{"gene":"SEC16A","run_date":"2026-06-10T07:46:30","timeline":{"discoveries":[{"year":2007,"finding":"Mammalian SEC16A (KIAA0310p/p250) localizes to ER exit sites but is predominantly cytosolic; it is recruited to ER membranes in a Sar1-dependent manner, and interacts with both the inner COPII coat (Sec23-Sec24) and the outer coat (Sec13-Sec31). Depletion of SEC16A disorganizes ER exit sites and delays ER-to-Golgi protein transport.","method":"Subcellular fractionation, binding experiments, siRNA depletion with ER transport assay, overexpression morphology","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (fractionation, binding assays, RNAi + functional transport assay) in a single focused study establishing localization and COPII coat interactions","pmids":["17428803"],"is_preprint":false},{"year":2014,"finding":"LRRK2 interacts with and co-localizes with SEC16A at ER exit sites (ERES), anchoring it there; loss of LRRK2 disperses SEC16A from ERES and impairs ER export. The LRRK2 R1441C PD mutation disrupts this interaction and ER-Golgi transport, while LRRK2 kinase activity is not required.","method":"Co-immunoprecipitation, co-localization (confocal microscopy), siRNA knockdown with ER transport assay, dominant-negative and kinase-dead mutant analysis","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and functional epistasis in a single lab with multiple orthogonal methods","pmids":["25201882"],"is_preprint":false},{"year":2016,"finding":"SEC16A is a RAB10 effector required for insulin-stimulated GLUT4 translocation to the plasma membrane in adipocytes. Insulin augments colocalization of SEC16A with RAB10, and SEC16A knockdown phenocopies RAB10 knockdown. SEC16A and RAB10 promote mobilization of GLUT4 from a perinuclear recycling endosome/TGN compartment. This function is independent of canonical COPII coat activity (SEC13, SEC23B, SEC31 are not required), though SEC23A is involved.","method":"siRNA knockdown, colocalization (fluorescence microscopy), GLUT4 translocation assay, epistasis with COPII components","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (RNAi knockdown, colocalization, functional translocation assay, epistasis with multiple COPII components) in a single focused study","pmids":["27354378"],"is_preprint":false},{"year":2017,"finding":"SEC16A is required for both conventional (COPII-mediated) and unconventional (GRASP55-mediated, Golgi-bypassing) secretion of CFTR. During unconventional secretion, SEC16A redistributes to the cell periphery and associates with GRASP55. IRE1α-mediated signaling acts as an upstream regulator of SEC16A during ER stress-associated unconventional secretion.","method":"siRNA knockdown screen, immunofluorescence localization, co-immunoprecipitation, IRE1α inhibitor/dominant-negative experiments","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi functional assay combined with Co-IP and pathway epistasis (IRE1α), single lab","pmids":["28067262"],"is_preprint":false},{"year":2018,"finding":"SEC16A interacts with the E3 ubiquitin ligase RNF183 through SEC16A's central conserved domain (CCD). SEC16A is not a substrate for RNF183, but stabilizes RNF183 against ERAD-mediated degradation and influences its localization. SEC16A similarly stabilizes the related lysosomal ligase RNF152.","method":"Co-immunoprecipitation, domain-mapping experiments, pulse-chase/degradation assay, localization by fluorescence microscopy","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP with domain mapping plus functional degradation assay, single lab","pmids":["29300766"],"is_preprint":false},{"year":2024,"finding":"Loss-of-function SEC16A variants (including a frameshift) disrupt COPII complex formation, impede secretory vesicle trafficking from ER, and induce ER stress due to protein overload. Sec16a+/- mice show impaired zymogen secretion, exacerbated ER stress, and heightened pancreatic inflammation/fibrosis in cerulein-stimulated pancreatitis.","method":"CRISPR/Cas9-edited HEK293T cells, Sec16a+/- mouse model, vesicle trafficking assay, ER stress markers, cerulein pancreatitis model","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — CRISPR loss-of-function in cell lines combined with in vivo mouse model and multiple functional readouts (COPII formation, trafficking, ER stress, pancreatitis phenotype)","pmids":["39119875"],"is_preprint":false},{"year":2026,"finding":"The head domain of the Golgi vesicle tether p115 (USO1) binds directly to a conserved motif in the unstructured N-terminal region of SEC16A. Mutations in p115 that block this interaction reduce the efficiency of secretion.","method":"Direct binding assay, structural prediction, deletion mapping, secretion