{"gene":"AGAP3","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2013,"finding":"AGAP3 is a component of the NMDA receptor complex, containing a GTPase-like domain, a pleckstrin homology domain, and an ArfGAP domain. It links NMDA receptor activation to Ras/ERK and Arf6 signaling pathways during chemically induced LTP, and knockdown of AGAP3 occludes AMPA receptor trafficking to the synapse during LTP.","method":"Co-immunoprecipitation (NMDA receptor complex identification), shRNA knockdown in rat primary neuronal cultures with AMPA receptor trafficking readout, chemical LTP induction with ERK/Arf6 pathway assays","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, clean KD with defined cellular phenotype, multiple orthogonal methods in single study","pmids":["23904596"],"is_preprint":false},{"year":2011,"finding":"CRAG (a short splicing variant of centaurin-γ3/AGAP3) facilitates degradation of expanded polyglutamine protein via the nuclear ubiquitin-proteasome pathway and activates c-Fos-dependent AP-1 via serum response factor (SRF). The nuclear localization signal and both N- and C-terminal regions of CRAG are critical for SRF-dependent c-Fos activation. CRAG knockdown attenuates c-Fos activation triggered by polyQ or proteasome inhibition.","method":"Mutation analysis, siRNA knockdown, dominant-negative mutant expression, reporter assays for AP-1/SRF activity","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (mutagenesis, KD, DN mutant) with defined phenotypic readouts, moderate evidence","pmids":["21832068"],"is_preprint":false},{"year":2019,"finding":"CRAG (splice variant of AGAP3) has an essential GTPase activity, interacts with ELK1 (a co-activator of SRF), and activates SRF in an ELK1-dependent manner at promyelocytic leukaemia (PML) bodies through SUMO-interacting motifs. CRAG/centaurin-γ3 knockout mice show suppressed kainic acid-induced c-fos expression in hippocampus.","method":"GTPase activity assay, co-immunoprecipitation (CRAG-ELK1 interaction), knockout mouse model with in vivo kainic acid stimulation, SUMO-interacting motif mutational analysis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1-2 — enzymatic assay, Co-IP, KO mouse with defined phenotype, multiple orthogonal methods","pmids":["31882856"],"is_preprint":false},{"year":2021,"finding":"Forebrain-specific CRAG/Centaurin-γ3 (AGAP3) knockout mice show maturational abnormality of hippocampal granule cells (increased doublecortin-positive immature neurons, decreased calbindin-positive mature neurons) and hyperactivity, demonstrating CRAG is required for dentate gyrus neuron maturation.","method":"Conditional (forebrain-specific) knockout mouse, immunohistochemistry for doublecortin and calbindin, open-field behavioral testing","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular and behavioral phenotypes, multiple readouts","pmids":["33811862"],"is_preprint":false},{"year":2017,"finding":"AGAP3 is identified as a binding partner (co-immunoprecipitates) of CLIP2 in the CLASP2 interactome in adipocytes, suggesting AGAP3 preferentially associates with CLIP2 over CLASP2 within the microtubule-associated protein network.","method":"Affinity purification coupled with mass spectrometry (AP-MS), co-immunoprecipitation, SAINT bioinformatics analysis","journal":"Molecular & cellular proteomics","confidence":"Medium","confidence_rationale":"Tier 3 — single co-IP/AP-MS identification without functional follow-up for AGAP3 specifically","pmids":["28550165"],"is_preprint":false},{"year":2019,"finding":"Insulin regulates phosphorylation of AGAP3 as part of the CLASP2 microtubule plus-end tracking protein network in adipocytes, placing AGAP3 in an insulin-responsive microtubule-associated signaling system.","method":"Protein-specific targeted quantitative phosphoproteomics in 3T3-L1 adipocytes after insulin stimulation","journal":"Molecular & cellular proteomics","confidence":"Medium","confidence_rationale":"Tier 2 — quantitative phosphoproteomics with defined stimulus, but functional consequence of AGAP3 phosphorylation not directly tested","pmids":["31018989"],"is_preprint":false},{"year":2020,"finding":"AGAP3-BRAF fusion protein promotes canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region of BRAF. The 5' AGAP3 partner influences subcellular localization and intracellular signaling capacity of the fusion, activating distinct downstream signaling pathways and conferring resistance to EGFR-targeted monotherapy.","method":"Expression of AGAP3-BRAF fusion in patient-derived colorectal cancer organoids, downstream signaling assays, drug sensitivity