{"gene":"SNX15","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":2000,"finding":"SNX15 is found on membranes and in the cytosol; the PX (phox homology) domain is required for membrane association and for association with the platelet-derived growth factor receptor (PDGFR). Overexpression of SNX15 disrupts normal trafficking of proteins from the plasma membrane to recycling endosomes or the trans-Golgi network, leading to mislocalization of furin and decreased processing of insulin and hepatocyte growth factor receptors.","method":"Subcellular fractionation, immunofluorescence, co-immunoprecipitation, overexpression in mammalian cells with functional readouts (receptor processing, furin localization)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (fractionation, co-IP, IF, biochemical processing assays) in original characterization paper","pmids":["11085978"],"is_preprint":false},{"year":2000,"finding":"Overexpression of SNX15 in COS-7 cells alters endosomal compartment morphology (generating large, amorphous membrane-limited structures containing lysosomal, late endosomal, early endosomal, and TGN markers), severely inhibits transferrin endocytosis, and slows endocytosis and recycling of tac-TGN38 and tac-furin, establishing SNX15 as a regulator of endocytic pathway trafficking.","method":"Transient transfection of myc-tagged SNX15, immunofluorescence microscopy, transferrin endocytosis assay, tac-TGN38/tac-furin trafficking assays in COS-7 cells","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal functional assays (morphology, endocytosis, recycling) with loss- and gain-of-function readouts","pmids":["11208079"],"is_preprint":false},{"year":2013,"finding":"SNX15 associates with early endosomes via its PX domain in a phosphatidylinositol 3-phosphate (PtdIns3P)-dependent manner, and also associates directly with clathrin-coated pits and clathrin-coated vesicles through a non-canonical clathrin-binding box. SNX15 depletion (RNAi) delays EGF receptor degradative sorting by impairing movement of newly internalized EGFR-labelled vesicles into early endosomes. Live-cell imaging shows that SNX15-labelled endocytic vesicles fuse directly with Rab5-positive early endosomes independently of the APPL1 compartment.","method":"RNAi loss-of-function screen, live-cell imaging, direct clathrin-binding assay, PtdIns3P-binding PX-domain experiments, co-localization with endosomal markers","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (RNAi, live imaging, direct binding, endosomal marker co-localization) with clear mechanistic pathway placement","pmids":["23986476"],"is_preprint":false},{"year":2013,"finding":"The MIT domain of SNX15 (and SNX15a splice variant) binds phosphoinositides in a Ca2+-dependent manner, with Ca2+ coordinated by the loop between the first and second α-helices of the MIT domain, suggesting the MIT domain is a membrane-associating module involved in endosomal trafficking.","method":"In vitro Ca2+-binding assay, phosphoinositide-binding assay, domain analysis of recombinant MIT domains from Vps4b and SNX15a","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 — in vitro biochemical assays, but single study with limited mutagenesis validation","pmids":["23423459"],"is_preprint":false},{"year":2015,"finding":"SNX15 localizes to peripheral Hrs (ESCRT-0)-labelled endosomes that are distinct from APPL1-containing endosomes and serve as intermediates in transporting EGFR from the cell surface to more central early endosomes (EEA1-positive). RNA silencing of ESCRT-0 and ESCRT-I impairs EGF transit to EEA1 endosomes, consistent with SNX15 marking an APPL1-independent transit route.","method":"Sub-pixel resolution localization software, particle-based co-localization analysis, RNA silencing, live-cell imaging of endosomal markers","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 — co-localization at subpixel resolution plus RNAi functional validation, single lab","pmids":["25588841"],"is_preprint":false},{"year":2015,"finding":"SNX15 regulates cell surface recycling of APP: overexpression of SNX15 increases APP at the cell surface by accelerating its recycling, while SNX15 knockdown has the opposite effect. This shifts APP processing away from BACE1/γ-secretase, reducing Aβ production. AAV-mediated SNX15 overexpression in mouse hippocampus reduces Aβ pathology and improves working memory in APPswe/PSEN1dE9 AD model mice.","method":"Overexpression and siRNA knockdown in cell lines, cell-surface APP assay, Aβ ELISA, AAV injection in transgenic AD mice with behavioral testing","journal":"Molecular neurobiology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple