{"gene":"TMEM41B","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2018,"finding":"TMEM41B is an ER-localized multispanning membrane protein required for autophagosome formation at an early step; its deletion causes accumulation of ATG proteins and small vesicles but no elongating autophagosome-like structures, and also causes lipid droplet accumulation.","method":"Genome-wide CRISPR screen with GFP-LC3-RFP reporter, knockout cell analysis, fluorescence microscopy","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide forward genetic screen independently replicated by three labs (PMIDs 30093494, 30126924, 30933966) with consistent phenotypic readouts","pmids":["30093494"],"is_preprint":false},{"year":2018,"finding":"TMEM41B physically interacts with VMP1 (another ER multispanning membrane protein essential for autophagy) both in vivo (co-immunoprecipitation) and in vitro, and overexpression of VMP1 can restore autophagic flux in TMEM41B-KO cells.","method":"Co-immunoprecipitation, in vitro binding assay, rescue experiment by VMP1 overexpression in TMEM41B-KO cells","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus in vitro binding plus functional rescue, replicated in follow-up studies (PMIDs 30773971, 35044051)","pmids":["30093494","30773971"],"is_preprint":false},{"year":2018,"finding":"TMEM41B localizes to the endoplasmic reticulum (ER) as a multi-spanning membrane protein; its absence causes stalled autophagosome biogenesis with LC3 accumulating at WIPI2- and DFCP1-positive isolation membranes, and results in enlarged lipid droplets and reduced fatty acid mobilization and β-oxidation.","method":"Pooled CRISPR screens, immunostaining, interaction proteomics, lipid droplet assays, β-oxidation assay","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (CRISPR screen, microscopy, proteomics, metabolic assays), replicated across labs","pmids":["30126924"],"is_preprint":false},{"year":2018,"finding":"TMEM41B (Stasimon) localizes to mitochondria-associated ER membranes (MAM), as determined by subcellular fractionation and super-resolution microscopy, and its interactome (identified by immunoprecipitation-mass spectrometry) includes components of the ER, mitochondria, and COPI vesicle trafficking machinery.","method":"Immunoprecipitation-mass spectrometry, subcellular fractionation, super-resolution microscopy","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal localization methods (fractionation + super-resolution microscopy) plus MS interactome, single lab","pmids":["30352685"],"is_preprint":false},{"year":2019,"finding":"TMEM41B is an integral ER membrane protein required for phagophore maturation; it plays related but not fully overlapping roles with VMP1 in autophagosome biogenesis.","method":"Genome-wide CRISPR screen, quantitative microscopy, biochemical analyses, genetic complementation","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — quantitative microscopy and biochemical validation, independently replicating prior findings across multiple labs","pmids":["30933966"],"is_preprint":false},{"year":2020,"finding":"TMEM41B is required for infection by all tested members of the Flaviviridae family and by SARS-CoV-2 (Coronaviridae); it associates with viral proteins and is proposed to facilitate membrane curvature to create flavivirus RNA replication complexes. SNPs in TMEM41B present at ~20% in East Asian populations reduce flavivirus infection.","method":"Genome-wide loss-of-function CRISPR-Cas9 screens, infection assays, mechanistic studies with viral protein co-association","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide CRISPR screen validated with mechanistic follow-up, multiple virus families tested, peer-reviewed publication","pmids":["33338421"],"is_preprint":false},{"year":2021,"finding":"TMEM41B is an ER-resident host factor required at an early, post-receptor-engagement stage of coronavirus (HCoV-229E, SARS-CoV-2) replication; mechanistic studies suggest it contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate membrane expansion and curvature, though the protein was not enriched at replication complexes.","method":"Genome-wide loss-of-function CRISPR screen, infection stage assays, lipid mobilization experiments, KO cell analysis","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (CRISPR screen, stage-specific infection assays, lipid analysis), single lab","pmids":["34043740"],"is_preprint":false},{"year":2021,"finding":"TMEM41B-KO cells are unable to form double-membrane vesicles (DMVs) required for coronavirus (TGEV) replication, establishing that TMEM41B contributes to formation of CoV replication organelles.","method":"Genome-scale CRISPR KO screen, electron microscopy of DMV formation, mouse infection model","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO phenotype with EM validation and in vivo mouse model, single lab","pmids":["34871328"],"is_preprint":false},{"year":2022,"finding":"TMEM41B and VMP1 are required for DMV biogenesis during β-coronavirus infection, but function at distinct steps: TMEM41B facilitates the nsp3-nsp4 interaction and ER zippering, while VMP1 is required for closing the paired ER into DMVs.","method":"KO cell analysis, expression of viral nsp3/nsp4, co-immunoprecipitation of nsp3-nsp4, electron microscopy of DMV formation","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — distinct mechanistic steps dissected by Co-IP, EM, and genetic KO with orthogonal validation, replicated in companion Autophagy paper (PMID 35900889)","pmids":["35536318","35900889"],"is_preprint":false},{"year":2022,"finding":"TMEM41B and VMP1 possess lipid scramblase activity, demonstrated by in vitro fluorescent liposome-based phospholipid scrambling assays and in vivo metabolic labeling with alkyne-choline in living cells.","method":"In vitro liposome-based phospholipid scrambling assay, in vivo metabolic labeling with alkyne-choline","journal":"STAR protocols","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution assay for scramblase activity, protocol