Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
16-7333052-T-C		Idiopathic generalized epilepsy	Likely benign (Sep 22, 2023)
16-7333055-A-G		Idiopathic generalized epilepsy	Likely benign (Jul 25, 2021)
16-7333056-C-T		Idiopathic generalized epilepsy	Uncertain significance (Dec 01, 2023)
16-7333057-C-G		Idiopathic generalized epilepsy	Uncertain significance (Jun 06, 2021)
16-7333057-C-T		Idiopathic generalized epilepsy • Inborn genetic diseases	Uncertain significance (Jan 17, 2024)

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
0.953	0.0474	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

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.748
• ghis: 0.536

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

Mouse Genome Informatics

• Gene name: Rbfox1
• 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); 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

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