assays, cross-comparison with other BRAF fusion partners","journal":"Molecular cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — functional characterization in organoids with signaling and drug response readouts, single lab","pmids":["31911540"],"is_preprint":false},{"year":2017,"finding":"Expression of the AGAP3-BRAF fusion gene in BRAFV600E mutant melanoma cells induces resistance to vemurafenib (BRAF inhibitor) while maintaining sensitivity to MEK inhibitors, demonstrating the AGAP3-BRAF fusion activates MAPK signaling downstream of the BRAF inhibitor target.","method":"Expression of AGAP3-BRAF fusion in BRAFV600E melanoma cell lines, drug sensitivity assays, comprehensive genomic profiling of serial biopsies","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — functional expression experiment with drug sensitivity readout, supported by clinical correlate","pmids":["28539463"],"is_preprint":false},{"year":2019,"finding":"CRAG (splice variant of AGAP3) overexpression upregulates c-Jun expression and significantly increases cell proliferation and colony formation in colorectal cancer cells, acting via AP-1 activation.","method":"Overexpression experiments in colorectal cancer cells, proliferation and colony formation assays, c-Jun protein expression measurement","journal":"Anticancer research","confidence":"Low","confidence_rationale":"Tier 3 — single overexpression experiment with cellular phenotype but limited mechanistic depth","pmids":["30591445"],"is_preprint":false},{"year":2024,"finding":"In Srrm2+/- mice (model of schizophrenia), Agap3 undergoes abnormal splicing and shows elevated expression, and Agap3 is identified as a SynGAP interactor, placing AGAP3 in the postsynaptic SynGAP signaling complex.","method":"RNA-seq splicing analysis in Srrm2+/- mouse brain, protein interaction identification","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 — preprint, single genetic model, interaction not yet validated by direct biochemical method in this study","pmids":[],"is_preprint":true}],"current_model":"AGAP3 (and its short splice variant CRAG) functions as a multidomain signaling scaffold (GTPase-like, PH, and ArfGAP domains) within the NMDA receptor complex, where it couples NMDA receptor activation to Ras/ERK and Arf6 signaling to drive AMPA receptor trafficking during synaptic potentiation; CRAG additionally translocates to the nucleus to activate SRF/c-Fos via ELK1 at PML bodies, promoting neuronal survival and maturation, while AGAP3 also participates in insulin-responsive microtubule-associated protein networks in adipocytes, and AGAP3-BRAF gene fusions drive oncogenic MAPK signaling by replacing the auto-inhibitory N-terminal region of BRAF."},"narrative":{"teleology":[{"year":2011,"claim":"Establishing that the CRAG splice variant couples nuclear ubiquitin-proteasome function to SRF/c-Fos transcriptional activation answered how AGAP3 isoforms participate in nuclear signaling, revealing a nuclear localization signal and domain requirements for SRF activation.","evidence":"Mutagenesis, siRNA knockdown, dominant-negative expression, and SRF/AP-1 reporter assays in cultured cells","pmids":["21832068"],"confidence":"High","gaps":["Direct nuclear substrates of CRAG's ArfGAP or GTPase domains were not identified","In vivo physiological relevance of polyQ-triggered CRAG activity not yet demonstrated"]},{"year":2013,"claim":"Identification of AGAP3 as an NMDA receptor complex component that bridges NMDA receptor activation to Ras/ERK and Arf6 pathways answered how synaptic activity drives AMPA receptor insertion during LTP.","evidence":"Co-immunoprecipitation with NMDA receptor complex, shRNA knockdown in rat primary neurons with chemical LTP induction and AMPA receptor trafficking assays","pmids":["23904596"],"confidence":"High","gaps":["Whether AGAP3's ArfGAP catalytic activity is required for LTP trafficking was not tested","Specific Arf6 substrates or effectors downstream of AGAP3 in LTP remain unidentified"]},{"year":2017,"claim":"Demonstration that AGAP3-BRAF fusions activate MAPK signaling and confer BRAF inhibitor resistance while preserving MEK inhibitor sensitivity established how AGAP3 genomic rearrangements contribute to oncogenic bypass signaling.","evidence":"Expression of AGAP3-BRAF fusion in BRAFV600E melanoma cells with drug sensitivity assays; parallel characterization in patient-derived colorectal cancer organoids","pmids":["28539463","31911540"],"confidence":"Medium","gaps":["Whether the AGAP3 portion contributes signaling or merely membrane localization to the fusion is incompletely resolved","In vivo