paper referencing prior Huang et al. 2021 study, single lab","pmids":["35496801"],"is_preprint":false},{"year":2022,"finding":"VMP1 and TMEM41B contain a DedA domain predicted to adopt a structure with two reentrant loops, and both proteins have experimentally demonstrated lipid scrambling activity; they regulate formation of multiple ER-derived structures including autophagosomes, lipid droplets, lipoproteins, and viral DMVs.","method":"Review of experimental data; DedA domain structural prediction; scramblase activity assays referenced","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — review/synthesis paper citing experimental scramblase activity data; DedA structural prediction is computational","pmids":["35044051"],"is_preprint":false},{"year":2022,"finding":"TMEM41B deficiency impairs DENV replication organelle formation; the inhibitory effect of TMEM41B deficiency on DENV replication (but not HCoV-OC43) can be partially reversed by exogenous fatty acid supplementation, linking TMEM41B's lipid mobilization function to flavivirus replication.","method":"KO cell infection assays, fatty acid supplementation rescue, metabolomic/lipidomic profiling, mitochondrial function assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (infection assay, metabolomics, rescue experiment), single lab","pmids":["35939522"],"is_preprint":false},{"year":2023,"finding":"Loss of TMEM41B (an ER-localized lipid scramblase) delays ER-to-Golgi transport of GPI-anchored proteins and transmembrane proteins, slows PGAP1 turnover via ER-associated degradation, and thereby promotes PGAP1-dependent GPI-inositol deacylation through PGAP1 stabilization.","method":"KO cell analysis, PI-PLC sensitivity assay, protein transport assays, PGAP1 turnover assays","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays (transport, enzymatic activity, protein stability) in KO cells, single lab","pmids":["37279648"],"is_preprint":false},{"year":2023,"finding":"TMEM41B is an interferon-stimulated gene (ISG); its knockdown blocks PRV entry by affecting lipid synthesis via downregulation of key lipid synthesis enzymes and by altering clathrin-coated pit (CCP) dynamics; lipid replenishment restores CCP dynamics and PRV entry in TMEM41B knockdown cells.","method":"IFN induction experiments, KO/knockdown/overexpression cell assays, PRV life cycle stage assays, CCP dynamics analysis, lipid replenishment rescue","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional assays (stage-specific infection, CCP imaging, rescue), single lab","pmids":["37255475"],"is_preprint":false},{"year":2024,"finding":"VMP1 and TMEM41B (as lipid scramblases) are required for primitive endoderm specification; mechanistically, their loss reduces FZD2 (WNT receptor) at the plasma membrane, impairing WNT signaling, and transgenic FZD2 expression rescues XEN differentiation.","method":"ESC knockout generation, differentiation assays, cell surface proteome profiling, transgenic rescue experiment","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with defined cellular phenotype, surface proteomics, and genetic rescue, single lab","pmids":["39695329"],"is_preprint":false},{"year":2024,"finding":"miR-660-5p directly targets TMEM41B; inhibition of miR-660-5p increases TMEM41B protein levels in breast cancer cells, and TMEM41B was validated as a direct miR-660-5p target by dual-luciferase reporter assay and Western blot.","method":"Dual-luciferase reporter assay, Western blot, miRNA inhibitor experiments","journal":"Hereditas","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, two methods but limited mechanistic follow-up on TMEM41B function itself","pmids":["39709500"],"is_preprint":false},{"year":2025,"finding":"Purified recombinant TMEM41B forms a concentration-dependent Ca2+ channel in single-channel electrophysiology assays; TMEM41B deficiency causes ER Ca2+ overload while overexpression depletes ER Ca2+, establishing TMEM41B as an ER Ca2+ release channel. ER Ca2+ overload in TMEM41B-deficient naive T cells upregulates IL-2/IL-7 receptors and activates JAK-STAT, AKT-mTOR, and MAPK pathways, lowering the T cell activation threshold.","method":"Single-channel electrophysiology with purified recombinant protein, ER Ca2+ measurement in KO and overexpression cells, T cell signaling pathway analysis","journal":"Cell discovery","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution (single-channel electrophysiology with purified protein) plus cellular gain/loss-of-function, single lab","pmids":["40038246"],"is_preprint":false},{"year":2025,"finding":"TMEM41B stabilizes fatty acid synthase (FASN) in vascular smooth muscle cells by inhibiting its ubiquitination and degradation, thereby promoting lipid synthesis and intracellular lipid storage; this TMEM41B-FASN axis drives foam cell-like features in VSMCs.","method":"TMEM41B silencing/overexpression in VSMCs, ubiquitination assay, lipidomics, FASN protein stability assays","journal":"Metabolism: clinical and experimental","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO/OE phenotype with ubiquitination mechanistic assay and lipidomics, single lab","pmids":["41297878"],"is_preprint":false},{"year":2025,"finding":"TMEM41B and VMP1 localize at mitochondria-associated membranes (MAM) in hepatocytes; loss of hepatic TMEM41B impairs VLDL secretion and reduces phospholipid (PC and PE) levels; TMEM41B and VMP1 have overlapping but distinct roles in hepatic lipoprotein secretion and autophagy.","method":"Liver-specific KO and KI mouse models, lipidomics, metabolomics, VLDL secretion assay, EM ultrastructural analysis, MAM fractionation","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple genetic mouse models with functional lipidomic and ultrastructural assays, preprint status","pmids":["40291711"],"is_preprint":true},{"year":2025,"finding":"VMP1 and TMEM41B scramblase activity is required for the maturation and stability of FZD2/FRIZZLED2 (a WNT receptor), linking ER lipid metabolism to protein trafficking and WNT signaling during