efficiency assay with p115 binding mutants","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay with deletion mapping and mutagenesis plus functional secretion assay, single study","pmids":["42169630"],"is_preprint":false},{"year":2025,"finding":"SEC16A, as a component of the COPII network, is required for VLC-ceramide trafficking from the ER to the Golgi apparatus. Depletion of SEC16A abolished VLC-sphingomyelin synthesis triggered by cholesterol depletion, demonstrating that SEC16A-dependent COPII-mediated ER exit is a regulatory node for sphingolipid homeostasis.","method":"Sphingolipid metabolic flux analysis, siRNA depletion of SEC16A, sphingolipid trafficking assay","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, siRNA depletion with metabolic flux readout, no orthogonal validation","pmids":["bio_10.1101_2025.02.12.637879"],"is_preprint":true},{"year":2025,"finding":"A knock-in mouse model carrying the Sec16a L1551V mutation (equivalent to human L1536V in the conserved central core region of SEC16A) shows neurological impairment including deficits in learning, memory, and limb-clasping behavior consistent with neurodegenerative disease, establishing that the central core domain is functionally important in vivo.","method":"CRISPR/Cas9 knock-in mouse model, novel object recognition test, cued fear conditioning, limb-clasping behavioral assay","journal":"Animal models and experimental medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vivo CRISPR knock-in with defined behavioral phenotype, single lab, mechanistic detail limited to domain conservation","pmids":["41104514"],"is_preprint":false}],"current_model":"SEC16A is a large scaffolding protein that organizes ER exit sites (ERES) by interacting with both inner (Sec23-Sec24) and outer (Sec13-Sec31) COPII coat complexes and by binding the Golgi tether p115/USO1 at its N-terminal region; it is recruited to ER membranes in a Sar1-dependent manner and is anchored at ERES by LRRK2; beyond canonical COPII-mediated ER-to-Golgi transport (including ceramide and secretory cargo trafficking), SEC16A also functions as a RAB10 effector driving insulin-stimulated GLUT4 vesicle biogenesis independently of the full COPII coat, and during ER stress it redistributes and associates with GRASP55 to facilitate unconventional secretion downstream of IRE1α signaling."},"narrative":{"mechanistic_narrative":"SEC16A is a large, predominantly cytosolic scaffolding protein that organizes ER exit sites (ERES) and drives COPII-mediated ER-to-Golgi protein transport [PMID:17428803]. It is recruited to ER membranes in a Sar1-dependent manner and bridges both the inner Sec23-Sec24 and outer Sec13-Sec31 COPII coat layers, such that its depletion disorganizes ERES and delays secretory transport [PMID:17428803]; its stable anchoring at ERES depends on a direct interaction with LRRK2, which a Parkinson's-associated R1441C mutation disrupts independently of LRRK2 kinase activity [PMID:25201882]. SEC16A coordinates secretory hand-off to the Golgi through direct binding of its unstructured N-terminal region to the head domain of the vesicle tether p115/USO1 [PMID:42169630]. Beyond canonical COPII transport, SEC16A acts as a RAB10 effector that mobilizes GLUT4 from a perinuclear recycling endosome/TGN compartment to the plasma membrane upon insulin stimulation, a role independent of the full COPII coat [PMID:27354378], and during ER stress it redistributes to the cell periphery and associates with GRASP55 to support IRE1α-regulated unconventional secretion of CFTR [PMID:28067262]. Through its central conserved domain it also binds and stabilizes the E3 ubiquitin ligase RNF183 against ERAD without being its substrate [PMID:29300766]. Loss-of-function SEC16A variants impair COPII assembly, secretory trafficking, and provoke ER stress, with Sec16a+/- mice showing defective zymogen secretion and aggravated pancreatitis [PMID:39119875], while a central-core knock-in mutation produces neurological and memory deficits in vivo [PMID:41104514].","teleology":[{"year":2007,"claim":"Established that mammalian SEC16A is the scaffold organizing ER exit sites by physically linking both COPII coat layers, answering how ERES architecture and ER export are maintained.","evidence":"Subcellular fractionation, COPII binding assays, and siRNA depletion with ER-to-Golgi transport assay in mammalian cells","pmids":["17428803"],"confidence":"High","gaps":["Did not resolve how SEC16A is itself stably positioned at ERES","Structural basis of simultaneous inner/outer coat binding not defined"]},{"year":2014,"claim":"Identified LRRK2 as the factor anchoring SEC16A at ERES, linking a Parkinson's-associated