complementary methods (gain- and loss-of-function, in vivo AAV, biochemical readouts) in single lab","pmids":["26115702"],"is_preprint":false},{"year":2023,"finding":"IST1 interacts with the MIT domain-containing SNX15 on endosomes. SNX15 and IST1 co-occupy a clathrin-containing subdomain on the endosomal perimeter distinct from retromer or ESCRT degradation subdomains. Live-cell microscopy shows that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or to the base of endosomal tubules, indicating SNX15 participates in a subset of recycling pathways from early/sorting endosomes.","method":"Co-immunoprecipitation/binding partner identification, live-cell microscopy, kinetic and spatial co-localization analysis in cells depleted of IST1","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal interaction plus live-cell spatial/kinetic analysis, replicated across peer-reviewed and preprint versions from same lab","pmids":["37926552","37577466"],"is_preprint":false},{"year":2022,"finding":"A novel in-frame RARA-SNX15 fusion protein (RARA-SNX15L) is generated by chromosomal rearrangement and RNA mis-splicing in APL. RARA-SNX15L contains the SNX15 PX (phox homology) domain and, by co-immunoprecipitation, directly associates with wild-type SNX15 and with itself (self-association), demonstrating that the PX domain mediates protein-protein interactions.","method":"Massive parallel RNA sequencing, co-immunoprecipitation in cells expressing RARA-SNX15L","journal":"International journal of hematology","confidence":"Low","confidence_rationale":"Tier 3 — single Co-IP in a disease context, single lab, no functional mutagenesis","pmids":["35854096"],"is_preprint":false}],"current_model":"SNX15 is a sorting nexin that uses its PX domain to bind phosphatidylinositol 3-phosphate on early endosomal membranes and a non-canonical clathrin-binding box to associate with clathrin-coated pits/vesicles, thereby linking clathrin-mediated endocytosis to direct fusion of SNX15-decorated vesicles with Rab5-positive early endosomes (independently of the APPL1 pathway); it additionally regulates recycling of cargoes such as APP to the cell surface and interacts via its MIT domain with IST1/CHMP1B at a distinct clathrin-containing endosomal subdomain to facilitate a subset of endosomal recycling pathways."},"narrative":{"teleology":[{"year":2000,"claim":"Initial characterization established SNX15 as a PX-domain-dependent membrane-associated protein whose overexpression disrupts endosomal compartment morphology and receptor trafficking, placing it as a regulator of endocytic sorting.","evidence":"Subcellular fractionation, co-IP with PDGFR, immunofluorescence of endosomal markers, transferrin endocytosis and furin/receptor processing assays in COS-7 and other mammalian cells","pmids":["11085978","11208079"],"confidence":"High","gaps":["Mechanism of action unclear—overexpression phenotypes do not distinguish direct trafficking role from dominant-negative effects","Endogenous binding partners beyond PDGFR not identified","Loss-of-function data not yet available"]},{"year":2013,"claim":"RNAi and live imaging resolved the specific step at which SNX15 acts: it binds PtdIns3P on early endosomes and clathrin on coated vesicles, mediating direct fusion of newly internalized vesicles with Rab5-positive early endosomes—bypassing the APPL1 intermediate compartment—and its depletion delays EGFR degradative sorting.","evidence":"RNAi loss-of-function, live-cell imaging of vesicle fusion, clathrin-binding and PtdIns3P-binding assays, co-localization with Rab5/APPL1 markers","pmids":["23986476"],"confidence":"High","gaps":["Structural basis of the non-canonical clathrin-binding box not determined","Whether SNX15 is required for all clathrin-coated vesicle–early endosome fusion events or only a subset is unclear"]},{"year":2013,"claim":"The MIT domain of SNX15 was shown to bind phosphoinositides in a Ca²⁺-dependent manner, revealing a second membrane-interaction module beyond the PX domain.","evidence":"In vitro Ca²⁺-binding and phosphoinositide-binding assays with recombinant MIT domains","pmids":["23423459"],"confidence":"Medium","gaps":["Ca²⁺-dependent binding not validated by mutagenesis in cells","Relative contributions of PX and MIT domains to membrane targeting in vivo not dissected"]},{"year":2015,"claim":"Sub-pixel localization placed SNX15 on peripheral Hrs/ESCRT-0-positive endosomes distinct from APPL1 endosomes, defining a specific endosomal transit route from the cell surface to EEA1-positive central early endosomes that depends on ESCRT-0/ESCRT-I.","evidence":"Sub-pixel resolution co-localization, RNA