primitive endoderm development.","method":"ESC knockout analysis, protein trafficking assays, FZD2 maturation/stability assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic link between scramblase activity and receptor maturation established in KO ESCs, single lab, replicates PMID 39695329","pmids":["39968886"],"is_preprint":false},{"year":2025,"finding":"The antibiotic carrimycin directly binds TMEM41B and induces its K48-ubiquitination and proteasomal degradation, thereby inhibiting coronavirus (including SARS-CoV-2) replication by disrupting DMV formation; TMEM41B overexpression partially reverses carrimycin's antiviral effect.","method":"Direct binding assay, ubiquitination assay, overexpression rescue experiment, viral replication assays, DMV formation analysis","journal":"Acta pharmacologica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding plus ubiquitination assay plus functional rescue, single lab","pmids":["40374896"],"is_preprint":false}],"current_model":"TMEM41B is an ER-resident multispanning membrane protein with a DedA/VTT domain that functions as a lipid scramblase (demonstrated in vitro) and an ER Ca2+ release channel; it physically interacts with VMP1 to facilitate early autophagosome formation (phagophore maturation), lipid droplet mobilization, ER-to-Golgi protein trafficking, VLDL secretion, and viral replication organelle (DMV) biogenesis by remodeling ER membrane lipid distribution, while also regulating WNT receptor (FZD2) trafficking, GPI-anchored protein processing, and naive T cell Ca2+ homeostasis."},"narrative":{"mechanistic_narrative":"TMEM41B is an ER-resident multispanning membrane protein that remodels the lipid composition of the ER membrane to enable the biogenesis of multiple ER-derived structures [PMID:30093494, PMID:30126924]. It carries a DedA/VTT domain predicted to adopt a two-reentrant-loop fold and functions as a phospholipid scramblase, demonstrated by in vitro liposome scrambling assays and in-cell metabolic labeling [PMID:35496801, PMID:35044051]. The protein physically interacts with the related scramblase VMP1, with which it cooperates—at related but distinct steps—to drive phagophore maturation during autophagosome formation; loss of TMEM41B stalls autophagy after ATG/WIPI2/DFCP1 recruitment to isolation membranes and causes lipid droplet accumulation with reduced fatty acid mobilization and β-oxidation [PMID:30093494, PMID:30773971, PMID:30126924, PMID:30933966, PMID:35536318, PMID:35900889]. Through this lipid-mobilizing activity, TMEM41B supports a broad range of membrane processes: ER-to-Golgi transport and GPI-anchored protein processing via PGAP1 stabilization [PMID:37279648], maturation and plasma-membrane delivery of the WNT receptor FZD2 to enable primitive endoderm specification [PMID:39695329, PMID:39968886], hepatic VLDL secretion and phospholipid homeostasis [PMID:40291711], and stabilization of fatty acid synthase to promote lipid storage [PMID:41297878]. TMEM41B is also a host dependency factor for diverse viruses, including Flaviviridae and coronaviruses, where it facilitates double-membrane vesicle replication-organelle biogenesis by promoting the nsp3-nsp4 interaction and ER zippering and by mobilizing cholesterol and other lipids [PMID:33338421, PMID:34871328, PMID:35536318, PMID:35900889]. Independently of its lipid role, purified recombinant TMEM41B forms a Ca2+ release channel that governs ER Ca2+ homeostasis, with loss causing ER Ca2+ overload that lowers the naive T cell activation threshold [PMID:40038246].","teleology":[{"year":2018,"claim":"Established TMEM41B as a previously uncharacterized ER membrane protein essential at an early step of autophagosome formation, defining its core cellular role.","evidence":"Genome-wide CRISPR screens with autophagy flux reporters, knockout microscopy and lipid droplet assays across three independent labs","pmids":["30093494","30126924","30933966"],"confidence":"High","gaps":["Molecular activity at the membrane not yet defined","Relationship between autophagy defect and lipid droplet accumulation unresolved"]},{"year":2018,"claim":"Placed TMEM41B in a functional partnership with VMP1, showing the two proteins interact and share an autophagy pathway.","evidence":"Reciprocal co-immunoprecipitation, in vitro binding, and VMP1-overexpression rescue of TMEM41B-KO cells","pmids":["30093494","30773971"],"confidence":"High","gaps":["Whether they act in a stable stoichiometric complex unclear","Mechanistic basis of the functional overlap unknown at this stage"]},{"year":2018,"claim":"Localized TMEM41B to mitochondria-associated ER membranes and identified ER, mitochondrial, and COPI trafficking interactors, hinting at roles beyond autophagy.","evidence":"Subcellular fractionation, super-resolution microscopy, and IP-mass spectrometry interactome","pmids":["30352685"],"confidence":"Medium","gaps":["Single-lab interactome without functional validation","Significance of MAM localization for autophagy not tested"]},{"year":2020,"claim":"Revealed TMEM41B as a pan-viral host dependency factor required for Flaviviridae and SARS-CoV-2 infection, extending its membrane-remodeling role to viral replication.","evidence":"Genome-wide CRISPR screens, infection assays, and viral protein co-association with population SNP analysis","pmids":["33338421"],"confidence":"High","gaps":["Whether TMEM41B acts directly at replication complexes not resolved","Mechanism linking membrane curvature to viral RNA replication not defined"]},{"year":2022,"claim":"Demonstrated that TMEM41B (and VMP1) possess intrinsic phospholipid scramblase activity, providing the biochemical activity underlying their membrane-shaping functions.","evidence":"In vitro liposome-based scrambling assays and in-cell alkyne-choline metabolic labeling; DedA-domain structural prediction","pmids":["35496801","35044051"],"confidence":"Medium","gaps":["Single-lab reconstitution","Substrate specificity and directionality of scrambling not fully mapped"]},{"year":2022,"claim":"Dissected