tumorigenic potential of the AGAP3-BRAF fusion not tested in animal models"]},{"year":2019,"claim":"Demonstrating that CRAG possesses intrinsic GTPase activity and activates SRF via ELK1 at PML bodies through SUMO-interacting motifs resolved the enzymatic basis and subnuclear site of CRAG-mediated transcriptional activation; knockout mice confirmed in vivo relevance for c-fos induction.","evidence":"GTPase activity assay, Co-IP of CRAG-ELK1, SUMO-interacting motif mutagenesis, centaurin-γ3 knockout mice with kainic acid stimulation","pmids":["31882856"],"confidence":"High","gaps":["GTP hydrolysis rate constants and nucleotide specificity not quantitatively determined","Whether GTPase and ArfGAP activities are independently regulated is unknown"]},{"year":2019,"claim":"Identification of AGAP3 as an insulin-responsive phosphoprotein within the CLASP2/CLIP2 microtubule plus-end tracking network in adipocytes expanded AGAP3 function beyond neurons to metabolic signaling.","evidence":"Affinity purification–mass spectrometry and targeted quantitative phosphoproteomics in 3T3-L1 adipocytes after insulin stimulation","pmids":["28550165","31539989"],"confidence":"Medium","gaps":["Functional consequence of AGAP3 phosphorylation on microtubule dynamics or GLUT4 trafficking not tested","Whether AGAP3 ArfGAP activity is relevant in adipocytes is unknown"]},{"year":2021,"claim":"Forebrain-specific CRAG knockout causing hippocampal granule cell maturation arrest and hyperactivity established AGAP3/CRAG as essential for postnatal neuronal maturation in vivo.","evidence":"Conditional knockout mice, doublecortin/calbindin immunohistochemistry, open-field behavioral testing","pmids":["33811862"],"confidence":"High","gaps":["Downstream transcriptional targets mediating maturation are not identified","Whether the maturation defect arises from impaired SRF/c-Fos signaling or AMPA receptor trafficking is unresolved"]},{"year":null,"claim":"It remains unknown how AGAP3's GTPase, PH, and ArfGAP domains are coordinately regulated, whether its ArfGAP catalytic activity is required for synaptic plasticity, and what distinguishes the functional roles of full-length AGAP3 versus the CRAG splice variant in different cellular contexts.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of AGAP3 exists","Domain-specific catalytic contributions to LTP versus transcription are not separated","Isoform-specific interactomes have not been systematically compared"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,6,7]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[0,2,3]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2]}],"complexes":["NMDA receptor complex"],"partners":["GRIN1","ELK1","CLIP2","BRAF"],"other_free_text":[]},"mechanistic_narrative":"AGAP3 is a multidomain signaling scaffold in excitatory synapses that couples neurotransmitter receptor activation to intracellular signal transduction and synaptic plasticity. It resides in the NMDA receptor complex and, through its GTPase-like, pleckstrin homology, and ArfGAP domains, links NMDA receptor activation to Ras/ERK and Arf6 signaling, thereby controlling AMPA receptor trafficking to synapses during long-term potentiation [PMID:23904596]. Its short splice variant CRAG possesses intrinsic GTPase activity, interacts with ELK1 at PML bodies to activate SRF-dependent c-Fos transcription, and is required for hippocampal granule cell maturation, as forebrain-specific knockout mice display arrested dentate gyrus neuron maturation and hyperactivity [PMID:31882856, PMID:33811862]. AGAP3-BRAF gene fusions, in which AGAP3 replaces the auto-inhibitory N-terminus of BRAF, constitutively activate MAPK signaling and confer resistance to BRAF inhibitors while retaining sensitivity to MEK inhibitors in melanoma and colorectal cancer models [PMID:28539463, PMID:31911540]."},"prefetch_data":{"uniprot":{"accession":"Q96P47","full_name":"Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3","aliases":["CRAM-associated GTPase","CRAG","Centaurin-gamma-3","Cnt-g3","MR1-interacting protein","MRIP-1"],"length_aa":875,"mass_kda":95.0,"function":"GTPase-activating protein for the ADP ribosylation factor family (Potential). GTPase which may be involved in the degradation of expanded polyglutamine proteins through the ubiquitin-proteasome