silencing of ESCRT-0/I, live-cell imaging","pmids":["25588841"],"confidence":"Medium","gaps":["Whether SNX15 is a passive marker or an active driver of this ESCRT-dependent transit route is unresolved","Cargo specificity of this pathway beyond EGFR not tested"]},{"year":2015,"claim":"A functional role for SNX15 in cargo recycling was established: SNX15 promotes APP return to the cell surface, diverting it from amyloidogenic processing, with in vivo validation in an Alzheimer's disease mouse model.","evidence":"Overexpression and siRNA knockdown in cell lines, cell-surface APP assay, Aβ ELISA, AAV-mediated hippocampal overexpression in APPswe/PSEN1dE9 transgenic mice with behavioral testing","pmids":["26115702"],"confidence":"Medium","gaps":["Direct physical interaction between SNX15 and APP not demonstrated","Mechanism by which SNX15 accelerates recycling (coat assembly, tubule scission, adaptor recruitment) unknown","Relevance to non-APP recycling cargoes not explored"]},{"year":2023,"claim":"Identification of IST1 and CHMP1B as MIT-domain-dependent interaction partners localized SNX15 to a clathrin-containing endosomal subdomain spatially distinct from retromer and ESCRT degradation subdomains, linking SNX15 to a specific subset of endosomal recycling pathways.","evidence":"Co-immunoprecipitation, live-cell microscopy with kinetic and spatial co-localization analysis","pmids":["37926552","37577466"],"confidence":"Medium","gaps":["Cargoes recycled through the SNX15–IST1 subdomain not identified","Whether IST1 or CHMP1B provides membrane-remodeling activity at this subdomain is untested","Functional consequence of disrupting the SNX15–IST1 interaction on recycling efficiency not measured"]},{"year":null,"claim":"The specific cargoes sorted through the SNX15–IST1–clathrin endosomal subdomain, the structural basis for SNX15's dual membrane-binding mode (PX + MIT), and whether SNX15 actively drives membrane scission or tubule formation remain open questions.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of full-length SNX15 or its domain–membrane interactions","Cargo repertoire beyond EGFR and APP undefined","Reconstitution of SNX15-mediated vesicle–endosome fusion in a minimal system not achieved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,2,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,6]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1,2,4,6]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[2]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,2,4,5,6]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[2,5,6]}],"complexes":[],"partners":["IST1","CHMP1B","CLTC"],"other_free_text":[]},"mechanistic_narrative":"SNX15 is a sorting nexin that functions at the interface of clathrin-mediated endocytosis and early endosomal sorting, regulating the trafficking of receptors and transmembrane cargoes between the plasma membrane, early endosomes, and the trans-Golgi network. It binds phosphatidylinositol 3-phosphate via its PX domain and associates with clathrin-coated pits/vesicles through a non-canonical clathrin-binding box, enabling SNX15-decorated endocytic vesicles to fuse directly with Rab5-positive early endosomes independently of the APPL1 pathway [PMID:23986476, PMID:25588841]. SNX15 promotes cell-surface recycling of cargoes such as APP, shifting APP processing away from amyloidogenic cleavage and reducing Aβ production both in vitro and in vivo [PMID:26115702]. Its MIT domain interacts with IST1 and CHMP1B on a clathrin-containing endosomal subdomain distinct from retromer or ESCRT degradation domains, positioning SNX15 in a subset of endosomal recycling pathways [PMID:37926552]."},"prefetch_data":{"uniprot":{"accession":"Q9NRS6","full_name":"Sorting nexin-15","aliases":[],"length_aa":342,"mass_kda":38.3,"function":"May be involved in several stages of intracellular trafficking. Overexpression of SNX15 disrupts the normal trafficking of proteins from the plasma membrane to recycling endosomes or the TGN","subcellular_location":"Cytoplasm; Membrane; Cytoplasmic vesicle membrane","url":"https://www.uniprot.org/uniprotkb/Q9NRS6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SNX15","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":1208,"dependency_fraction":0.009105960264900662},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SNX15","total_profiled":1310},"omim":[{"mim_id":"619200","title":"SORTING NEXIN FAMILY, MEMBER 21; SNX21","url":"https://www.omim.org/entry/619200"},{"mim_id":"607111","title":"SPARTIN; SPART","url":"https://www.omim.org/entry/607111"},{"mim_id":"605964","title":"SORTING NEXIN 