distinct mechanistic steps for TMEM41B versus VMP1 in coronavirus DMV biogenesis, clarifying their non-redundant contributions.","evidence":"KO cell analysis, nsp3/nsp4 expression and co-IP, EM of DMV formation","pmids":["35536318","35900889"],"confidence":"High","gaps":["How scramblase activity mechanistically promotes ER zippering not resolved","Direct role in physiological autophagosome zippering versus viral DMVs not disentangled"]},{"year":2023,"claim":"Connected TMEM41B lipid function to secretory-pathway protein homeostasis, including GPI-anchored protein trafficking and PGAP1 stability.","evidence":"KO cell transport assays, PI-PLC sensitivity assays, and PGAP1 turnover assays","pmids":["37279648"],"confidence":"Medium","gaps":["Single-lab study","Direct versus indirect effect of lipid scrambling on transport kinetics unclear"]},{"year":2024,"claim":"Linked TMEM41B/VMP1 scramblase activity to developmental WNT signaling through FZD2 receptor maturation and surface delivery.","evidence":"ESC knockouts, differentiation assays, cell-surface proteomics, and transgenic FZD2 rescue","pmids":["39695329","39968886"],"confidence":"Medium","gaps":["Single-lab system","Whether FZD2 is a direct client of the scramblase or affected via general ER lipid changes unresolved"]},{"year":2025,"claim":"Identified an unanticipated channel function: purified TMEM41B forms an ER Ca2+ release channel controlling naive T cell activation threshold.","evidence":"Single-channel electrophysiology with purified recombinant protein, ER Ca2+ measurements in loss/gain-of-function cells, T cell signaling analysis","pmids":["40038246"],"confidence":"Medium","gaps":["Single lab; reconciliation of channel activity with scramblase activity not addressed","Structural basis of ion permeation unknown"]},{"year":2025,"claim":"Extended TMEM41B's lipid-handling role in vivo to hepatic VLDL secretion and to FASN stabilization driving lipid storage.","evidence":"Liver-specific KO/KI mouse models with lipidomics and EM (preprint); VSMC silencing/overexpression with ubiquitination and lipidomic assays","pmids":["40291711","41297878"],"confidence":"Medium","gaps":["Hepatic study is a preprint","Mechanism by which TMEM41B controls FASN ubiquitination not defined"]},{"year":2025,"claim":"Validated TMEM41B as a druggable antiviral target by showing carrimycin binds it and triggers its degradation to block DMV formation.","evidence":"Direct binding and K48-ubiquitination assays, overexpression rescue, and viral replication/DMV assays","pmids":["40374896"],"confidence":"Medium","gaps":["Single-lab study","Selectivity of carrimycin for TMEM41B versus off-targets not fully characterized"]},{"year":null,"claim":"How a single protein reconciles phospholipid scramblase activity with Ca2+ channel activity, and which structural features underlie each, remains unresolved.","evidence":"No experimental structure or unifying mechanistic model present in the corpus","pmids":[],"confidence":"Medium","gaps":["No high-resolution structure reported","Directionality/substrate range of scrambling incompletely defined","Whether scramblase and channel activities are mechanistically coupled is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[9,10]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[9,10]},{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[16]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,2,4]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[3,18]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,18,17]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[5,7,8]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[12,14,19]}],"complexes":[],"partners":["VMP1","FZD2","PGAP1","FASN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5BJD5","full_name":"Transmembrane protein 41B","aliases":["Protein stasimon"],"length_aa":291,"mass_kda":32.5,"function":"Phospholipid scramblase involved in lipid homeostasis and membrane dynamics processes (PubMed:33850023, PubMed:33929485, PubMed:34015269). Has phospholipid scramblase activity toward cholesterol and phosphatidylserine, as well as phosphatidylethanolamine and phosphatidylcholine (PubMed:33850023, PubMed:33929485, PubMed:34015269). Required for autophagosome formation: participates in early stages of autophagosome biogenesis at the endoplasmic reticulum (ER) membrane by reequilibrating the leaflets of the ER as lipids are extracted by ATG2 (ATG2A or ATG2B) to mediate autophagosome assembly (PubMed:30093494, PubMed:30126924, PubMed:30933966, PubMed:33850023, PubMed:33929485, PubMed:34015269, PubMed:34043740). In addition to autophagy, involved in other processes in which phospholipid scramblase activity is required (PubMed:33850023). Required for normal motor neuron development (By similarity) (Microbial infection) Critical host factor required for infection by human coronaviruses SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E, as well as all flaviviruses tested such as Zika virus and Yellow fever virus (PubMed:33338421, PubMed:33382968). Required post-entry of the virus to facilitate the ER membrane remodeling necessary to form replication organelles (PubMed:33382968)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q5BJD5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM41B","classification":"Not Classified","n_dependent_lines":326,"n_total_lines":1208,"dependency_fraction":0.26986754966887416},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TMEM41B","total_profiled":1310},"omim":[{"mim_id":"620271","title":"TRANSMEMBRANE PROTEIN 41B; TMEM41B","url":"https://www.omim.org/entry/620271"},{"mim_id":"611753","title":"VACUOLE MEMBRANE PROTEIN 1; VMP1","url":"https://www.omim.org/entry/611753"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Peroxisomes","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMEM41B"},"hgnc":{"alias_symbol":["KIAA0033"],"prev_symbol":[]},"alphafold":{"accession":"Q5BJD5","domains":[{"cath_id":"-","chopping":"57-174_238-271","consensus_level":"high","plddt":90.3431,"start":57,"end":271}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5BJD5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5BJD5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5BJD5-F1-predicted_aligned_error_v6.png","plddt_mean":82.