pathway","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q96P47/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/AGAP3","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000133612","cell_line_id":"CID000651","localizations":[{"compartment":"cell_contact","grade":3},{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"AGAP1","stoichiometry":10.0},{"gene":"C12ORF57","stoichiometry":0.2},{"gene":"UBE2O","stoichiometry":0.2},{"gene":"TANC1","stoichiometry":0.2},{"gene":"DCTN1;DKFZP686E0752","stoichiometry":0.2},{"gene":"AHCYL1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000651","total_profiled":1310},"omim":[{"mim_id":"621159","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 11, NONCODING; AGAP11","url":"https://www.omim.org/entry/621159"},{"mim_id":"621158","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 9; AGAP9","url":"https://www.omim.org/entry/621158"},{"mim_id":"621157","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 6; AGAP6","url":"https://www.omim.org/entry/621157"},{"mim_id":"621156","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 5; AGAP5","url":"https://www.omim.org/entry/621156"},{"mim_id":"621155","title":"ARF GTPase-ACTIVATING PROTEIN WITH GTPase DOMAIN, ANKYRIN REPEAT, AND PLECKSTRIN HOMOLOGY DOMAIN 4; AGAP4","url":"https://www.omim.org/entry/621155"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":264.6}],"url":"https://www.proteinatlas.org/search/AGAP3"},"hgnc":{"alias_symbol":[],"prev_symbol":["CENTG3"]},"alphafold":{"accession":"Q96P47","domains":[{"cath_id":"3.40.50.300","chopping":"90-257","consensus_level":"high","plddt":91.5896,"start":90,"end":257},{"cath_id":"2.30.29.30","chopping":"366-428_570-612","consensus_level":"medium","plddt":87.2513,"start":366,"end":612},{"cath_id":"1.10.220.150","chopping":"635-733","consensus_level":"medium","plddt":95.3881,"start":635,"end":733},{"cath_id":"1.25.40.20","chopping":"748-840","consensus_level":"medium","plddt":94.6637,"start":748,"end":840}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96P47","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96P47-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96P47-F1-predicted_aligned_error_v6.png","plddt_mean":70.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=AGAP3","jax_strain_url":"https://www.jax.org/strain/search?query=AGAP3"},"sequence":{"accession":"Q96P47","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96P47.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96P47/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96P47"}},"corpus_meta":[{"pmid":"23904596","id":"PMC_23904596","title":"AGAP3 and Arf6 regulate trafficking of AMPA receptors and synaptic plasticity.","date":"2013","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/23904596","citation_count":58,"is_preprint":false},{"pmid":"28539463","id":"PMC_28539463","title":"BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma.","date":"2017","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/28539463","citation_count":53,"is_preprint":false},{"pmid":"31018989","id":"PMC_31018989","title":"Insulin Induces Microtubule Stabilization and Regulates the Microtubule Plus-end Tracking Protein Network in Adipocytes.","date":"2019","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/31018989","citation_count":52,"is_preprint":false},{"pmid":"28550165","id":"PMC_28550165","title":"Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein.","date":"2017","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/28550165","citation_count":49,"is_preprint":false},{"pmid":"35871080","id":"PMC_35871080","title":"Identification of fusions with potential clinical significance in melanoma.","date":"2022","source":"Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc","url":"https://pubmed.ncbi.nlm.nih.gov/35871080","citation_count":28,"is_preprint":false},{"pmid":"34398495","id":"PMC_34398495","title":"Gastrointestinal stromal tumors with BRAF gene fusions. A report of two cases showing low or absent KIT expression resulting in diagnostic pitfalls.","date":"2021","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/34398495","citation_count":20,"is_preprint":false},{"pmid":"34568720","id":"PMC_34568720","title":"Spectrum of BRAF Mutations and Gene Rearrangements in Ovarian Serous Carcinoma.","date":"2021","source":"JCO precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34568720","citation_count":16,"is_preprint":false},{"pmid":"31911540","id":"PMC_31911540","title":"Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity.","date":"2020","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/31911540","citation_count":16,"is_preprint":false},{"pmid":"21832068","id":"PMC_21832068","title":"CRMP5-associated GTPase (CRAG) protein protects neuronal cells against cytotoxicity of expanded polyglutamine protein partially via c-Fos-dependent activator protein-1 activation.