15; SNX15","url":"https://www.omim.org/entry/605964"},{"mim_id":"173490","title":"PLATELET-DERIVED GROWTH FACTOR RECEPTOR, ALPHA; PDGFRA","url":"https://www.omim.org/entry/173490"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNX15"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9NRS6","domains":[{"cath_id":"3.30.1520.10","chopping":"8-132","consensus_level":"high","plddt":89.6446,"start":8,"end":132},{"cath_id":"1.20.58.80","chopping":"266-342","consensus_level":"medium","plddt":91.1808,"start":266,"end":342}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NRS6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NRS6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NRS6-F1-predicted_aligned_error_v6.png","plddt_mean":72.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNX15","jax_strain_url":"https://www.jax.org/strain/search?query=SNX15"},"sequence":{"accession":"Q9NRS6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NRS6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NRS6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NRS6"}},"corpus_meta":[{"pmid":"11085978","id":"PMC_11085978","title":"Identification and characterization of SNX15, a novel sorting nexin involved in protein trafficking.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11085978","citation_count":78,"is_preprint":false},{"pmid":"11208079","id":"PMC_11208079","title":"Overexpression of a novel sorting nexin, SNX15, affects endosome morphology and protein trafficking.","date":"2000","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/11208079","citation_count":43,"is_preprint":false},{"pmid":"20145299","id":"PMC_20145299","title":"Transcriptomic signature of cell lines isolated from canine mammary adenocarcinoma metastases to lungs.","date":"2010","source":"Journal of applied genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20145299","citation_count":42,"is_preprint":false},{"pmid":"16018968","id":"PMC_16018968","title":"Structural characterization of the MIT domain from human Vps4b.","date":"2005","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16018968","citation_count":30,"is_preprint":false},{"pmid":"23986476","id":"PMC_23986476","title":"SNX15 links clathrin endocytosis to the PtdIns3P early endosome independently of the APPL1 endosome.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23986476","citation_count":24,"is_preprint":false},{"pmid":"25588841","id":"PMC_25588841","title":"ESCRT-0 marks an APPL1-independent transit route for EGFR between the cell surface and the EEA1-positive early endosome.","date":"2015","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/25588841","citation_count":21,"is_preprint":false},{"pmid":"34831096","id":"PMC_34831096","title":"Transcriptomic-Based Identification of the Immuno-Oncogenic Signature of Cholangiocarcinoma for HLC-018 Multi-Target Therapy Exploration.","date":"2021","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/34831096","citation_count":21,"is_preprint":false},{"pmid":"33539531","id":"PMC_33539531","title":"A Genome-Wide Association Study Identifies Novel Susceptibility loci in Chronic Chagas Cardiomyopathy.","date":"2021","source":"Clinical infectious diseases : an official publication of the Infectious Diseases Society of America","url":"https://pubmed.ncbi.nlm.nih.gov/33539531","citation_count":16,"is_preprint":false},{"pmid":"26115702","id":"PMC_26115702","title":"SNX15 Regulates Cell Surface Recycling of APP and Aβ Generation.","date":"2015","source":"Molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/26115702","citation_count":14,"is_preprint":false},{"pmid":"37926552","id":"PMC_37926552","title":"IST1 regulates select recycling pathways.","date":"2023","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/37926552","citation_count":10,"is_preprint":false},{"pmid":"23423459","id":"PMC_23423459","title":"MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.","date":"2013","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23423459","citation_count":10,"is_preprint":false},{"pmid":"15372247","id":"PMC_15372247","title":"A clinical, genetic and candidate gene study of Silver syndrome, a complicated form of hereditary spastic paraplegia.","date":"2004","source":"Journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/15372247","citation_count":9,"is_preprint":false},{"pmid":"35854096","id":"PMC_35854096","title":"A novel RARA-SNX15 fusion in PML-RARA-positive acute promyelocytic leukemia with t(11;17;15)(q13;q21.2;q24.1).","date":"2022","source":"International journal of hematology","url":"https://pubmed.ncbi.nlm.nih.gov/35854096","citation_count":2,"is_preprint":false},{"pmid":"37577466","id":"PMC_37577466","title":"IST1 regulates select endosomal recycling pathways.