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM41B","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM41B"},"sequence":{"accession":"Q5BJD5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5BJD5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5BJD5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5BJD5"}},"corpus_meta":[{"pmid":"30093494","id":"PMC_30093494","title":"Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation.","date":"2018","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/30093494","citation_count":178,"is_preprint":false},{"pmid":"33338421","id":"PMC_33338421","title":"TMEM41B Is a Pan-flavivirus Host Factor.","date":"2020","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33338421","citation_count":174,"is_preprint":false},{"pmid":"30126924","id":"PMC_30126924","title":"TMEM41B is a novel regulator of autophagy and lipid mobilization.","date":"2018","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/30126924","citation_count":137,"is_preprint":false},{"pmid":"30933966","id":"PMC_30933966","title":"CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor.","date":"2019","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/30933966","citation_count":124,"is_preprint":false},{"pmid":"35536318","id":"PMC_35536318","title":"VMP1 and TMEM41B are essential for DMV formation during β-coronavirus infection.","date":"2022","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/35536318","citation_count":69,"is_preprint":false},{"pmid":"34043740","id":"PMC_34043740","title":"TMEM41B is a host factor required for the replication of diverse coronaviruses including SARS-CoV-2.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34043740","citation_count":58,"is_preprint":false},{"pmid":"34871328","id":"PMC_34871328","title":"Genome-scale CRISPR screen identifies TMEM41B as a multi-function host factor required for coronavirus replication.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34871328","citation_count":57,"is_preprint":false},{"pmid":"30773971","id":"PMC_30773971","title":"TMEM41B functions with VMP1 in autophagosome formation.","date":"2019","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/30773971","citation_count":44,"is_preprint":false},{"pmid":"35939522","id":"PMC_35939522","title":"TMEM41B and VMP1 modulate cellular lipid and energy metabolism for facilitating dengue virus infection.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/35939522","citation_count":38,"is_preprint":false},{"pmid":"35044051","id":"PMC_35044051","title":"Regulation of ER-derived membrane dynamics by the DedA domain-containing proteins VMP1 and TMEM41B.","date":"2022","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/35044051","citation_count":35,"is_preprint":false},{"pmid":"30352685","id":"PMC_30352685","title":"Stasimon/Tmem41b localizes to mitochondria-associated ER membranes and is essential for mouse embryonic development.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/30352685","citation_count":33,"is_preprint":false},{"pmid":"33520197","id":"PMC_33520197","title":"In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b.","date":"2020","source":"F1000Research","url":"https://pubmed.ncbi.nlm.nih.gov/33520197","citation_count":17,"is_preprint":false},{"pmid":"35900889","id":"PMC_35900889","title":"DMV biogenesis during β-coronavirus infection requires autophagy proteins VMP1 and TMEM41B.","date":"2022","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/35900889","citation_count":15,"is_preprint":false},{"pmid":"37255475","id":"PMC_37255475","title":"TMEM41B Is an Interferon-Stimulated Gene That Promotes Pseudorabies Virus Replication.","date":"2023","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/37255475","citation_count":9,"is_preprint":false},{"pmid":"38640735","id":"PMC_38640735","title":"Stasimon/Tmem41b is required for cell proliferation and adult mouse survival.","date":"2024","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/38640735","citation_count":6,"is_preprint":false},{"pmid":"40038246","id":"PMC_40038246","title":"TMEM41B is an endoplasmic reticulum Ca2+ release channel maintaining naive T cell quiescence and responsiveness.","date":"2025","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/40038246","citation_count":6,"is_preprint":false},{"pmid":"33052348","id":"PMC_33052348","title":"TMEM41B is a pan-flavivirus host factor.","date":"2020","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/33052348","citation_count":6,"is_preprint":false},{"pmid":"39695329","id":"PMC_39695329","title":"The scramblases VMP1 and TMEM41B are required for primitive endoderm specification by targeting WNT signaling.","date":"2024","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/39695329","citation_count":6,"is_preprint":false},{"pmid":"37279648","id":"PMC_37279648","title":"A lipid scramblase TMEM41B is involved in the processing and transport of GPI-anchored proteins.","date":"2023","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37279648","citation_count":5,"is_preprint":false},{"pmid":"35496801","id":"PMC_35496801","title":"In vitro and in vivo assay of the ER lipid scramblase TMEM41B.","date":"2022","source":"STAR protocols","url":"https://pubmed.ncbi.nlm.nih.gov/35496801","citation_count":4,"is_preprint":false},{"pmid":"40291711","id":"PMC_40291711","title":"Overlapping yet Distinct Functions of VMP1 and TMEM41B in Modulating Hepatic Lipoprotein Secretion and Autophagy.","date":"2025","source":"bioRxiv : the preprint server for 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Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40374896","citation_count":1,"is_preprint":false},{"pmid":"33884885","id":"PMC_33884885","title":"WITHDRAWN: Expression of Tmem41b and MMP13 associated with poor outcome in