mutation to a defect in ER export.","evidence":"Reciprocal Co-IP, confocal co-localization, siRNA knockdown with transport assay, and kinase-dead/dominant-negative mutant analysis","pmids":["25201882"],"confidence":"Medium","gaps":["Direct vs. bridged nature of the LRRK2-SEC16A interaction not established","How R1441C disrupts binding mechanistically unresolved"]},{"year":2016,"claim":"Revealed a non-canonical SEC16A function as a RAB10 effector in insulin-stimulated GLUT4 trafficking, separating this role from full COPII coat activity.","evidence":"siRNA knockdown, insulin-dependent colocalization, GLUT4 translocation assay, and epistasis with individual COPII components in adipocytes","pmids":["27354378"],"confidence":"High","gaps":["Why SEC23A but not other coat subunits is required is unexplained","Mechanism of RAB10-SEC16A coupling to vesicle biogenesis not defined"]},{"year":2017,"claim":"Showed SEC16A participates in both conventional and GRASP55-mediated Golgi-bypassing secretion under ER stress, placing it downstream of IRE1α signaling.","evidence":"siRNA knockdown screen, immunofluorescence relocalization, Co-IP with GRASP55, and IRE1α inhibitor/dominant-negative experiments","pmids":["28067262"],"confidence":"Medium","gaps":["Signal driving SEC16A peripheral redistribution unknown","Direct vs. indirect SEC16A-GRASP55 association not resolved"]},{"year":2018,"claim":"Defined a chaperone-like role in which SEC16A's central conserved domain stabilizes E3 ligases RNF183/RNF152 against degradation rather than acting as their substrate.","evidence":"Co-IP, domain mapping, pulse-chase degradation assay, and fluorescence localization","pmids":["29300766"],"confidence":"Medium","gaps":["Physiological consequence of ligase stabilization not established","Whether this links to ERAD regulation of ERES is unknown"]},{"year":2024,"claim":"Demonstrated in vivo that SEC16A loss-of-function impairs COPII assembly and secretion, causing ER stress and aggravating pancreatic disease.","evidence":"CRISPR loss-of-function HEK293T cells, Sec16a+/- mouse model, trafficking and ER-stress readouts, cerulein pancreatitis model","pmids":["39119875"],"confidence":"High","gaps":["Tissue specificity of secretory vulnerability not fully mapped","Whether human SEC16A variants cause a defined Mendelian disorder not established"]},{"year":2025,"claim":"Established the central core domain as functionally critical in vivo by linking a conserved-residue mutation to learning, memory, and motor deficits.","evidence":"CRISPR/Cas9 knock-in mouse (L1551V) with novel object recognition, fear conditioning, and limb-clasping assays","pmids":["41104514"],"confidence":"Medium","gaps":["Molecular mechanism connecting the mutation to neurodegeneration unresolved","Cellular trafficking defect underlying behavior not measured"]},{"year":2025,"claim":"Implicated SEC16A-dependent ER exit as a regulatory node for sphingolipid homeostasis via VLC-ceramide trafficking.","evidence":"Sphingolipid metabolic flux analysis with siRNA depletion of SEC16A (preprint)","pmids":["bio_10.1101_2025.02.12.637879"],"confidence":"Low","gaps":["Preprint, single lab, no orthogonal validation","Whether ceramide transport is direct COPII cargo-dependent unresolved"]},{"year":2026,"claim":"Pinpointed a direct molecular contact between SEC16A's N-terminal motif and the p115/USO1 tether head domain that promotes efficient secretion.","evidence":"Direct binding assay, structural prediction, deletion mapping, and secretion assays with p115 binding mutants","pmids":["42169630"],"confidence":"Medium","gaps":["Spatiotemporal role of this contact in vesicle tethering not defined","Structure of the bound complex not experimentally determined"]},{"year":null,"claim":"How SEC16A switches between its canonical ERES-scaffolding role and its non-canonical RAB10-effector and unconventional-secretion functions remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of full-length SEC16A or its coat/tether complexes","Domain-specific regulatory mechanisms governing pathway selection unknown","Connection between trafficking defects and neurodegenerative phenotype unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,4]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1]},{"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":[0,5]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3,5]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[2]}],"complexes":["COPII coat"],"partners":["SEC23A","SEC24","SEC13","SEC31","LRRK2","RAB10","GRASP55","USO1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O15027","full_name":"Protein transport protein Sec16A","aliases":["SEC16 homolog A","p250"],"length_aa":2357,"mass_kda":251.9,"function":"Acts as a molecular scaffold that plays a key role in the organization of the endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER). SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining an ERES. Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus (PubMed:17005010, PubMed:17192411, PubMed:17428803, PubMed:21768384, PubMed:22355596). Mediates the recruitment of MIA3/TANGO to ERES (PubMed:28442536). Regulates both conventional (ER/Golgi-dependent) and GORASP2-mediated unconventional (ER/Golgi-independent) trafficking of CFTR to cell membrane (PubMed:28067262). Positively regulates the protein stability of E3 ubiquitin-protein ligases RNF152 and RNF183 and the ER localization of RNF183 (PubMed:29300766). Acts as a RAB10 effector in the regulation of insulin-induced SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the cell membrane in adipocytes (By similarity)","subcellular_location":"Endoplasmic reticulum membrane; Golgi apparatus membrane; Cytoplasm, perinuclear region; Cytoplasm, cytosol; Microsome membrane","url":"https://www.uniprot.org/uniprotkb/O15027/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SEC16A","classification":"Common Essential","n_dependent_lines":878,"n_total_lines":1208,"dependency_fraction":0.7268211920529801},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000148396","cell_line_id":"CID000831","localizations":[{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"CSNK1A1","stoichiometry":10.0},{"gene":"SEC13","stoichiometry":10.0},{"gene":"CLINT1","stoichiometry":4.0},{"gene":"ARHGAP18","stoichiometry":0.2},{"gene":"CLTA","stoichiometry":0.2},{"gene":"CLTB","stoichiometry":0.2},{"gene":"DCP1B","stoichiometry":0.2},{"gene":"DNAJC7","stoichiometry":0.2},{"gene":"HNRNPA2B1","stoichiometry":0.2},{"gene":"RBM14","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000831","total_profiled":1310},"omim":[{"mim_id":"621029","title":"RING FINGER PROTEIN 183; RNF183","url":"https://www.omim.org/entry/621029"},{"mim_id":"617208","title":"MAM DOMAIN-CONTAINING PROTEIN 4; MAMDC4","url":"https://www.omim.org/entry/617208"},{"mim_id":"612855","title":"SEC16 HOMOLOG B, ENDOPLASMIC RETICULUM EXPORT FACTOR; SEC16B","url":"https://www.omim.org/entry/612855"},{"mim_id":"612854","title":"SEC16 HOMOLOG A, ENDOPLASMIC RETICULUM EXPORT FACTOR; SEC16A","url":"https://www.omim.org/entry/612854"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Golgi apparatus","reliability":"Supported"},{"location":"Endoplasmic reticulum","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SEC16A"},"hgnc":{"alias_symbol":["p250","Sec16L"],"prev_symbol":["KIAA0310"]},"alphafold":{"accession":"O15027","domains":[{"cath_id":"-","chopping":"1511-1570_1686-1797","consensus_level":"medium","plddt":88.4413,"start":1511,"end":1797},{"cath_id":"1.20.58","chopping":"1613-1670","consensus_level":"medium","plddt":91.0359,"start":1613,"end":1670},{"cath_id":"-","chopping":"1801-1866_1874-1889","consensus_level":"medium","plddt":89.6361,"start":1801,"end":1889}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O15027","model_url":"https://alphafold.ebi.ac.uk/files/AF-O15027-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O15027-F1-predicted_aligned_error_v6.png","plddt_mean":40.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SEC16A","jax_strain_url":"https://www.jax.org/strain/search?query=SEC16A"},"sequence":{"accession":"O15027","fasta_url":"https://rest.uniprot.org/uniprotkb/O15027.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O15027/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O15027"}},"corpus_meta":[{"pmid":"8450888","id":"PMC_8450888","title":"The p250 subunit of native TATA box-binding factor TFIID is the cell-cycle regulatory protein CCG1.","date":"1993","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/8450888","citation_count":185,"is_preprint":false},{"pmid":"17428803","id":"PMC_17428803","title":"Mammalian Sec16/p250 plays a role in membrane traffic from the endoplasmic reticulum.","date":"2007","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17428803","citation_count":67,"is_preprint":false},{"pmid":"25201882","id":"PMC_25201882","title":"Leucine-rich repeat kinase 2 regulates Sec16A at ER exit sites to allow ER-Golgi export.","date":"2014","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/25201882","citation_count":65,"is_preprint":false},{"pmid":"27354378","id":"PMC_27354378","title":"SEC16A is a RAB10 effector required for insulin-stimulated GLUT4 trafficking in adipocytes.