CYFIP1

gene
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Also known as KIAA0068P140SRA-1SHYC

Summary

CYFIP1 (cytoplasmic FMR1 interacting protein 1, HGNC:13759) is a protein-coding gene on chromosome 15q11.2, encoding Cytoplasmic FMR1-interacting protein 1 (Q7L576). Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. It is a selective cancer dependency (DepMap: 11.8% of cell lines).

This gene encodes a protein that regulates cytoskeletal dynamics and protein translation. The encoded protein is a component of the WAVE regulatory complex (WRC), which promotes actin polymerization. This protein also interacts with the synaptic functional regulator FMR1 protein and translation initiation factor 4E to inhibit protein translation. A large chromosomal deletion including this gene is associated with increased risk of schizophrenia and epilepsy in human patients. Reduced expression of this gene has been observed in various human cancers and the encoded protein may inhibit tumor invasion.

Source: NCBI Gene 23191 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 455 total — 80 pathogenic, 8 likely-pathogenic
  • Phenotypes (HPO): 4
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 11.8% of screened cell lines
  • MANE Select transcript: NM_014608

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13759
Approved symbolCYFIP1
Namecytoplasmic FMR1 interacting protein 1
Location15q11.2
Locus typegene with protein product
StatusApproved
AliasesKIAA0068, P140SRA-1, SHYC
Ensembl geneENSG00000273749
Ensembl biotypeprotein_coding
OMIM606322
Entrez23191

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 33 protein_coding, 5 retained_intron, 2 nonsense_mediated_decay

ENST00000557890, ENST00000561263, ENST00000610365, ENST00000611832, ENST00000612288, ENST00000613006, ENST00000617556, ENST00000617928, ENST00000619037, ENST00000619290, ENST00000619348, ENST00000621036, ENST00000621105, ENST00000622576, ENST00000900858, ENST00000900859, ENST00000900860, ENST00000900861, ENST00000900862, ENST00000900863, ENST00000900864, ENST00000900865, ENST00000900866, ENST00000900867, ENST00000900868, ENST00000900869, ENST00000900870, ENST00000900871, ENST00000900872, ENST00000919971, ENST00000919972, ENST00000919973, ENST00000919974, ENST00000919975, ENST00000945409, ENST00000945410, ENST00000945411, ENST00000945412, ENST00000945413, ENST00000945414

RefSeq mRNA: 10 — MANE Select: NM_014608 NM_001033028, NM_001287810, NM_001324119, NM_001324120, NM_001324122, NM_001324123, NM_001324124, NM_001324125, NM_001324126, NM_014608

CCDS: CCDS73695, CCDS73696

Canonical transcript exons

ENST00000617928 — 31 exons

ExonStartEnd
ENSE000035080872287349122873729
ENSE000036877512287455022874644
ENSE000037135432294700322947092
ENSE000037166532291778822917935
ENSE000037219532294317322943354
ENSE000037224062287519922875271
ENSE000037237172290919422909313
ENSE000037238662293222322932340
ENSE000037316212298028722980368
ENSE000037321482292598222926107
ENSE000037327972291073722910813
ENSE000037335262293710422937208
ENSE000037346512293941122939507
ENSE000037363602292790622928028
ENSE000037383382291647722916630
ENSE000037384722290370622903905
ENSE000037427192294486222944939
ENSE000037436422291472622914882
ENSE000037441212287282522872972
ENSE000037443692294455822944659
ENSE000037452332291217922912275
ENSE000037460122288184622881936
ENSE000037467092293380222933893
ENSE000037506532293919222939320
ENSE000037509202291869222918858
ENSE000037509582289289022892977
ENSE000037514692288286822883011
ENSE000037518912287991322880043
ENSE000037520062286705222870192
ENSE000037533172291052022910628
ENSE000037548252294716922947291

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.7736 / max 428.8543, expressed in 1797 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
14898445.98841795
1489832.51321359
1489850.2604133
1489810.01162

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
esophagus squamous epitheliumUBERON:000692099.23gold quality
germinal epithelium of ovaryUBERON:000130499.03gold quality
epithelium of esophagusUBERON:000197699.03gold quality
gingival epitheliumUBERON:000194998.90gold quality
parietal pleuraUBERON:000240098.89gold quality
visceral pleuraUBERON:000240198.89gold quality
pleuraUBERON:000097798.76gold quality
gingivaUBERON:000182898.71gold quality
squamous epitheliumUBERON:000691498.58gold quality
oral cavityUBERON:000016798.42gold quality
tibiaUBERON:000097998.37gold quality
tongue squamous epitheliumUBERON:000691998.21gold quality
palpebral conjunctivaUBERON:000181298.20gold quality
skin of hipUBERON:000155498.07gold quality
colonic mucosaUBERON:000031797.95gold quality
mucosa of sigmoid colonUBERON:000499397.95gold quality
upper leg skinUBERON:000426297.69gold quality
caput epididymisUBERON:000435897.59gold quality
ileal mucosaUBERON:000033197.49gold quality
mammalian vulvaUBERON:000099797.45gold quality
metanephric glomerulusUBERON:000473697.43gold quality
epithelial cell of pancreasCL:000008397.41gold quality
epithelium of mammary glandUBERON:000324497.40gold quality
renal glomerulusUBERON:000007497.32gold quality
pericardiumUBERON:000240797.31gold quality
layer of synovial tissueUBERON:000761697.26gold quality
seminal vesicleUBERON:000099897.25gold quality
mammary ductUBERON:000176597.24gold quality
cauda epididymisUBERON:000436097.22gold quality
penisUBERON:000098997.15gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-35yes30.61
E-HCAD-25yes16.69
E-CURD-112yes14.79
E-ANND-3yes14.01
E-GEOD-111727no617.37
E-MTAB-2983no397.34
E-CURD-10no184.17