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37577466","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8090,"output_tokens":2321,"usd":0.029542},"stage2":{"model":"claude-opus-4-6","input_tokens":5609,"output_tokens":2131,"usd":0.12198},"total_usd":0.151522,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"SNX15 is found on membranes and in the cytosol; the PX (phox homology) domain is required for membrane association and for association with the platelet-derived growth factor receptor (PDGFR). Overexpression of SNX15 disrupts normal trafficking of proteins from the plasma membrane to recycling endosomes or the trans-Golgi network, leading to mislocalization of furin and decreased processing of insulin and hepatocyte growth factor receptors.\",\n      \"method\": \"Subcellular fractionation, immunofluorescence, co-immunoprecipitation, overexpression in mammalian cells with functional readouts (receptor processing, furin localization)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (fractionation, co-IP, IF, biochemical processing assays) in original characterization paper\",\n      \"pmids\": [\"11085978\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Overexpression of SNX15 in COS-7 cells alters endosomal compartment morphology (generating large, amorphous membrane-limited structures containing lysosomal, late endosomal, early endosomal, and TGN markers), severely inhibits transferrin endocytosis, and slows endocytosis and recycling of tac-TGN38 and tac-furin, establishing SNX15 as a regulator of endocytic pathway trafficking.\",\n      \"method\": \"Transient transfection of myc-tagged SNX15, immunofluorescence microscopy, transferrin endocytosis assay, tac-TGN38/tac-furin trafficking assays in COS-7 cells\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal functional assays (morphology, endocytosis, recycling) with loss- and gain-of-function readouts\",\n      \"pmids\": [\"11208079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SNX15 associates with early endosomes via its PX domain in a phosphatidylinositol 3-phosphate (PtdIns3P)-dependent manner, and also associates directly with clathrin-coated pits and clathrin-coated vesicles through a non-canonical clathrin-binding box. SNX15 depletion (RNAi) delays EGF receptor degradative sorting by impairing movement of newly internalized EGFR-labelled vesicles into early endosomes. Live-cell imaging shows that SNX15-labelled endocytic vesicles fuse directly with Rab5-positive early endosomes independently of the APPL1 compartment.\",\n      \"method\": \"RNAi loss-of-function screen, live-cell imaging, direct clathrin-binding assay, PtdIns3P-binding PX-domain experiments, co-localization with endosomal markers\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (RNAi, live imaging, direct binding, endosomal marker co-localization) with clear mechanistic pathway placement\",\n      \"pmids\": [\"23986476\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The MIT domain of SNX15 (and SNX15a splice variant) binds phosphoinositides in a Ca2+-dependent manner, with Ca2+ coordinated by the loop between the first and second α-helices of the MIT domain, suggesting the MIT domain is a membrane-associating module involved in endosomal trafficking.\",\n      \"method\": \"In vitro Ca2+-binding assay, phosphoinositide-binding assay, domain analysis of recombinant MIT domains from Vps4b and SNX15a\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro biochemical assays, but single study with limited mutagenesis validation\",\n      \"pmids\": [\"23423459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SNX15 localizes to peripheral Hrs (ESCRT-0)-labelled endosomes that are distinct from APPL1-containing endosomes and serve as intermediates in transporting EGFR from the cell surface to more central early endosomes (EEA1-positive). RNA silencing of ESCRT-0 and ESCRT-I impairs EGF transit to EEA1 endosomes, consistent with SNX15 marking an APPL1-independent transit route.\",\n      \"method\": \"Sub-pixel resolution localization software, particle-based co-localization analysis, RNA silencing, live-cell imaging of endosomal markers\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — co-localization at subpixel resolution plus RNAi functional validation, single lab\",\n      \"pmids\": [\"25588841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SNX15 regulates cell surface recycling of APP: overexpression of SNX15 increases APP at the cell surface by accelerating its recycling, while SNX15 knockdown has the opposite effect. This shifts APP processing away from BACE1/γ-secretase, reducing Aβ production. AAV-mediated SNX15 overexpression in mouse hippocampus reduces Aβ pathology and improves working memory in APPswe/PSEN1dE9 AD model mice.