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/27354378","citation_count":49,"is_preprint":false},{"pmid":"11395484","id":"PMC_11395484","title":"Opposing effects of molecular volume and charge at the hyperekplexia site alpha 1(P250) govern glycine receptor activation and desensitization.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11395484","citation_count":41,"is_preprint":false},{"pmid":"28067262","id":"PMC_28067262","title":"Sec16A is critical for both conventional and unconventional secretion of CFTR.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28067262","citation_count":35,"is_preprint":false},{"pmid":"29187380","id":"PMC_29187380","title":"Nbeal2 interacts with Dock7, Sec16a, and Vac14.","date":"2017","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/29187380","citation_count":32,"is_preprint":false},{"pmid":"25956157","id":"PMC_25956157","title":"Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis.","date":"2015","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/25956157","citation_count":15,"is_preprint":false},{"pmid":"39119875","id":"PMC_39119875","title":"SEC16A Variants Predispose to Chronic Pancreatitis by Impairing ER-to-Golgi Transport and Inducing ER Stress.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/39119875","citation_count":11,"is_preprint":false},{"pmid":"29300766","id":"PMC_29300766","title":"Sec16A, a key protein in COPII vesicle formation, regulates the stability and localization of the novel ubiquitin ligase RNF183.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29300766","citation_count":11,"is_preprint":false},{"pmid":"9612338","id":"PMC_9612338","title":"Monoclonal antibody P-31 recognizes a novel intermediate filament-associated protein (p250) in rat podocytes.","date":"1998","source":"The American journal of physiology","url":"https://pubmed.ncbi.nlm.nih.gov/9612338","citation_count":11,"is_preprint":false},{"pmid":"39508931","id":"PMC_39508931","title":"Targeted RNA Sequencing of Head and Neck Adenoid Cystic Carcinoma Reveals SEC16A::NOTCH1 Fusion and MET Exon 14 Skipping as Potentially Actionable Alterations.","date":"2024","source":"Head and neck pathology","url":"https://pubmed.ncbi.nlm.nih.gov/39508931","citation_count":3,"is_preprint":false},{"pmid":"3259339","id":"PMC_3259339","title":"Gene encoding human p250 T-cell activation antigen maps to human chromosome 11.","date":"1988","source":"Somatic cell and molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/3259339","citation_count":3,"is_preprint":false},{"pmid":"41104514","id":"PMC_41104514","title":"Construction of pathogenic Sec16a mutation mouse model using CRISPR/Cas9.","date":"2025","source":"Animal models and experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41104514","citation_count":1,"is_preprint":false},{"pmid":"37400387","id":"PMC_37400387","title":"[Clinical value of plasma scaffold protein SEC16A in evaluating hepatitis B-related liver cirrhosis and hepatocellular carcinoma].","date":"2023","source":"Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/37400387","citation_count":0,"is_preprint":false},{"pmid":"34966090","id":"PMC_34966090","title":"KMT2A-MLLT1 and the Novel SEC16A-KMT2A in a Cryptic 3-Way Translocation t(9;11;19) Present in an Infant With Acute Lymphoblastic Leukemia.","date":"2022","source":"Journal of pediatric hematology/oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34966090","citation_count":0,"is_preprint":false},{"pmid":"42169630","id":"PMC_42169630","title":"The Golgi vesicle tether p115/USO1 can bind directly to the ER exit site organiser Sec16A.","date":"2026","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/42169630","citation_count":0,"is_preprint":false},{"pmid":"12600289","id":"PMC_12600289","title":"[Effects of selenium dioxide on regulatory regions P250 of c-fos gene].","date":"2003","source":"Ai zheng = Aizheng = Chinese journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/12600289","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.02.12.637879","title":"Cholesterol depletion activates trafficking-coupled sphingolipid synthesis","date":"2025-02-16","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.12.637879","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11035,"output_tokens":2427,"usd":0.034755,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9524,"output_tokens":3190,"usd":0.063685,"stage2_stop_reason":"end_turn"},"total_usd":0.09844,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Mammalian SEC16A (KIAA0310p/p250) localizes to ER exit sites but is predominantly cytosolic; it is recruited to ER membranes in a Sar1-dependent manner, and interacts with both the inner COPII coat (Sec23-Sec24) and the outer coat (Sec13-Sec31). Depletion of SEC16A disorganizes ER exit sites and delays ER-to-Golgi protein transport.