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EOMES

miRNA regulators (miRDB)

29 targeting CYFIP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-8485100.0077.574731
HSA-MIR-340-5P100.0072.504437
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-590-3P99.9674.346478
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-806799.8669.592260
HSA-MIR-442299.7272.072908
HSA-MIR-570099.6469.882280
HSA-MIR-4756-3P99.6266.301319
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-582-5P99.4770.792635
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-133A-5P99.2869.13941
HSA-MIR-196A-3P99.1967.341204
HSA-MIR-806599.1970.381289
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-1304-3P98.2966.441207
HSA-MIR-4659A-5P98.0366.42819
HSA-MIR-4659B-5P98.0366.84979
HSA-MIR-1285-5P98.0168.71779
HSA-MIR-124397.0765.44719
HSA-MIR-6839-5P96.7468.291088
HSA-MIR-4695-3P96.7167.21836
HSA-MIR-378J96.4466.201020
HSA-MIR-2114-5P96.0064.56617
HSA-MIR-573988.0963.94123

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 28)

  • located in the genomic domain between break points 1 and 2 on chromosome 15, of the Prader-Willi/Angelman syndromes (PMID:14508708)
  • CRMP-2 transports the Sra-1/WAVE1 complex to axons in a kinesin-1-dependent manner and thereby regulates axon outgrowth and formation (PMID:16260607)
  • quantitated mRNA levels of NIPA2, NIPA2,l CYFIP1, and GCP5 in Prader-Willi syndrome and correlated levels with psychological and behavior scales (PMID:16982806)
  • Study found that Cyfip1, a subunit of the WAVE complex, which regulates cytoskeletal dynamics, is commonly deleted in human epithelial cancers. (PMID:19524508)
  • Protein complexes containing CYFIP/Sra/PIR121 coordinate Arf1 and Rac1 signalling during clathrin-AP-1-coated carrier biogenesis at the trans-golgi network. (PMID:20228810)
  • An imbalance of specific isoforms of CYFIP1, an FMRP interaction partner, and CAMK4, a transcriptional regulator of the FMRP gene, modulates risk for autism spectrum disorders. (PMID:24442360)
  • haploinsufficiency causes cell polarity defects via WAVE complex destabilization; genetic polymorphism is associated with schizophrenia (PMID:24996170)
  • This study confirmed that CYFIP2 were altered in postsynaptic density in patient with schizophrenia. (PMID:25048004)
  • Data confirm that CYFIP1 is upregulated in transformed lymphoblastoid cell lines and demonstrate its upregulation in the post-mortem brain from 15q11-13 duplication patients for the first time (PMID:25311365)
  • Both mRNA and protein expression levels of Cyfip1 were significantly lower in ALL patients. (PMID:26779626)
  • Reduced CYFIP1 in human neural progenitors results in dysregulation of schizophrenia and epilepsy gene networks. (PMID:26824476)
  • Hippocampal synapses with reduced Cyfip1 are larger and release neurotransmitter more rapidly. (PMID:26843638)
  • rs4778298, a common variant at CYFIP1 is associated with inter-individual variation in surface area across the left supramarginal gyrus. (PMID:27351196)
  • we show that stapled peptides targeting the interface between NCKAP1 and CYFIP1 destabilize the WASF3 complex… thereby suppressing invasion and metastasis of breast cancer cells. (PMID:27432794)
  • The studies suggest that MNK-eiF4E axis controls the translation of specific mRNAs in cancer metastasis and neuronal synaptic plasticity by a novel mechanism involving the regulation of the translational repressor, CYFIP1. (Review) (PMID:27527252)
  • Surprisingly, Rac1 is not located at the binding site on the Sra1 subunit of the WAVE regulatory complex previously identified by mutagenesis and biochemical data. Rather, it binds to a distinct, conserved site on the opposite end of Sra1. (PMID:28949297)
  • The expression level of Cyfip1 mRNA was significantly lower in patients with nasopharyngeal carcinoma than in the control samples. Low expression level of Cyfip1 mRNA was significantly associated with invasive range, lymph node metastasis, distant metastases, and clinical stage. (PMID:29534591)
  • A novel regulatory mechanism of p53 in early onset breast cancer progression through GAS7-CYFIP1-mediated signaling pathways. (PMID:29706651)
  • The current study provides further supports for contribution of CYFIP1/2 in the pathogenesis of autism spectrum disorder (ASD) and potentiates it as a peripheral marker for ASD diagnosis. (PMID:29752658)
  • CYFIP1 gene expression was upregulated in the blood of epileptic patients. (PMID:29992499)
  • this research identifies the behavioral and molecular consequences of CYFIP1 overexpression. (PMID:31198525)
  • The human studies revealed profound deficits in grammatical reasoning, arithmetic reasoning, and working memory in BP1-BP2 (TUBGCP5, CYFIP1, NIPA2, and NIPA1) deletion carriers. (PMID:31202490)
  • Evidence for a Contribution of the Nlgn3/Cyfip1/Fmr1 Pathway in the Pathophysiology of Autism Spectrum Disorders. (PMID:31705895)
  • Haploinsufficiency of the schizophrenia and autism risk gene Cyfip1 causes abnormal postnatal hippocampal neurogenesis through microglial and Arp2/3 mediated actin dependent mechanisms. (PMID:34031371)
  • Cytoplasmic FMR1 interacting protein (CYFIP) family members and their function in neural development and disorders. (PMID:34327661)
  • Loss of Function in the Neurodevelopmental Disease and Schizophrenia-Associated Gene CYFIP1 in Human Microglia-like Cells Supports a Functional Role in Synaptic Engulfment. (PMID:37573007)
  • Different dysregulations of CYFIP1 and CYFIP2 in distinct types of dementia. (PMID:38128786)
  • Integrated machine learning-driven disulfidptosis profiling: CYFIP1 and EMILIN1 as therapeutic nodes in neuroblastoma. (PMID:38427078)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocyfip1ENSDARG00000044345
mus_musculusCyfip1ENSMUSG00000030447
rattus_norvegicusCyfip1ENSRNOG00000011945
drosophila_melanogasterCyfipFBGN0038320
caenorhabditis_elegansWBGENE00001579