\",\n      \"method\": \"Overexpression and siRNA knockdown in cell lines, cell-surface APP assay, Aβ ELISA, AAV injection in transgenic AD mice with behavioral testing\",\n      \"journal\": \"Molecular neurobiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple complementary methods (gain- and loss-of-function, in vivo AAV, biochemical readouts) in single lab\",\n      \"pmids\": [\"26115702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"IST1 interacts with the MIT domain-containing SNX15 on endosomes. SNX15 and IST1 co-occupy a clathrin-containing subdomain on the endosomal perimeter distinct from retromer or ESCRT degradation subdomains. Live-cell microscopy shows that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or to the base of endosomal tubules, indicating SNX15 participates in a subset of recycling pathways from early/sorting endosomes.\",\n      \"method\": \"Co-immunoprecipitation/binding partner identification, live-cell microscopy, kinetic and spatial co-localization analysis in cells depleted of IST1\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction plus live-cell spatial/kinetic analysis, replicated across peer-reviewed and preprint versions from same lab\",\n      \"pmids\": [\"37926552\", \"37577466\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A novel in-frame RARA-SNX15 fusion protein (RARA-SNX15L) is generated by chromosomal rearrangement and RNA mis-splicing in APL. RARA-SNX15L contains the SNX15 PX (phox homology) domain and, by co-immunoprecipitation, directly associates with wild-type SNX15 and with itself (self-association), demonstrating that the PX domain mediates protein-protein interactions.\",\n      \"method\": \"Massive parallel RNA sequencing, co-immunoprecipitation in cells expressing RARA-SNX15L\",\n      \"journal\": \"International journal of hematology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP in a disease context, single lab, no functional mutagenesis\",\n      \"pmids\": [\"35854096\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNX15 is a sorting nexin that uses its PX domain to bind phosphatidylinositol 3-phosphate on early endosomal membranes and a non-canonical clathrin-binding box to associate with clathrin-coated pits/vesicles, thereby linking clathrin-mediated endocytosis to direct fusion of SNX15-decorated vesicles with Rab5-positive early endosomes (independently of the APPL1 pathway); it additionally regulates recycling of cargoes such as APP to the cell surface and interacts via its MIT domain with IST1/CHMP1B at a distinct clathrin-containing endosomal subdomain to facilitate a subset of endosomal recycling pathways.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SNX15 is a sorting nexin that functions at the interface of clathrin-mediated endocytosis and early endosomal sorting, regulating the trafficking of receptors and transmembrane cargoes between the plasma membrane, early endosomes, and the trans-Golgi network. It binds phosphatidylinositol 3-phosphate via its PX domain and associates with clathrin-coated pits/vesicles through a non-canonical clathrin-binding box, enabling SNX15-decorated endocytic vesicles to fuse directly with Rab5-positive early endosomes independently of the APPL1 pathway [PMID:23986476, PMID:25588841]. SNX15 promotes cell-surface recycling of cargoes such as APP, shifting APP processing away from amyloidogenic cleavage and reducing Aβ production both in vitro and in vivo [PMID:26115702]. Its MIT domain interacts with IST1 and CHMP1B on a clathrin-containing endosomal subdomain distinct from retromer or ESCRT degradation domains, positioning SNX15 in a subset of endosomal recycling pathways [PMID:37926552].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Initial characterization established SNX15 as a PX-domain-dependent membrane-associated protein whose overexpression disrupts endosomal compartment morphology and receptor trafficking, placing it as a regulator of endocytic sorting.\",\n      \"evidence\": \"Subcellular fractionation, co-IP with PDGFR, immunofluorescence of endosomal markers, transferrin endocytosis and furin/receptor processing assays in COS-7 and other mammalian cells\",\n      \"pmids\": [\"11085978\", \"11208079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism of action unclear—overexpression phenotypes do not distinguish direct trafficking role from dominant-negative effects\",\n        \"Endogenous binding partners beyond PDGFR not identified\",\n        \"Loss-of-function data not yet available\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"RNAi and live imaging resolved the specific step at which SNX15 acts: it binds PtdIns3P on early endosomes and clathrin on coated vesicles, mediating direct fusion of newly internalized vesicles with Rab5-positive early endosomes—bypassing the APPL1 intermediate compartment—and its depletion delays EGFR degradative sorting.