osteosarcomas.","date":"2023","source":"Neoplasma","url":"https://pubmed.ncbi.nlm.nih.gov/33884885","citation_count":1,"is_preprint":false},{"pmid":"39658195","id":"PMC_39658195","title":"Commentary for: a lipid scramblase TMEM41B is involved in the processing and transport of GPI-anchored proteins.","date":"2025","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39658195","citation_count":1,"is_preprint":false},{"pmid":"39968886","id":"PMC_39968886","title":"Scrambling stem cell development: VMP1 and TMEM41B regulate FZD2/FRIZZLED2 secretion during primitive endoderm specification.","date":"2025","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/39968886","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14405,"output_tokens":4776,"usd":0.057427,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12935,"output_tokens":3628,"usd":0.077688,"stage2_stop_reason":"end_turn"},"total_usd":0.135115,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B is an ER-localized multispanning membrane protein required for autophagosome formation at an early step; its deletion causes accumulation of ATG proteins and small vesicles but no elongating autophagosome-like structures, and also causes lipid droplet accumulation.\",\n      \"method\": \"Genome-wide CRISPR screen with GFP-LC3-RFP reporter, knockout cell analysis, fluorescence microscopy\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide forward genetic screen independently replicated by three labs (PMIDs 30093494, 30126924, 30933966) with consistent phenotypic readouts\",\n      \"pmids\": [\"30093494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B physically interacts with VMP1 (another ER multispanning membrane protein essential for autophagy) both in vivo (co-immunoprecipitation) and in vitro, and overexpression of VMP1 can restore autophagic flux in TMEM41B-KO cells.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assay, rescue experiment by VMP1 overexpression in TMEM41B-KO cells\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus in vitro binding plus functional rescue, replicated in follow-up studies (PMIDs 30773971, 35044051)\",\n      \"pmids\": [\"30093494\", \"30773971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B localizes to the endoplasmic reticulum (ER) as a multi-spanning membrane protein; its absence causes stalled autophagosome biogenesis with LC3 accumulating at WIPI2- and DFCP1-positive isolation membranes, and results in enlarged lipid droplets and reduced fatty acid mobilization and β-oxidation.\",\n      \"method\": \"Pooled CRISPR screens, immunostaining, interaction proteomics, lipid droplet assays, β-oxidation assay\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (CRISPR screen, microscopy, proteomics, metabolic assays), replicated across labs\",\n      \"pmids\": [\"30126924\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B (Stasimon) localizes to mitochondria-associated ER membranes (MAM), as determined by subcellular fractionation and super-resolution microscopy, and its interactome (identified by immunoprecipitation-mass spectrometry) includes components of the ER, mitochondria, and COPI vesicle trafficking machinery.\",\n      \"method\": \"Immunoprecipitation-mass spectrometry, subcellular fractionation, super-resolution microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal localization methods (fractionation + super-resolution microscopy) plus MS interactome, single lab\",\n      \"pmids\": [\"30352685\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMEM41B is an integral ER membrane protein required for phagophore maturation; it plays related but not fully overlapping roles with VMP1 in autophagosome biogenesis.\",\n      \"method\": \"Genome-wide CRISPR screen, quantitative microscopy, biochemical analyses, genetic complementation\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — quantitative microscopy and biochemical validation, independently replicating prior findings across multiple labs\",\n      \"pmids\": [\"30933966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TMEM41B is required for infection by all tested members of the Flaviviridae family and by SARS-CoV-2 (Coronaviridae); it associates with viral proteins and is proposed to facilitate membrane curvature to create flavivirus RNA replication complexes. SNPs in TMEM41B present at ~20% in East Asian populations reduce flavivirus infection.\",\n      \"method\": \"Genome-wide loss-of-function CRISPR-Cas9 screens, infection assays, mechanistic studies with viral protein co-association\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide CRISPR screen validated with mechanistic follow-up, multiple virus families tested, peer-reviewed publication\",\n      \"pmids\": [\"33338421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMEM41B is an ER-resident host factor required at an early, post-receptor-engagement stage of coronavirus (HCoV-229E, SARS-CoV-2) replication; mechanistic studies suggest it contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate membrane expansion and curvature, though the protein was not enriched at replication complexes.\",\n      \"method\": \"Genome-wide loss-of-function CRISPR screen, infection stage assays, lipid mobilization experiments, KO cell analysis\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (CRISPR screen, stage-specific infection assays, lipid analysis), single lab\",\n      \"pmids\": [\"34043740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMEM41B-KO cells are unable to form double-membrane vesicles (DMVs) required for coronavirus (TGEV) replication, establishing that TMEM41B contributes to formation of CoV replication organelles.\",\n      \"method\": \"Genome-scale CRISPR KO screen, electron microscopy of DMV formation, mouse infection model\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO phenotype with EM validation and in vivo mouse model, single lab\",\n      \"pmids\": [\"34871328\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B and VMP1 are required for DMV biogenesis during β-coronavirus infection, but function at distinct steps: TMEM41B facilitates the nsp3-nsp4 interaction and ER zippering, while VMP1 is required for closing the paired ER into DMVs.