Paralogs (1): CYFIP2 (ENSG00000055163)

Protein

Protein identifiers

Cytoplasmic FMR1-interacting protein 1Q7L576 (reviewed: Q7L576)

Alternative names: Specifically Rac1-associated protein 1, p140sra-1

All UniProt accessions (7): A0A087WU52, A0A087WVZ5, Q7L576, A0A087WWL1, A0A087WWY5, A0A087WZ89, H0YL50

UniProt curated annotations — full annotation on UniProt →

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. 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. May act as an invasion suppressor in cancers.

Subunit / interactions. Component of the WAVE1 complex composed of ABI2, CYFIP1 or CYFIP2, BRK1, NCKAP1 and WASF1/WAVE1. Within the complex, a heterodimer containing NCKAP1 and CYFIP1 interacts with a heterotrimer formed by WAVE1, ABI2 and BRK1. Component of the CYFIP1-EIF4E-FMR1 complex which is composed of CYFIP, EIF4E and FMR1. Interacts with FMR1 but does not bind to related proteins FXR1 or FXR2. Interaction with EIF4E stimulates FMR1 binding. Component of the WAVE2 complex composed of ABI1, CYFIP1/SRA1, NCKAP1/NAP1 (NCKAP1l/HEM1 in hematopoietic cells) and WASF2/WAVE2. Interacts with the active GTP-bound form of RAC1. Interacts through its C-terminus with the C-terminus of DPYSL2/CRMP2 which is necessary for DPYSL2-induced axon outgrowth. Interacts with NYAP1, NYAP2 and MYO16. Interacts with TMEM108 (via N-terminus); the interaction associates TMEM108 with the WAVE1 complex.

Subcellular location. Cytoplasm. Perinuclear region. Cell projection. Lamellipodium. Ruffle. Synapse. Synaptosome.

Miscellaneous. Breakpoint hotspot for the Prader-Willi/Angelman syndromes and may be implicated in autism. Commonly altered in tumors.

Similarity. Belongs to the CYFIP family.

Isoforms (3)

UniProt IDNamesCanonical?
Q7L576-11, 3yes
Q7L576-22, 4
Q7L576-33, 5

RefSeq proteins (10): NP_001028200, NP_001274739, NP_001311048, NP_001311049, NP_001311051, NP_001311052, NP_001311053, NP_001311054, NP_001311055, NP_055423* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008081Cytoplasmic_FMR1-intFamily
IPR009828CYRIA/CYRIB_Rac1-bdDomain

Pfam: PF05994, PF07159

UniProt features (119 total): helix 68, strand 19, turn 10, mutagenesis site 9, sequence conflict 4, splice variant 3, sequence variant 3, modified residue 2, chain 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
3P8CX-RAY DIFFRACTION2.29
4N78X-RAY DIFFRACTION2.43
7USCELECTRON MICROSCOPY3
7USDELECTRON MICROSCOPY3
7USEELECTRON MICROSCOPY3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7L576-F190.240.72

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 583, 1234

Mutagenesis-validated functional residues (9):