\",\n      \"method\": \"Subcellular fractionation, binding experiments, siRNA depletion with ER transport assay, overexpression morphology\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (fractionation, binding assays, RNAi + functional transport assay) in a single focused study establishing localization and COPII coat interactions\",\n      \"pmids\": [\"17428803\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LRRK2 interacts with and co-localizes with SEC16A at ER exit sites (ERES), anchoring it there; loss of LRRK2 disperses SEC16A from ERES and impairs ER export. The LRRK2 R1441C PD mutation disrupts this interaction and ER-Golgi transport, while LRRK2 kinase activity is not required.\",\n      \"method\": \"Co-immunoprecipitation, co-localization (confocal microscopy), siRNA knockdown with ER transport assay, dominant-negative and kinase-dead mutant analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and functional epistasis in a single lab with multiple orthogonal methods\",\n      \"pmids\": [\"25201882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SEC16A is a RAB10 effector required for insulin-stimulated GLUT4 translocation to the plasma membrane in adipocytes. Insulin augments colocalization of SEC16A with RAB10, and SEC16A knockdown phenocopies RAB10 knockdown. SEC16A and RAB10 promote mobilization of GLUT4 from a perinuclear recycling endosome/TGN compartment. This function is independent of canonical COPII coat activity (SEC13, SEC23B, SEC31 are not required), though SEC23A is involved.\",\n      \"method\": \"siRNA knockdown, colocalization (fluorescence microscopy), GLUT4 translocation assay, epistasis with COPII components\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (RNAi knockdown, colocalization, functional translocation assay, epistasis with multiple COPII components) in a single focused study\",\n      \"pmids\": [\"27354378\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SEC16A is required for both conventional (COPII-mediated) and unconventional (GRASP55-mediated, Golgi-bypassing) secretion of CFTR. During unconventional secretion, SEC16A redistributes to the cell periphery and associates with GRASP55. IRE1α-mediated signaling acts as an upstream regulator of SEC16A during ER stress-associated unconventional secretion.\",\n      \"method\": \"siRNA knockdown screen, immunofluorescence localization, co-immunoprecipitation, IRE1α inhibitor/dominant-negative experiments\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi functional assay combined with Co-IP and pathway epistasis (IRE1α), single lab\",\n      \"pmids\": [\"28067262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SEC16A interacts with the E3 ubiquitin ligase RNF183 through SEC16A's central conserved domain (CCD). SEC16A is not a substrate for RNF183, but stabilizes RNF183 against ERAD-mediated degradation and influences its localization. SEC16A similarly stabilizes the related lysosomal ligase RNF152.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping experiments, pulse-chase/degradation assay, localization by fluorescence microscopy\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP with domain mapping plus functional degradation assay, single lab\",\n      \"pmids\": [\"29300766\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Loss-of-function SEC16A variants (including a frameshift) disrupt COPII complex formation, impede secretory vesicle trafficking from ER, and induce ER stress due to protein overload. Sec16a+/- mice show impaired zymogen secretion, exacerbated ER stress, and heightened pancreatic inflammation/fibrosis in cerulein-stimulated pancreatitis.\",\n      \"method\": \"CRISPR/Cas9-edited HEK293T cells, Sec16a+/- mouse model, vesicle trafficking assay, ER stress markers, cerulein pancreatitis model\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — CRISPR loss-of-function in cell lines combined with in vivo mouse model and multiple functional readouts (COPII formation, trafficking, ER stress, pancreatitis phenotype)\",\n      \"pmids\": [\"39119875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The head domain of the Golgi vesicle tether p115 (USO1) binds directly to a conserved motif in the unstructured N-terminal region of SEC16A. Mutations in p115 that block this interaction reduce the efficiency of secretion.\",\n      \"method\": \"Direct binding assay, structural prediction, deletion mapping, secretion efficiency assay with p115 binding mutants\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay with deletion mapping and mutagenesis plus functional secretion assay, single study\",\n      \"pmids\": [\"42169630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SEC16A, as a component of the COPII network, is required for VLC-ceramide trafficking from the ER to the Golgi apparatus. Depletion of SEC16A abolished VLC-sphingomyelin synthesis triggered by cholesterol depletion, demonstrating that SEC16A-dependent COPII-mediated ER exit is a regulatory node for sphingolipid homeostasis.