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21832068","citation_count":14,"is_preprint":false},{"pmid":"30591445","id":"PMC_30591445","title":"CRMP5-associated GTPase (CRAG) Is a Candidate Driver Gene for Colorectal Cancer Carcinogenesis.","date":"2019","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/30591445","citation_count":12,"is_preprint":false},{"pmid":"36110430","id":"PMC_36110430","title":"Integrated analysis and identification of hub genes as novel biomarkers for Alzheimer's disease.","date":"2022","source":"Frontiers in aging neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/36110430","citation_count":10,"is_preprint":false},{"pmid":"33289181","id":"PMC_33289181","title":"Whole-exome sequencing reveals novel vacuolar ATPase genes' variants and variants in genes involved in lysosomal biology and autophagosomal formation in oral granular cell tumors.","date":"2020","source":"Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology","url":"https://pubmed.ncbi.nlm.nih.gov/33289181","citation_count":10,"is_preprint":false},{"pmid":"35949061","id":"PMC_35949061","title":"AGAP3: A novel BRAF fusion partner in pediatric pancreatic-type acinar cell carcinoma.","date":"2022","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35949061","citation_count":9,"is_preprint":false},{"pmid":"31698611","id":"PMC_31698611","title":"Exome sequencing identifies predisposing and fusion gene in ganglioneuroma, ganglioneuroblastoma and neuroblastoma.","date":"2019","source":"Mathematical biosciences and engineering : MBE","url":"https://pubmed.ncbi.nlm.nih.gov/31698611","citation_count":6,"is_preprint":false},{"pmid":"31882856","id":"PMC_31882856","title":"Critical role of CRAG, a splicing variant of centaurin-γ3/AGAP3, in ELK1-dependent SRF activation at PML bodies.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31882856","citation_count":4,"is_preprint":false},{"pmid":"33811862","id":"PMC_33811862","title":"Forebrain-specific deficiency of the GTPase CRAG/Centaurin-γ3 leads to immature dentate gyri and hyperactivity in mice.","date":"2021","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33811862","citation_count":4,"is_preprint":false},{"pmid":"37749596","id":"PMC_37749596","title":"Novelty-induced memory consolidation is accompanied by increased Agap3 transcription: a cross-species study.","date":"2023","source":"Molecular brain","url":"https://pubmed.ncbi.nlm.nih.gov/37749596","citation_count":3,"is_preprint":false},{"pmid":"39986469","id":"PMC_39986469","title":"Clinical, Morphologic, and Genomic Findings in Spitz Tumors With RET Fusion: A Series of 31 Cases.","date":"2025","source":"Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc","url":"https://pubmed.ncbi.nlm.nih.gov/39986469","citation_count":3,"is_preprint":false},{"pmid":"38255294","id":"PMC_38255294","title":"Cannabinerol (CBNR) Influences Synaptic Genes Associated with Cytoskeleton and Ion Channels in NSC-34 Cell Line: A Transcriptomic Study.","date":"2024","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/38255294","citation_count":3,"is_preprint":false},{"pmid":"40616715","id":"PMC_40616715","title":"Primary pigmented papillary epithelial tumor of the sella: case report and literature review.","date":"2025","source":"Brain tumor pathology","url":"https://pubmed.ncbi.nlm.nih.gov/40616715","citation_count":2,"is_preprint":false},{"pmid":"37113989","id":"PMC_37113989","title":"Whole transcriptome sequencing reveals HOXD11-AGAP3, a novel fusion transcript in the Indian acute leukemia cohort.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37113989","citation_count":1,"is_preprint":false},{"pmid":"38586706","id":"PMC_38586706","title":"Pulmonary Erdheim-Chester Disease With BRAF-AGAP3 Fusion: Late-Onset Osteolytic Femoral Lesions Despite Long-Term Pulmonary Stabilization With Corticosteroid.","date":"2024","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/38586706","citation_count":1,"is_preprint":false},{"pmid":"39687148","id":"PMC_39687148","title":"Rare BRAF gene fusions in metastatic early-onset colon cancer: A case report.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/39687148","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.10.617460","title":"Reduction of SynGAP-γ, disrupted splicing of<i>Agap3</i>, and oligodendrocyte deficits in<i>Srrm2</i>mice, a genetic model of schizophrenia and neurodevelopmental disorder","date":"2024-10-12","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.10.617460","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14660,"output_tokens":2444,"usd":0.04032},"stage2":{"model":"claude-opus-4-6","input_tokens":5751,"output_tokens":2093,"usd":0.12162},"total_usd":0.16194,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"AGAP3 is a component of the NMDA receptor complex, containing a GTPase-like domain, a pleckstrin homology domain, and an ArfGAP domain. It links NMDA receptor activation to Ras/ERK and Arf6 signaling pathways during chemically induced LTP, and knockdown of AGAP3 occludes AMPA receptor trafficking to the synapse during LTP.