PositionPhenotype
190reduced interaction with rac1.
434reduced interaction with rac1; when associated with a-626.
626reduced interaction with rac1; when associated with k-434.
632reduced interaction with rac1.
697constitutive induction of the formation of actin filaments; when associated with d-704.
704constitutive induction of the formation of actin filaments; when associated with d-697.
841constitutive induction of the formation of actin filaments; when associated with 844-a-a-845.
844–845constitutive induction of the formation of actin filaments; when associated with a-841.
179reduced interaction with rac1.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

IDPathway
R-HSA-2029482Regulation of actin dynamics for phagocytic cup formation
R-HSA-4420097VEGFA-VEGFR2 Pathway
R-HSA-5663213RHO GTPases Activate WASPs and WAVEs
R-HSA-6798695Neutrophil degranulation
R-HSA-9013149RAC1 GTPase cycle
R-HSA-9013404RAC2 GTPase cycle
R-HSA-9013408RHOG GTPase cycle
R-HSA-9013423RAC3 GTPase cycle
R-HSA-9664422FCGR3A-mediated phagocytosis

MSigDB gene sets: 385 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_COGNITION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_NEURON_PROJECTION_EXTENSION, GOBP_REGULATION_OF_ACTIN_NUCLEATION, GOCC_SECRETORY_GRANULE, GOBP_GROWTH, GOBP_NEUROGENESIS, GOCC_RUFFLE, GOMF_GTPASE_BINDING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS

GO Biological Process (20): cell morphogenesis (GO:0000902), regulation of translation (GO:0006417), axon guidance (GO:0007411), regulation of cell shape (GO:0008360), positive regulation of lamellipodium assembly (GO:0010592), Rac protein signal transduction (GO:0016601), lamellipodium assembly (GO:0030032), regulation of actin filament polymerization (GO:0030833), ruffle organization (GO:0031529), axon extension (GO:0048675), cognition (GO:0050890), positive regulation of neurotrophin TRK receptor signaling pathway (GO:0051388), dendrite extension (GO:0097484), regulation of translation at postsynapse, modulating synaptic transmission (GO:0099578), regulation of modification of postsynaptic actin cytoskeleton (GO:1905274), positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601), nervous system development (GO:0007399), negative regulation of translation (GO:0017148), cell differentiation (GO:0030154), neuron projection development (GO:0031175)

GO Molecular Function (6): RNA 7-methylguanosine cap binding (GO:0000340), translation repressor activity (GO:0030371), small GTPase binding (GO:0031267), actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (17): ruffle (GO:0001726), extracellular region (GO:0005576), cytosol (GO:0005829), focal adhesion (GO:0005925), lamellipodium (GO:0030027), SCAR complex (GO:0031209), secretory granule lumen (GO:0034774), specific granule lumen (GO:0035580), neuron projection (GO:0043005), synapse (GO:0045202), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), postsynapse (GO:0098794), tertiary granule lumen (GO:1904724), cytoplasm (GO:0005737), cell leading edge (GO:0031252), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
RHO GTPase cycle4
Fcgamma receptor (FCGR) dependent phagocytosis1
Signaling by VEGF1
RHO GTPase Effectors1
Innate Immune System1
Leishmania phagocytosis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure7
translation3
plasma membrane bounded cell projection3
cytoplasm3
axonogenesis2
plasma membrane bounded cell projection organization2
neuron projection extension2
cell leading edge2
anatomical structure morphogenesis1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
neuron projection guidance1
regulation of cell morphogenesis1
regulation of biological quality1
regulation of lamellipodium assembly1
lamellipodium assembly1
positive regulation of plasma membrane bounded cell projection assembly1
positive regulation of lamellipodium organization1
small GTPase-mediated signal transduction1
lamellipodium organization1
plasma membrane bounded cell projection assembly1
regulation of actin polymerization or depolymerization1
actin filament polymerization1
regulation of protein polymerization1
nervous system process1
positive regulation of signal transduction1
neurotrophin TRK receptor signaling pathway1
regulation of neurotrophin TRK receptor signaling pathway1
chemical synaptic transmission1
postsynapse1
postsynaptic modulation of chemical synaptic transmission1
regulation of translation at synapse, modulating synaptic transmission1
regulation of translation at postsynapse1
modification of postsynaptic actin cytoskeleton1
regulation of modification of postsynaptic structure1
Arp2/3 complex-mediated actin nucleation1
regulation of Arp2/3 complex-mediated actin nucleation1
positive regulation of actin nucleation1
system development1
regulation of translation1

Protein interactions and networks

STRING

1668 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYFIP1NCKAP1Q9Y2A7998
CYFIP1FMR1Q06787998
CYFIP1BRK1Q8WUW1998
CYFIP1FXR2P51116997
CYFIP1ABI1Q8IZP0997
CYFIP1ABI2Q9NYB9996
CYFIP1FXR1P51114996
CYFIP1NCKAP1LP55160995
CYFIP1WASF1Q92558995
CYFIP1EIF4EP06730988
CYFIP1WASF2Q9Y6W5981
CYFIP1NIPA2Q8N8Q9973
CYFIP1TUBGCP5Q96RT8973
CYFIP1NIPA1Q7RTP0965
CYFIP1ABI3Q9P2A4963