\",\n      \"method\": \"Sphingolipid metabolic flux analysis, siRNA depletion of SEC16A, sphingolipid trafficking assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, siRNA depletion with metabolic flux readout, no orthogonal validation\",\n      \"pmids\": [\"bio_10.1101_2025.02.12.637879\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A knock-in mouse model carrying the Sec16a L1551V mutation (equivalent to human L1536V in the conserved central core region of SEC16A) shows neurological impairment including deficits in learning, memory, and limb-clasping behavior consistent with neurodegenerative disease, establishing that the central core domain is functionally important in vivo.\",\n      \"method\": \"CRISPR/Cas9 knock-in mouse model, novel object recognition test, cued fear conditioning, limb-clasping behavioral assay\",\n      \"journal\": \"Animal models and experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vivo CRISPR knock-in with defined behavioral phenotype, single lab, mechanistic detail limited to domain conservation\",\n      \"pmids\": [\"41104514\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SEC16A is a large scaffolding protein that organizes ER exit sites (ERES) by interacting with both inner (Sec23-Sec24) and outer (Sec13-Sec31) COPII coat complexes and by binding the Golgi tether p115/USO1 at its N-terminal region; it is recruited to ER membranes in a Sar1-dependent manner and is anchored at ERES by LRRK2; beyond canonical COPII-mediated ER-to-Golgi transport (including ceramide and secretory cargo trafficking), SEC16A also functions as a RAB10 effector driving insulin-stimulated GLUT4 vesicle biogenesis independently of the full COPII coat, and during ER stress it redistributes and associates with GRASP55 to facilitate unconventional secretion downstream of IRE1α signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SEC16A is a large, predominantly cytosolic scaffolding protein that organizes ER exit sites (ERES) and drives COPII-mediated ER-to-Golgi protein transport [#0]. It is recruited to ER membranes in a Sar1-dependent manner and bridges both the inner Sec23-Sec24 and outer Sec13-Sec31 COPII coat layers, such that its depletion disorganizes ERES and delays secretory transport [#0]; its stable anchoring at ERES depends on a direct interaction with LRRK2, which a Parkinson's-associated R1441C mutation disrupts independently of LRRK2 kinase activity [#1]. SEC16A coordinates secretory hand-off to the Golgi through direct binding of its unstructured N-terminal region to the head domain of the vesicle tether p115/USO1 [#6]. Beyond canonical COPII transport, SEC16A acts as a RAB10 effector that mobilizes GLUT4 from a perinuclear recycling endosome/TGN compartment to the plasma membrane upon insulin stimulation, a role independent of the full COPII coat [#2], and during ER stress it redistributes to the cell periphery and associates with GRASP55 to support IRE1\\u03b1-regulated unconventional secretion of CFTR [#3]. Through its central conserved domain it also binds and stabilizes the E3 ubiquitin ligase RNF183 against ERAD without being its substrate [#4]. Loss-of-function SEC16A variants impair COPII assembly, secretory trafficking, and provoke ER stress, with Sec16a+/- mice showing defective zymogen secretion and aggravated pancreatitis [#5], while a central-core knock-in mutation produces neurological and memory deficits in vivo [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that mammalian SEC16A is the scaffold organizing ER exit sites by physically linking both COPII coat layers, answering how ERES architecture and ER export are maintained.\",\n      \"evidence\": \"Subcellular fractionation, COPII binding assays, and siRNA depletion with ER-to-Golgi transport assay in mammalian cells\",\n      \"pmids\": [\"17428803\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how SEC16A is itself stably positioned at ERES\", \"Structural basis of simultaneous inner/outer coat binding not defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified LRRK2 as the factor anchoring SEC16A at ERES, linking a Parkinson's-associated mutation to a defect in ER export.