\",\n      \"method\": \"KO cell analysis, expression of viral nsp3/nsp4, co-immunoprecipitation of nsp3-nsp4, electron microscopy of DMV formation\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — distinct mechanistic steps dissected by Co-IP, EM, and genetic KO with orthogonal validation, replicated in companion Autophagy paper (PMID 35900889)\",\n      \"pmids\": [\"35536318\", \"35900889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B and VMP1 possess lipid scramblase activity, demonstrated by in vitro fluorescent liposome-based phospholipid scrambling assays and in vivo metabolic labeling with alkyne-choline in living cells.\",\n      \"method\": \"In vitro liposome-based phospholipid scrambling assay, in vivo metabolic labeling with alkyne-choline\",\n      \"journal\": \"STAR protocols\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution assay for scramblase activity, protocol paper referencing prior Huang et al. 2021 study, single lab\",\n      \"pmids\": [\"35496801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VMP1 and TMEM41B contain a DedA domain predicted to adopt a structure with two reentrant loops, and both proteins have experimentally demonstrated lipid scrambling activity; they regulate formation of multiple ER-derived structures including autophagosomes, lipid droplets, lipoproteins, and viral DMVs.\",\n      \"method\": \"Review of experimental data; DedA domain structural prediction; scramblase activity assays referenced\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — review/synthesis paper citing experimental scramblase activity data; DedA structural prediction is computational\",\n      \"pmids\": [\"35044051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B deficiency impairs DENV replication organelle formation; the inhibitory effect of TMEM41B deficiency on DENV replication (but not HCoV-OC43) can be partially reversed by exogenous fatty acid supplementation, linking TMEM41B's lipid mobilization function to flavivirus replication.\",\n      \"method\": \"KO cell infection assays, fatty acid supplementation rescue, metabolomic/lipidomic profiling, mitochondrial function assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (infection assay, metabolomics, rescue experiment), single lab\",\n      \"pmids\": [\"35939522\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Loss of TMEM41B (an ER-localized lipid scramblase) delays ER-to-Golgi transport of GPI-anchored proteins and transmembrane proteins, slows PGAP1 turnover via ER-associated degradation, and thereby promotes PGAP1-dependent GPI-inositol deacylation through PGAP1 stabilization.\",\n      \"method\": \"KO cell analysis, PI-PLC sensitivity assay, protein transport assays, PGAP1 turnover assays\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays (transport, enzymatic activity, protein stability) in KO cells, single lab\",\n      \"pmids\": [\"37279648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM41B is an interferon-stimulated gene (ISG); its knockdown blocks PRV entry by affecting lipid synthesis via downregulation of key lipid synthesis enzymes and by altering clathrin-coated pit (CCP) dynamics; lipid replenishment restores CCP dynamics and PRV entry in TMEM41B knockdown cells.\",\n      \"method\": \"IFN induction experiments, KO/knockdown/overexpression cell assays, PRV life cycle stage assays, CCP dynamics analysis, lipid replenishment rescue\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional assays (stage-specific infection, CCP imaging, rescue), single lab\",\n      \"pmids\": [\"37255475\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VMP1 and TMEM41B (as lipid scramblases) are required for primitive endoderm specification; mechanistically, their loss reduces FZD2 (WNT receptor) at the plasma membrane, impairing WNT signaling, and transgenic FZD2 expression rescues XEN differentiation.\",\n      \"method\": \"ESC knockout generation, differentiation assays, cell surface proteome profiling, transgenic rescue experiment\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with defined cellular phenotype, surface proteomics, and genetic rescue, single lab\",\n      \"pmids\": [\"39695329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"miR-660-5p directly targets TMEM41B; inhibition of miR-660-5p increases TMEM41B protein levels in breast cancer cells, and TMEM41B was validated as a direct miR-660-5p target by dual-luciferase reporter assay and Western blot.\",\n      \"method\": \"Dual-luciferase reporter assay, Western blot, miRNA inhibitor experiments\",\n      \"journal\": \"Hereditas\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, two methods but limited mechanistic follow-up on TMEM41B function itself\",\n      \"pmids\": [\"39709500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Purified recombinant TMEM41B forms a concentration-dependent Ca2+ channel in single-channel electrophysiology assays; TMEM41B deficiency causes ER Ca2+ overload while overexpression depletes ER Ca2+, establishing TMEM41B as an ER Ca2+ release channel. ER Ca2+ overload in TMEM41B-deficient naive T cells upregulates IL-2/IL-7 receptors and activates JAK-STAT, AKT-mTOR, and MAPK pathways, lowering the T cell activation threshold.\",\n      \"method\": \"Single-channel electrophysiology with purified recombinant protein, ER Ca2+ measurement in KO and overexpression cells, T cell signaling pathway analysis\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution (single-channel electrophysiology with purified protein) plus cellular gain/loss-of-function, single lab\",\n      \"pmids\": [\"40038246\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TMEM41B stabilizes fatty acid synthase (FASN) in vascular smooth muscle cells by inhibiting its ubiquitination and degradation, thereby promoting lipid synthesis and intracellular lipid storage; this TMEM41B-FASN axis drives foam cell-like features in VSMCs.