IntAct

218 interactions, top by confidence:

ABTypeScore
NCKAP1CYFIP1psi-mi:“MI:0915”(physical association)0.900
CYFIP1NCKAP1psi-mi:“MI:0407”(direct interaction)0.900
CYFIP1NCKAP1psi-mi:“MI:0915”(physical association)0.900
EIF4Epsi-mi:“MI:0914”(association)0.880
ABI2CYFIP1psi-mi:“MI:0915”(physical association)0.870
BAIAP2YWHAQpsi-mi:“MI:0914”(association)0.740
BRK1HSBP1psi-mi:“MI:0914”(association)0.740
CYFIP1ABI1psi-mi:“MI:0915”(physical association)0.740
NCKAP1YWHAHpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
IKBIPSNAPINpsi-mi:“MI:0914”(association)0.670
NCK2SH3PXD2Bpsi-mi:“MI:0914”(association)0.640
WASF1CYFIP1psi-mi:“MI:0914”(association)0.640
BRK1CYFIP1psi-mi:“MI:0914”(association)0.640

BioGRID (270): CYFIP1 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), CYFIP1 (Affinity Capture-MS), BZW2 (Co-fractionation), CYFIP1 (Co-fractionation), CYFIP1 (Co-fractionation), CYFIP1 (Co-fractionation), CYFIP1 (Co-fractionation), CYFIP1 (Co-fractionation), CYFIP1 (Co-fractionation), FNBP1L (Co-fractionation), TRIP10 (Co-fractionation)

ESM2 similar proteins: A1CGW7, A1CXW3, A1Z7L1, A7RU46, B0S6R1, F1QJX5, F1QN74, F6WXT2, O44518, P28660, P55160, P55161, P55162, P55163, Q0CL68, Q16X15, Q23658, Q24134, Q299G2, Q2UG94, Q4WNQ6, Q54IR8, Q54R74, Q5R414, Q5S2C3, Q5SQX6, Q5U430, Q5XHG1, Q60PC0, Q640K3, Q6GQD1, Q6PFJ7, Q6PI53, Q6UK63, Q6ZBH9, Q7L576, Q7Q6D9, Q7TMB8, Q869Q3, Q8IQV9

Diamond homologs: O44518, Q299G2, Q5R414, Q5SQX6, Q6GQD1, Q6UK63, Q7L576, Q7TMB8, Q90YM8, Q96F07, Q9VF87, Q5S2C3

SIGNOR signaling

3 interactions.

AEffectBMechanism
CYFIP1“form complex”“WRC complex”binding
CYFIP1“up-regulates activity”NHSbinding
CYFIP1“form complex”“WAVE complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 168 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
RHO GTPases Activate WASPs and WAVEs1542.9×8e-19
Activation of BAD and translocation to mitochondria534.3×8e-06
Parasite infection1031.2×5e-11
Leishmania phagocytosis1031.2×5e-11
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex530.3×1e-05
SARS-CoV-1 targets host intracellular signalling and regulatory pathways530.3×1e-05
FCGR3A-mediated phagocytosis1627.0×7e-17
Regulation of actin dynamics for phagocytic cup formation1626.6×7e-17

GO biological processes:

GO termPartnersFoldFDR
Rac protein signal transduction727.3×3e-06
positive regulation of lamellipodium assembly520.9×6e-04
lamellipodium assembly618.5×2e-04
positive regulation of actin filament polymerization716.1×1e-04
cell motility513.9×2e-03
neuron projection morphogenesis713.4×2e-04
small GTPase-mediated signal transduction67.6×9e-03
intracellular protein localization107.3×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

455 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic80
Likely pathogenic8
Uncertain significance233
Likely benign34
Benign37