\",\n      \"method\": \"Co-immunoprecipitation (NMDA receptor complex identification), shRNA knockdown in rat primary neuronal cultures with AMPA receptor trafficking readout, chemical LTP induction with ERK/Arf6 pathway assays\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, clean KD with defined cellular phenotype, multiple orthogonal methods in single study\",\n      \"pmids\": [\"23904596\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"CRAG (a short splicing variant of centaurin-γ3/AGAP3) facilitates degradation of expanded polyglutamine protein via the nuclear ubiquitin-proteasome pathway and activates c-Fos-dependent AP-1 via serum response factor (SRF). The nuclear localization signal and both N- and C-terminal regions of CRAG are critical for SRF-dependent c-Fos activation. CRAG knockdown attenuates c-Fos activation triggered by polyQ or proteasome inhibition.\",\n      \"method\": \"Mutation analysis, siRNA knockdown, dominant-negative mutant expression, reporter assays for AP-1/SRF activity\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (mutagenesis, KD, DN mutant) with defined phenotypic readouts, moderate evidence\",\n      \"pmids\": [\"21832068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CRAG (splice variant of AGAP3) has an essential GTPase activity, interacts with ELK1 (a co-activator of SRF), and activates SRF in an ELK1-dependent manner at promyelocytic leukaemia (PML) bodies through SUMO-interacting motifs. CRAG/centaurin-γ3 knockout mice show suppressed kainic acid-induced c-fos expression in hippocampus.\",\n      \"method\": \"GTPase activity assay, co-immunoprecipitation (CRAG-ELK1 interaction), knockout mouse model with in vivo kainic acid stimulation, SUMO-interacting motif mutational analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — enzymatic assay, Co-IP, KO mouse with defined phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"31882856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Forebrain-specific CRAG/Centaurin-γ3 (AGAP3) knockout mice show maturational abnormality of hippocampal granule cells (increased doublecortin-positive immature neurons, decreased calbindin-positive mature neurons) and hyperactivity, demonstrating CRAG is required for dentate gyrus neuron maturation.\",\n      \"method\": \"Conditional (forebrain-specific) knockout mouse, immunohistochemistry for doublecortin and calbindin, open-field behavioral testing\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular and behavioral phenotypes, multiple readouts\",\n      \"pmids\": [\"33811862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"AGAP3 is identified as a binding partner (co-immunoprecipitates) of CLIP2 in the CLASP2 interactome in adipocytes, suggesting AGAP3 preferentially associates with CLIP2 over CLASP2 within the microtubule-associated protein network.\",\n      \"method\": \"Affinity purification coupled with mass spectrometry (AP-MS), co-immunoprecipitation, SAINT bioinformatics analysis\",\n      \"journal\": \"Molecular & cellular proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single co-IP/AP-MS identification without functional follow-up for AGAP3 specifically\",\n      \"pmids\": [\"28550165\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Insulin regulates phosphorylation of AGAP3 as part of the CLASP2 microtubule plus-end tracking protein network in adipocytes, placing AGAP3 in an insulin-responsive microtubule-associated signaling system.\",\n      \"method\": \"Protein-specific targeted quantitative phosphoproteomics in 3T3-L1 adipocytes after insulin stimulation\",\n      \"journal\": \"Molecular & cellular proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — quantitative phosphoproteomics with defined stimulus, but functional consequence of AGAP3 phosphorylation not directly tested\",\n      \"pmids\": [\"31018989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"AGAP3-BRAF fusion protein promotes canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region of BRAF. The 5' AGAP3 partner influences subcellular localization and intracellular signaling capacity of the fusion, activating distinct downstream signaling pathways and conferring resistance to EGFR-targeted monotherapy.