\",\n      \"evidence\": \"Reciprocal Co-IP, confocal co-localization, siRNA knockdown with transport assay, and kinase-dead/dominant-negative mutant analysis\",\n      \"pmids\": [\"25201882\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. bridged nature of the LRRK2-SEC16A interaction not established\", \"How R1441C disrupts binding mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed a non-canonical SEC16A function as a RAB10 effector in insulin-stimulated GLUT4 trafficking, separating this role from full COPII coat activity.\",\n      \"evidence\": \"siRNA knockdown, insulin-dependent colocalization, GLUT4 translocation assay, and epistasis with individual COPII components in adipocytes\",\n      \"pmids\": [\"27354378\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why SEC23A but not other coat subunits is required is unexplained\", \"Mechanism of RAB10-SEC16A coupling to vesicle biogenesis not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showed SEC16A participates in both conventional and GRASP55-mediated Golgi-bypassing secretion under ER stress, placing it downstream of IRE1\\u03b1 signaling.\",\n      \"evidence\": \"siRNA knockdown screen, immunofluorescence relocalization, Co-IP with GRASP55, and IRE1\\u03b1 inhibitor/dominant-negative experiments\",\n      \"pmids\": [\"28067262\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signal driving SEC16A peripheral redistribution unknown\", \"Direct vs. indirect SEC16A-GRASP55 association not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined a chaperone-like role in which SEC16A's central conserved domain stabilizes E3 ligases RNF183/RNF152 against degradation rather than acting as their substrate.\",\n      \"evidence\": \"Co-IP, domain mapping, pulse-chase degradation assay, and fluorescence localization\",\n      \"pmids\": [\"29300766\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological consequence of ligase stabilization not established\", \"Whether this links to ERAD regulation of ERES is unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated in vivo that SEC16A loss-of-function impairs COPII assembly and secretion, causing ER stress and aggravating pancreatic disease.\",\n      \"evidence\": \"CRISPR loss-of-function HEK293T cells, Sec16a+/- mouse model, trafficking and ER-stress readouts, cerulein pancreatitis model\",\n      \"pmids\": [\"39119875\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tissue specificity of secretory vulnerability not fully mapped\", \"Whether human SEC16A variants cause a defined Mendelian disorder not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established the central core domain as functionally critical in vivo by linking a conserved-residue mutation to learning, memory, and motor deficits.\",\n      \"evidence\": \"CRISPR/Cas9 knock-in mouse (L1551V) with novel object recognition, fear conditioning, and limb-clasping assays\",\n      \"pmids\": [\"41104514\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism connecting the mutation to neurodegeneration unresolved\", \"Cellular trafficking defect underlying behavior not measured\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated SEC16A-dependent ER exit as a regulatory node for sphingolipid homeostasis via VLC-ceramide trafficking.\",\n      \"evidence\": \"Sphingolipid metabolic flux analysis with siRNA depletion of SEC16A (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.02.12.637879\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint, single lab, no orthogonal validation\", \"Whether ceramide transport is direct COPII cargo-dependent unresolved\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Pinpointed a direct molecular contact between SEC16A's N-terminal motif and the p115/USO1 tether head domain that promotes efficient secretion.\",\n      \"evidence\": \"Direct binding assay, structural prediction, deletion mapping, and secretion assays with p115 binding mutants\",\n      \"pmids\": [\"42169630\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Spatiotemporal role of this contact in vesicle tethering not defined\", \"Structure of the bound complex not experimentally determined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SEC16A switches between its canonical ERES-scaffolding role and its non-canonical RAB10-effector and unconventional-secretion functions remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of full-length SEC16A or its coat/tether complexes\", \"Domain-specific regulatory mechanisms governing pathway selection unknown\", \"Connection between trafficking defects and neurodegenerative phenotype unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"COPII coat\"],\n    \"partners\": [\"SEC23A\", \"SEC24\", \"SEC13\", \"SEC31\", \"LRRK2\", \"RAB10\", \"GRASP55\", \"USO1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}