RBFOX2

RNA binding fox-1 homolog 2, the group of RNA binding motif containing

Basic information

Region (hg38): 22:35738735-36028824

Previous symbols: [ "RBM9" ]

Links

ENSG00000100320 ∙ NCBI:23543 ∙ OMIM:612149 ∙ HGNC:9906 ∙ Uniprot:O43251 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBFOX2 gene.

• not provided (35 variants)
• Inborn genetic diseases (11 variants)
• Hypoplastic left heart syndrome (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBFOX2 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				10	5	15
missense			18	1	2	21
nonsense			1			1
start loss			1			1
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding				1	3	4
Total	1	0	21	12	10

Variants in RBFOX2

This is a list of pathogenic ClinVar variants found in the RBFOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-35744211-G-C			Likely benign (Apr 19, 2023)
22-35744254-A-G			Likely benign (Dec 20, 2018)
22-35745947-G-A		Inborn genetic diseases	Likely benign (Dec 20, 2023)
22-35745952-G-A		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
22-35745960-G-C			Uncertain significance (Jun 19, 2023)
22-35746474-C-A			Uncertain significance (Jan 04, 2024)
22-35746475-G-T		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
22-35746492-C-A			Uncertain significance (Jan 04, 2024)
22-35756109-A-G			Uncertain significance (Nov 26, 2022)
22-35756129-G-A			Likely benign (Mar 14, 2021)
22-35759881-C-T			Likely benign (Jul 12, 2022)
22-35759889-C-T		not specified	Uncertain significance (May 04, 2022)
22-35759892-G-C		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
22-35759920-C-T			Likely benign (Jun 01, 2022)
22-35759931-C-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
22-35760003-G-A		Inborn genetic diseases	Uncertain significance (May 11, 2022)
22-35761247-G-A			Uncertain significance (Nov 18, 2016)
22-35761250-CTGCTGCATCAT-C			Uncertain significance (Nov 28, 2022)
22-35761272-C-T			Benign (Jan 06, 2024)
22-35761299-T-C			Uncertain significance (Jul 24, 2023)
22-35761304-T-G			Benign (Jan 14, 2024)
22-35761428-C-T			Likely benign (Jun 10, 2023)
22-35765379-TTTACACAAGAATAAACACTCTTTCGAAGA-T			Likely benign (Apr 06, 2023)
22-35765404-G-A			Likely benign (May 28, 2022)
22-35765411-A-G			Benign (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBFOX2	protein_coding	protein_coding	ENST00000438146	14	289691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000981	124485	0	1	124486	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	144	262	0.550	0.0000161	2844
Missense in Polyphen		39	119.69	0.32584		1201
Synonymous	-0.278	109	105	1.03	0.00000720	935
Loss of Function	4.40	1	24.5	0.0408	0.00000121	293

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)	0.00000885	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Prevents binding of U2AF2 to the 3'-splice site. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis (By similarity). RNA-binding protein that seems to act as a coregulatory factor of ER-alpha. {ECO:0000250, ECO:0000269|PubMed:11875103}.
• Pathway: FGFR2 alternative splicing;Signaling by FGFR2;Signal Transduction;Signaling by FGFR;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.0922

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.467
• hipred: Y
• hipred_score: 0.725
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Rbfox2
• Phenotype: growth/size/body region phenotype; cellular phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: rbfox2
• Affected structure: skeletal muscle
• Phenotype tag: abnormal
• Phenotype quality: decreased force

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;nervous system development;RNA splicing;fibroblast growth factor receptor signaling pathway;regulation of definitive erythrocyte differentiation;RNA metabolic process;radial glia guided migration of Purkinje cell;intracellular estrogen receptor signaling pathway;regulation of cell population proliferation;negative regulation of transcription, DNA-templated;dendrite morphogenesis;neuromuscular process controlling balance
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: transcription corepressor activity;RNA binding;mRNA binding;protein binding;transcription factor binding