\",\n      \"method\": \"Expression of AGAP3-BRAF fusion in patient-derived colorectal cancer organoids, downstream signaling assays, drug sensitivity assays, cross-comparison with other BRAF fusion partners\",\n      \"journal\": \"Molecular cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional characterization in organoids with signaling and drug response readouts, single lab\",\n      \"pmids\": [\"31911540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Expression of the AGAP3-BRAF fusion gene in BRAFV600E mutant melanoma cells induces resistance to vemurafenib (BRAF inhibitor) while maintaining sensitivity to MEK inhibitors, demonstrating the AGAP3-BRAF fusion activates MAPK signaling downstream of the BRAF inhibitor target.\",\n      \"method\": \"Expression of AGAP3-BRAF fusion in BRAFV600E melanoma cell lines, drug sensitivity assays, comprehensive genomic profiling of serial biopsies\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional expression experiment with drug sensitivity readout, supported by clinical correlate\",\n      \"pmids\": [\"28539463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CRAG (splice variant of AGAP3) overexpression upregulates c-Jun expression and significantly increases cell proliferation and colony formation in colorectal cancer cells, acting via AP-1 activation.\",\n      \"method\": \"Overexpression experiments in colorectal cancer cells, proliferation and colony formation assays, c-Jun protein expression measurement\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single overexpression experiment with cellular phenotype but limited mechanistic depth\",\n      \"pmids\": [\"30591445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Srrm2+/- mice (model of schizophrenia), Agap3 undergoes abnormal splicing and shows elevated expression, and Agap3 is identified as a SynGAP interactor, placing AGAP3 in the postsynaptic SynGAP signaling complex.\",\n      \"method\": \"RNA-seq splicing analysis in Srrm2+/- mouse brain, protein interaction identification\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, single genetic model, interaction not yet validated by direct biochemical method in this study\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"AGAP3 (and its short splice variant CRAG) functions as a multidomain signaling scaffold (GTPase-like, PH, and ArfGAP domains) within the NMDA receptor complex, where it couples NMDA receptor activation to Ras/ERK and Arf6 signaling to drive AMPA receptor trafficking during synaptic potentiation; CRAG additionally translocates to the nucleus to activate SRF/c-Fos via ELK1 at PML bodies, promoting neuronal survival and maturation, while AGAP3 also participates in insulin-responsive microtubule-associated protein networks in adipocytes, and AGAP3-BRAF gene fusions drive oncogenic MAPK signaling by replacing the auto-inhibitory N-terminal region of BRAF.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"AGAP3 is a multidomain signaling scaffold in excitatory synapses that couples neurotransmitter receptor activation to intracellular signal transduction and synaptic plasticity. It resides in the NMDA receptor complex and, through its GTPase-like, pleckstrin homology, and ArfGAP domains, links NMDA receptor activation to Ras/ERK and Arf6 signaling, thereby controlling AMPA receptor trafficking to synapses during long-term potentiation [PMID:23904596]. Its short splice variant CRAG possesses intrinsic GTPase activity, interacts with ELK1 at PML bodies to activate SRF-dependent c-Fos transcription, and is required for hippocampal granule cell maturation, as forebrain-specific knockout mice display arrested dentate gyrus neuron maturation and hyperactivity [PMID:31882856, PMID:33811862]. AGAP3-BRAF gene fusions, in which AGAP3 replaces the auto-inhibitory N-terminus of BRAF, constitutively activate MAPK signaling and confer resistance to BRAF inhibitors while retaining sensitivity to MEK inhibitors in melanoma and colorectal cancer models [PMID:28539463, PMID:31911540].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing that the CRAG splice variant couples nuclear ubiquitin-proteasome function to SRF/c-Fos transcriptional activation answered how AGAP3 isoforms participate in nuclear signaling, revealing a nuclear localization signal and domain requirements for SRF activation.