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1012382GRCh37/hg19 15q11.2-12(chr15:22833525-27193380)x4Pathogenic
1175875GRCh37/hg19 15q11.2(chr15:22833525-23264865)x1Pathogenic
1328464GRCh37/hg19 15q11.2(chr15:22832874-23223352)x1Pathogenic
1330198GRCh37/hg19 15q11.2(chr15:22743127-23246000)x1Pathogenic
1339977GRCh37/hg19 15q11.2(chr15:22770421-23625677)x1Pathogenic
1340320GRCh37/hg19 15q11.2(chr15:22770422-23195725)x1Pathogenic
146208GRCh38/hg38 15q11.2(chr15:22787972-23107440)x1Pathogenic
1694765GRCh37/hg19 15q11.2(chr15:22833525-23265556)x1Pathogenic
1705939GRCh37/hg19 15q11.2(chr15:22770421-25648680)x1Pathogenic
1707411Single allelePathogenic
1708197GRCh37/hg19 15q11.2(chr15:22770421-23288487)x3Pathogenic
1708267Single allelePathogenic
1711393GRCh37/hg19 15q11.2(chr15:22736246-23265381)x1Pathogenic
1808466GRCh37/hg19 15q11.2(chr15:22770422-23082442)x1Pathogenic
1808506GRCh37/hg19 15q11.2(chr15:22770422-23082328)x1Pathogenic
1879312GRCh37/hg19 15q11.2(chr15:22833525-23262343)x1Pathogenic
1879313GRCh37/hg19 15q11.2(chr15:22833525-23264190)x1Pathogenic
2498628GRCh37/hg19 15q11.2(chr15:22070540-23262343)x1Pathogenic
2506528GRCh37/hg19 15q11.2(chr15:22833525-23412276)Pathogenic
252972GRCh37/hg19 15q11.2(chr15:22427966-23226254)x1Pathogenic
2570914GRCh37/hg19 15q11.2(chr15:22833499-23577516)x1Pathogenic
2570915GRCh37/hg19 15q11.2(chr15:22833525-23412276)x1Pathogenic
2574676GRCh37/hg19 15q11.2(chr15:22770421-23282799)Pathogenic
2574691GRCh37/hg19 15q11.2(chr15:22770421-23195725)Pathogenic
2580327GRCh37/hg19 15q11.2(chr15:22744149-23246340)x1Pathogenic
2663903GRCh38/hg38 15q11.2(chr15:22542702-23121344)x1Pathogenic
2671614Single allelePathogenic
2685502GRCh37/hg19 15q11.2(chr15:22770422-23679133)x1Pathogenic
3024383GRCh38/hg38 15q11.2(chr15:22633497-23084434)Pathogenic
3024585GRCh37/hg19 15q11.2(chr15:22757538-23411062)x1Pathogenic

SpliceAI

6245 predictions. Top by Δscore:

VariantEffectΔscore
15:22870191:G:GGacceptor_gain1.0000
15:22870191:GCC:Gacceptor_gain1.0000
15:22870192:A:AGacceptor_gain1.0000
15:22870199:T:TAacceptor_gain1.0000
15:22872842:A:Gdonor_gain1.0000
15:22872971:GGCA:Gacceptor_gain1.0000
15:22873488:G:GGdonor_gain1.0000
15:22873490:GA:Gdonor_gain1.0000
15:22873493:GTCGA:Gdonor_gain1.0000
15:22874643:G:GGacceptor_gain1.0000
15:22874644:A:AGacceptor_gain1.0000
15:22875195:T:Gdonor_loss1.0000
15:22875196:G:Tdonor_loss1.0000
15:22875197:GGT:Gdonor_loss1.0000
15:22875198:AGG:Adonor_loss1.0000
15:22875199:AAGG:Adonor_loss1.0000
15:22875270:G:Cacceptor_loss1.0000
15:22875270:G:GAacceptor_gain1.0000
15:22875270:GT:Gacceptor_gain1.0000
15:22875270:GTCT:Gacceptor_gain1.0000
15:22875271:A:AGacceptor_gain1.0000
15:22875273:CTA:Cacceptor_loss1.0000
15:22875274:TCTA:Tacceptor_loss1.0000
15:22879910:G:Adonor_loss1.0000
15:22879910:G:GGdonor_gain1.0000
15:22879911:GG:Gdonor_gain1.0000
15:22879912:TG:Tdonor_gain1.0000
15:22879912:TGG:Tdonor_loss1.0000
15:22879913:CTG:Cdonor_gain1.0000
15:22879914:CCTG:Cdonor_gain1.0000

AlphaMissense

8315 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:22872956:C:AG1156W1.000
15:22872961:C:AG1154V1.000
15:22872961:C:TG1154D1.000
15:22873544:A:CS1132R1.000
15:22873544:A:TS1132R1.000
15:22873546:T:GS1132R1.000
15:22873549:A:GW1131R1.000
15:22873549:A:TW1131R1.000
15:22875249:A:GL1022P1.000
15:22879949:G:CN1002K1.000
15:22879949:G:TN1002K1.000
15:22879953:C:TG1001E1.000
15:22879954:C:AG1001W1.000
15:22879954:C:GG1001R1.000
15:22879954:C:TG1001R1.000
15:22879962:C:GR998P1.000
15:22880016:A:GL980P1.000
15:22881858:A:GY967H1.000
15:22903706:C:GR863P1.000
15:22903754:A:GL847P1.000
15:22910806:A:GL697P1.000
15:22912184:C:GA693P1.000
15:22914775:A:GW646R1.000
15:22914775:A:TW646R1.000
15:22914797:G:CF638L1.000
15:22914797:G:TF638L1.000
15:22914798:A:GF638S1.000
15:22914799:A:GF638L1.000
15:22914822:A:GL630P1.000
15:22914828:A:GL628P1.000

dbSNP variants (sampled 300 via entrez): RS1000047677 (15:22897596 G>A), RS1000050554 (15:22917952 G>A,C), RS1000081339 (15:22978462 A>C), RS1000117353 (15:22898827 C>T), RS1000118346 (15:22953587 T>A), RS1000131523 (15:22973267 T>C), RS1000137424 (15:22962665 A>C), RS1000166391 (15:22889509 C>A), RS1000179803 (15:22928290 G>C), RS1000214019 (15:22949044 C>G,T), RS1000218608 (15:22966280 G>A), RS1000243436 (15:22869054 A>T), RS1000244864 (15:22928185 A>G), RS1000260259 (15:22932428 G>A,T), RS1000293716 (15:22879361 C>T)

