CYFIP1

cytoplasmic FMR1 interacting protein 1, the group of SCAR/WAVE complex

Basic information

Region (hg38): 15:22867051-22981063

Links

ENSG00000273749 ∙ NCBI:23191 ∙ OMIM:606322 ∙ HGNC:13759 ∙ Uniprot:Q7L576 ∙ 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 CYFIP1 gene.

• Inborn genetic diseases (45 variants)
• not provided (43 variants)
• 6 conditions (2 variants)
• CYFIP1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYFIP1 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				21	10	31
missense			49	2	4	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding					1	1
Total	0	0	49	23	15

Variants in CYFIP1

This is a list of pathogenic ClinVar variants found in the CYFIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-22870057-G-A		not specified	Uncertain significance (Oct 27, 2022)
15-22870093-C-T		not specified	Likely benign (Jun 16, 2023)
15-22870098-C-T		not specified	Uncertain significance (Jul 26, 2022)
15-22870120-T-C		not specified	Uncertain significance (Dec 21, 2023)
15-22870131-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-22870134-A-G		not specified	Uncertain significance (Aug 10, 2021)
15-22870187-C-T			Benign (Dec 31, 2019)
15-22872904-C-T		not specified	Uncertain significance (Nov 08, 2022)
15-22872970-T-A		not specified	Uncertain significance (Aug 13, 2021)
15-22873540-T-A		not specified	Uncertain significance (Oct 16, 2023)
15-22873570-A-G		not specified	Uncertain significance (Jan 30, 2024)
15-22873573-C-T		not specified	Uncertain significance (Nov 09, 2023)
15-22873574-G-A			Likely benign (Dec 31, 2019)
15-22873585-T-C		not specified	Uncertain significance (Jan 23, 2024)
15-22873604-A-G			Likely benign (Dec 13, 2017)
15-22873610-G-A			Likely benign (Dec 31, 2019)
15-22873638-C-A		not specified	Uncertain significance (Jun 16, 2023)
15-22873645-G-A		not specified	Uncertain significance (Aug 30, 2022)
15-22873665-A-G		not specified	Uncertain significance (Aug 16, 2022)
15-22873720-T-C		CYFIP1-related disorder	Uncertain significance (Oct 06, 2023)
15-22874544-C-T		CYFIP1-related disorder	Likely benign (Jan 20, 2021)
15-22874593-G-A		not specified	Uncertain significance (Jun 29, 2023)
15-22874595-G-A			Likely benign (May 12, 2018)
15-22874598-G-A			Benign/Likely benign (Jan 01, 2023)
15-22874625-G-A			Likely benign (Jun 06, 2018)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. In the CYFIP1-EIF4E-FMR1 complex this subunit is an adapter between EIF4E and FMR1. Promotes the translation repression activity of FMR1 in brain probably by mediating its association with EIF4E and mRNA (By similarity). Regulates formation of membrane ruffles and lamellipodia. Plays a role in axon outgrowth. Binds to F-actin but not to RNA. Part of the WAVE complex that regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. Regulator of epithelial morphogenesis. As component of the WAVE1 complex, required for BDNF-NTRK2 endocytic trafficking and signaling from early endosomes (By similarity). May act as an invasion suppressor in cancers. {ECO:0000250|UniProtKB:Q7TMB8, ECO:0000269|PubMed:16260607, ECO:0000269|PubMed:19524508, ECO:0000269|PubMed:21107423, ECO:0000269|PubMed:9417078}.
• Pathway: RNA transport - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Prader-Willi and Angelman Syndrome;G13 Signaling Pathway;Neutrophil degranulation;Signal Transduction;VEGFA-VEGFR2 Pathway;Fcgamma receptor (FCGR) dependent phagocytosis;TCR;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.520
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.99

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyfip1
• 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); embryo phenotype; 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)

Gene ontology

• Biological process: cell morphogenesis;regulation of translation;axon guidance;regulation of cell shape;Rac protein signal transduction;cell projection assembly;lamellipodium assembly;ruffle organization;cellular response to insulin stimulus;Fc-gamma receptor signaling pathway involved in phagocytosis;neutrophil degranulation;positive regulation of axon extension;vascular endothelial growth factor receptor signaling pathway;axon extension;cognition;positive regulation of neurotrophin TRK receptor signaling pathway;response to electrical stimulus;dendrite extension;modification of synaptic structure;regulation of translation at postsynapse, modulating synaptic transmission;positive regulation of dendrite development;positive regulation of ruffle assembly;negative regulation of synaptic vesicle recycling;regulation of modification of postsynaptic actin cytoskeleton;positive regulation of Arp2/3 complex-mediated actin nucleation
• Cellular component: ruffle;extracellular region;cytosol;mRNA cap binding complex;focal adhesion;lamellipodium;SCAR complex;filopodium tip;secretory granule lumen;specific granule lumen;neuron projection;neuronal cell body;terminal bouton;dendritic spine;dendritic growth cone;axonal growth cone;synapse;perinuclear region of cytoplasm;excitatory synapse;extracellular exosome;central region of growth cone;peripheral region of growth cone;tertiary granule lumen
• Molecular function: RNA 7-methylguanosine cap binding;protein binding;translation regulator activity;Rac GTPase binding;actin filament binding