\",\n      \"evidence\": \"Mutagenesis, siRNA knockdown, dominant-negative expression, and SRF/AP-1 reporter assays in cultured cells\",\n      \"pmids\": [\"21832068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct nuclear substrates of CRAG's ArfGAP or GTPase domains were not identified\",\n        \"In vivo physiological relevance of polyQ-triggered CRAG activity not yet demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identification of AGAP3 as an NMDA receptor complex component that bridges NMDA receptor activation to Ras/ERK and Arf6 pathways answered how synaptic activity drives AMPA receptor insertion during LTP.\",\n      \"evidence\": \"Co-immunoprecipitation with NMDA receptor complex, shRNA knockdown in rat primary neurons with chemical LTP induction and AMPA receptor trafficking assays\",\n      \"pmids\": [\"23904596\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether AGAP3's ArfGAP catalytic activity is required for LTP trafficking was not tested\",\n        \"Specific Arf6 substrates or effectors downstream of AGAP3 in LTP remain unidentified\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstration that AGAP3-BRAF fusions activate MAPK signaling and confer BRAF inhibitor resistance while preserving MEK inhibitor sensitivity established how AGAP3 genomic rearrangements contribute to oncogenic bypass signaling.\",\n      \"evidence\": \"Expression of AGAP3-BRAF fusion in BRAFV600E melanoma cells with drug sensitivity assays; parallel characterization in patient-derived colorectal cancer organoids\",\n      \"pmids\": [\"28539463\", \"31911540\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the AGAP3 portion contributes signaling or merely membrane localization to the fusion is incompletely resolved\",\n        \"In vivo tumorigenic potential of the AGAP3-BRAF fusion not tested in animal models\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that CRAG possesses intrinsic GTPase activity and activates SRF via ELK1 at PML bodies through SUMO-interacting motifs resolved the enzymatic basis and subnuclear site of CRAG-mediated transcriptional activation; knockout mice confirmed in vivo relevance for c-fos induction.\",\n      \"evidence\": \"GTPase activity assay, Co-IP of CRAG-ELK1, SUMO-interacting motif mutagenesis, centaurin-γ3 knockout mice with kainic acid stimulation\",\n      \"pmids\": [\"31882856\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"GTP hydrolysis rate constants and nucleotide specificity not quantitatively determined\",\n        \"Whether GTPase and ArfGAP activities are independently regulated is unknown\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identification of AGAP3 as an insulin-responsive phosphoprotein within the CLASP2/CLIP2 microtubule plus-end tracking network in adipocytes expanded AGAP3 function beyond neurons to metabolic signaling.\",\n      \"evidence\": \"Affinity purification–mass spectrometry and targeted quantitative phosphoproteomics in 3T3-L1 adipocytes after insulin stimulation\",\n      \"pmids\": [\"28550165\", \"31539989\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of AGAP3 phosphorylation on microtubule dynamics or GLUT4 trafficking not tested\",\n        \"Whether AGAP3 ArfGAP activity is relevant in adipocytes is unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Forebrain-specific CRAG knockout causing hippocampal granule cell maturation arrest and hyperactivity established AGAP3/CRAG as essential for postnatal neuronal maturation in vivo.\",\n      \"evidence\": \"Conditional knockout mice, doublecortin/calbindin immunohistochemistry, open-field behavioral testing\",\n      \"pmids\": [\"33811862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Downstream transcriptional targets mediating maturation are not identified\",\n        \"Whether the maturation defect arises from impaired SRF/c-Fos signaling or AMPA receptor trafficking is unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how AGAP3's GTPase, PH, and ArfGAP domains are coordinately regulated, whether its ArfGAP catalytic activity is required for synaptic plasticity, and what distinguishes the functional roles of full-length AGAP3 versus the CRAG splice variant in different cellular contexts.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of AGAP3 exists\",\n        \"Domain-specific catalytic contributions to LTP versus transcription are not separated\",\n        \"Isoform-specific interactomes have not been systematically compared\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 6, 7]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [\n      \"NMDA receptor complex\"\n    ],\n    \"partners\": [\n      \"GRIN1\",\n      \"ELK1\",\n      \"CLIP2\",\n      \"BRAF\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}