Disease associations

OMIM: gene MIM:606322 | disease phenotypes: MIM:615656, MIM:241550, MIM:257350, MIM:608636, MIM:209850, MIM:108800, MIM:176270, MIM:181500

GenCC curated gene-disease

Mondo (15): chromosome 15q11.2 deletion syndrome (MONDO:0014294), neurodevelopmental disorder (MONDO:0700092), hypoplastic left heart syndrome 1 (MONDO:0009433), cystic hygroma (MONDO:0009761), 15q11q13 microduplication syndrome (MONDO:0012081), epilepsy (MONDO:0005027), autism spectrum disorder (MONDO:0005258), strabismus (MONDO:0003432), autism (MONDO:0005260), atrial septal defect (MONDO:0006664), Prader-Willi syndrome (MONDO:0008300), thrombocytopenia (MONDO:0002049), hypertensive disorder (MONDO:0005044), obesity disorder (MONDO:0011122), schizophrenia (MONDO:0005090)

Orphanet (10): 15q11.2 microdeletion syndrome (Orphanet:261183), Hypoplastic left heart syndrome (Orphanet:2248), 15q11q13 microduplication syndrome (Orphanet:238446), Interatrial communication (Orphanet:1478), Prader-Willi syndrome (Orphanet:739), Obesity due to melanocortin 4 receptor deficiency (Orphanet:71529), Cystic hygroma (Orphanet:79486), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Non rare obesity (Orphanet:521399), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

4 total (4 of 4 shown, HPO-id order):

HPOTerm
HP:0000717Autism
HP:0000822Hypertension
HP:0001513Obesity
HP:0100753Schizophrenia

GWAS associations

6 associations (top):

StudyTraitp-value
GCST006979_1017Heel bone mineral density1.000000e-12
GCST009615_16Triglyceride levels x loop diuretics use interaction4.000000e-07
GCST009615_17Triglyceride levels x loop diuretics use interaction3.000000e-06
GCST010116_1World class endurance athleticism9.000000e-06
GCST012306_11Bipolar disorder1.000000e-06
GCST90002401_87Platelet distribution width1.000000e-21

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density
EFO:0004530triglyceride measurement
EFO:0007818athletic endurance measurement
EFO:0007984platelet component distribution width

MeSH disease descriptors (9)

DescriptorNameTree numbers
D001321Autistic DisorderF03.625.164.113.500
D004827EpilepsyC10.228.140.490
D006344Heart Septal Defects, AtrialC14.240.400.560.375; C14.280.400.560.375; C16.131.240.400.560.375
D006973HypertensionC14.907.489
D018191Lymphangioma, CysticC04.557.375.450.450
D065886Neurodevelopmental DisordersF03.625
D011218Prader-Willi SyndromeC10.597.606.360.690; C16.131.077.730; C16.131.260.700; C16.320.180.700; C16.320.447.500; C18.654.726.750.500.740
D013285StrabismusC10.292.562.887; C11.590.810
D013921ThrombocytopeniaC15.378.140.855; C15.378.243.937

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724762 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.25Kd5.638nMCHEMBL3752910
8.25ED505.638nMCHEMBL3752910
5.56Kd2745nMCHEMBL5653589
5.56ED502745nMCHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 10 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148189: Binding affinity to human CYFIP1 incubated for 45 mins by Kinobead based pull down assaykd0.0056uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148189: Binding affinity to human CYFIP1 incubated for 45 mins by Kinobead based pull down assaykd2.7453uM