\",\n      \"evidence\": \"RNAi loss-of-function, live-cell imaging of vesicle fusion, clathrin-binding and PtdIns3P-binding assays, co-localization with Rab5/APPL1 markers\",\n      \"pmids\": [\"23986476\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the non-canonical clathrin-binding box not determined\",\n        \"Whether SNX15 is required for all clathrin-coated vesicle–early endosome fusion events or only a subset is unclear\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The MIT domain of SNX15 was shown to bind phosphoinositides in a Ca²⁺-dependent manner, revealing a second membrane-interaction module beyond the PX domain.\",\n      \"evidence\": \"In vitro Ca²⁺-binding and phosphoinositide-binding assays with recombinant MIT domains\",\n      \"pmids\": [\"23423459\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Ca²⁺-dependent binding not validated by mutagenesis in cells\",\n        \"Relative contributions of PX and MIT domains to membrane targeting in vivo not dissected\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Sub-pixel localization placed SNX15 on peripheral Hrs/ESCRT-0-positive endosomes distinct from APPL1 endosomes, defining a specific endosomal transit route from the cell surface to EEA1-positive central early endosomes that depends on ESCRT-0/ESCRT-I.\",\n      \"evidence\": \"Sub-pixel resolution co-localization, RNA silencing of ESCRT-0/I, live-cell imaging\",\n      \"pmids\": [\"25588841\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether SNX15 is a passive marker or an active driver of this ESCRT-dependent transit route is unresolved\",\n        \"Cargo specificity of this pathway beyond EGFR not tested\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"A functional role for SNX15 in cargo recycling was established: SNX15 promotes APP return to the cell surface, diverting it from amyloidogenic processing, with in vivo validation in an Alzheimer's disease mouse model.\",\n      \"evidence\": \"Overexpression and siRNA knockdown in cell lines, cell-surface APP assay, Aβ ELISA, AAV-mediated hippocampal overexpression in APPswe/PSEN1dE9 transgenic mice with behavioral testing\",\n      \"pmids\": [\"26115702\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct physical interaction between SNX15 and APP not demonstrated\",\n        \"Mechanism by which SNX15 accelerates recycling (coat assembly, tubule scission, adaptor recruitment) unknown\",\n        \"Relevance to non-APP recycling cargoes not explored\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identification of IST1 and CHMP1B as MIT-domain-dependent interaction partners localized SNX15 to a clathrin-containing endosomal subdomain spatially distinct from retromer and ESCRT degradation subdomains, linking SNX15 to a specific subset of endosomal recycling pathways.\",\n      \"evidence\": \"Co-immunoprecipitation, live-cell microscopy with kinetic and spatial co-localization analysis\",\n      \"pmids\": [\"37926552\", \"37577466\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Cargoes recycled through the SNX15–IST1 subdomain not identified\",\n        \"Whether IST1 or CHMP1B provides membrane-remodeling activity at this subdomain is untested\",\n        \"Functional consequence of disrupting the SNX15–IST1 interaction on recycling efficiency not measured\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific cargoes sorted through the SNX15–IST1–clathrin endosomal subdomain, the structural basis for SNX15's dual membrane-binding mode (PX + MIT), and whether SNX15 actively drives membrane scission or tubule formation remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of full-length SNX15 or its domain–membrane interactions\",\n        \"Cargo repertoire beyond EGFR and APP undefined\",\n        \"Reconstitution of SNX15-mediated vesicle–endosome fusion in a minimal system not achieved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1, 2, 4, 6]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 2, 4, 5, 6]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [2, 5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"IST1\",\n      \"CHMP1B\",\n      \"CLTC\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}