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation4
bisphenol Aaffects cotreatment, increases methylation, increases expression2
entinostatdecreases expression, affects cotreatment2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment, increases expression2
Smokedecreases expression2
Tobacco Smoke Pollutionaffects expression, decreases expression2
pyrogallol 1,3-dimethyl etherdecreases expression, affects cotreatment1
beta-lapachonedecreases expression, increases expression1
arseniteaffects binding, decreases reaction1
sodium bichromatedecreases expression1
cobaltous chloridedecreases expression1
benzo(e)pyreneincreases methylation1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
belinostatdecreases expression1
bisphenol Bincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases expression1
LDN 193189increases expression, affects cotreatment1
Resveratrolaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Vorinostatdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, decreases methylation1
Benzoatesdecreases expression1
Caffeinedecreases phosphorylation1
Doxorubicinincreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651231BindingBinding affinity to human CYFIP1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT00004637PHASE4COMPLETEDDouble-Blind, Placebo-Controlled Trial of Vitamin E as Add-on Therapy for Children With Epilepsy
NCT00043914PHASE4COMPLETEDMeasurement Of Serum Levels Of Two Antiepileptic Drugs During Conversion In Patients With Epilepsy
NCT00132223PHASE4UNKNOWNEffects on the Diagnostic Accuracy of Magnetic Imaging Angiographies of the Supra-Aortic Vessels by Three Different Magnetic Resonance Contrast Agents in Patients
NCT00133081PHASE4UNKNOWNStudy to Improve the Treatment of Epilepsy (SITE)
NCT00137709PHASE4UNKNOWNHormone Profiles in Adults With Newly Diagnosed Epilepsy
NCT00154076PHASE4COMPLETEDA Multicenter Comparative Trial of Zonisamide and Topiramate as Initial Monotherapy in Untreated Epilepsies
NCT00165828PHASE4TERMINATEDEfficacy and Safety of an add-on Treatment With Zonisamide in Adults With Focal Epileptic Seizures With or Without Secondary Generalization
NCT00181116PHASE4COMPLETEDLevetiracetam for Benign Rolandic Epilepsy
NCT00207935PHASE4COMPLETEDUse of Sustained Release Antiepileptic Medication (Depakote® ER) for Pediatric Epilepsy in a Mental Retardation/Developmental Disorder Population
NCT00215592PHASE4COMPLETEDOpen Label, Zonegran (Zonisamide) In Partial Onset Seizures
NCT00266604PHASE4COMPLETEDA Study to Evaluate the Dosing, Effectiveness and Safety of Topiramate for the Treatment of Epilepsy
NCT00288639PHASE4COMPLETEDLyrica (Pregabalin) Administered as an Add-on Therapy for Partial Seizures (LEADER).
NCT00312676PHASE4UNKNOWNCompare Tolerability of an Overnight Switch to Gradual Switch Between Two Different Forms of Depakote
NCT00323947PHASE4COMPLETEDMethylphenidate for Treating Attention Deficit Hyperactivity Disorder in Children With Both ADHD and Epilepsy
NCT00385411PHASE4COMPLETEDStudy of Valproate in Young Patients Suffering From Epilepsy
NCT00522418PHASE4TERMINATEDStudy Comparing Best Medical Practice With or Without VNS Therapy in Pharmacoresistant Partial Epilepsy Patients
NCT00537940PHASE4COMPLETEDComparative Study Of Pregabalin And Gabapentin As Adjunctive Therapy In Subjects With Partial Seizures
NCT00552526PHASE4UNKNOWNKetogenic Diet vs.Antiepileptic Drug Treatment in Drug Resistant Epilepsy
NCT00564915PHASE4COMPLETEDRCT of the Efficacy of the Ketogenic Diet in the Treatment of Epilepsy
NCT00571155PHASE4COMPLETEDTrial of Levetiracetam in Patients With Primary Brain Tumors and Symptomatic Seizures Who Undergo Surgery
NCT00572195PHASE4COMPLETEDRNS® System LTT Study
NCT00610532PHASE4TERMINATEDEvaluating the Transporter Protein Inhibitor Probenecid In Patients With Epilepsy
NCT00630357PHASE4COMPLETEDTrial to Evaluate the Safety and Efficacy of Keppra After Conversion to Mono-therapy in Subjects With Partial Epilepsy
NCT00630630PHASE4COMPLETEDStudy on Safety and Efficacy of Levetiracetam in the Adjunctive Treatment of Female Subjects With C1 Catamenial Epilepsy
NCT00630968PHASE4COMPLETEDS.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy
NCT00631150PHASE4COMPLETEDA Phase IV-Pharmacovigilance Study of Keppra Greece - S.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy
NCT00659958PHASE4COMPLETEDZAGAL Study: Evaluating Effectiveness and Tolerability of Zonisamide as Adjunctive Therapy in Patients With Partial Onset Seizures Treated With Two Antiepileptic Drugs
NCT00713622PHASE4COMPLETEDComparing The Effect On Cognition Of Adjunctive Therapy With Zonisamide Versus Sodium Valproate
NCT00807989PHASE4COMPLETEDThe Efficacy and Safety of Low Dose Combination of LTG and VPA Compared to CBZ Monotherapy
NCT00832884PHASE4COMPLETEDThe Safety of Intravenous Lacosamide
NCT00869622PHASE4COMPLETEDAntiepileptic Drugs and Osteoporotic Prevention Trial
NCT00896987PHASE4COMPLETEDLamotrigine Cognitive Function Study in Adult Untreated Epilepsies
NCT00952081PHASE4COMPLETEDA Pilot Study to Evaluate Efficacy and Safety of Clevidipine in Neurosurgical Patients
NCT01118455PHASE4TERMINATEDTrial to Assess Vagus Nerve Stimulation Therapy vs. Anti-Epileptic Drug (AED) Treatment in Children With Refractory Seizures
NCT01127165PHASE4COMPLETEDLow and High Dose Zonisamide in Children as Monotherapy
NCT01127256PHASE4COMPLETEDComparative Study of Zonisamide and Carbamazepine as an Initial Monotherapy: Efficacy and Safety Evaluation
NCT01140867PHASE4COMPLETEDOpen-label, Multi-center Trial of Zonisamide as Adjunctive Therapy in Patients With Uncontrolled Partial Epilepsy
NCT01175954PHASE4COMPLETEDCognitive and Behavioral Effects of Lacosamide