\",\n      \"method\": \"TMEM41B silencing/overexpression in VSMCs, ubiquitination assay, lipidomics, FASN protein stability assays\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO/OE phenotype with ubiquitination mechanistic assay and lipidomics, single lab\",\n      \"pmids\": [\"41297878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TMEM41B and VMP1 localize at mitochondria-associated membranes (MAM) in hepatocytes; loss of hepatic TMEM41B impairs VLDL secretion and reduces phospholipid (PC and PE) levels; TMEM41B and VMP1 have overlapping but distinct roles in hepatic lipoprotein secretion and autophagy.\",\n      \"method\": \"Liver-specific KO and KI mouse models, lipidomics, metabolomics, VLDL secretion assay, EM ultrastructural analysis, MAM fractionation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genetic mouse models with functional lipidomic and ultrastructural assays, preprint status\",\n      \"pmids\": [\"40291711\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VMP1 and TMEM41B scramblase activity is required for the maturation and stability of FZD2/FRIZZLED2 (a WNT receptor), linking ER lipid metabolism to protein trafficking and WNT signaling during primitive endoderm development.\",\n      \"method\": \"ESC knockout analysis, protein trafficking assays, FZD2 maturation/stability assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic link between scramblase activity and receptor maturation established in KO ESCs, single lab, replicates PMID 39695329\",\n      \"pmids\": [\"39968886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The antibiotic carrimycin directly binds TMEM41B and induces its K48-ubiquitination and proteasomal degradation, thereby inhibiting coronavirus (including SARS-CoV-2) replication by disrupting DMV formation; TMEM41B overexpression partially reverses carrimycin's antiviral effect.\",\n      \"method\": \"Direct binding assay, ubiquitination assay, overexpression rescue experiment, viral replication assays, DMV formation analysis\",\n      \"journal\": \"Acta pharmacologica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding plus ubiquitination assay plus functional rescue, single lab\",\n      \"pmids\": [\"40374896\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMEM41B is an ER-resident multispanning membrane protein with a DedA/VTT domain that functions as a lipid scramblase (demonstrated in vitro) and an ER Ca2+ release channel; it physically interacts with VMP1 to facilitate early autophagosome formation (phagophore maturation), lipid droplet mobilization, ER-to-Golgi protein trafficking, VLDL secretion, and viral replication organelle (DMV) biogenesis by remodeling ER membrane lipid distribution, while also regulating WNT receptor (FZD2) trafficking, GPI-anchored protein processing, and naive T cell Ca2+ homeostasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMEM41B is an ER-resident multispanning membrane protein that remodels the lipid composition of the ER membrane to enable the biogenesis of multiple ER-derived structures [#0, #2]. It carries a DedA/VTT domain predicted to adopt a two-reentrant-loop fold and functions as a phospholipid scramblase, demonstrated by in vitro liposome scrambling assays and in-cell metabolic labeling [#9, #10]. The protein physically interacts with the related scramblase VMP1, with which it cooperates—at related but distinct steps—to drive phagophore maturation during autophagosome formation; loss of TMEM41B stalls autophagy after ATG/WIPI2/DFCP1 recruitment to isolation membranes and causes lipid droplet accumulation with reduced fatty acid mobilization and β-oxidation [#1, #2, #4, #8]. Through this lipid-mobilizing activity, TMEM41B supports a broad range of membrane processes: ER-to-Golgi transport and GPI-anchored protein processing via PGAP1 stabilization [#12], maturation and plasma-membrane delivery of the WNT receptor FZD2 to enable primitive endoderm specification [#14, #19], hepatic VLDL secretion and phospholipid homeostasis [#18], and stabilization of fatty acid synthase to promote lipid storage [#17]. TMEM41B is also a host dependency factor for diverse viruses, including Flaviviridae and coronaviruses, where it facilitates double-membrane vesicle replication-organelle biogenesis by promoting the nsp3-nsp4 interaction and ER zippering and by mobilizing cholesterol and other lipids [#5, #7, #8]. Independently of its lipid role, purified recombinant TMEM41B forms a Ca2+ release channel that governs ER Ca2+ homeostasis, with loss causing ER Ca2+ overload that lowers the naive T cell activation threshold [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Established TMEM41B as a previously uncharacterized ER membrane protein essential at an early step of autophagosome formation, defining its core cellular role.\",\n      \"evidence\": \"Genome-wide CRISPR screens with autophagy flux reporters, knockout microscopy and lipid droplet assays across three independent labs\",\n      \"pmids\": [\"30093494\", \"30126924\", \"30933966\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular activity at the membrane not yet defined\", \"Relationship between autophagy defect and lipid droplet accumulation unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placed TMEM41B in a functional partnership with VMP1, showing the two proteins interact and share an autophagy pathway.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, in vitro binding, and VMP1-overexpression rescue of TMEM41B-KO cells\",\n      \"pmids\": [\"30093494\", \"30773971\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether they act in a stable stoichiometric complex unclear\", \"Mechanistic basis of the functional overlap unknown at this stage\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Localized TMEM41B to mitochondria-associated ER membranes and identified ER, mitochondrial, and COPI trafficking interactors, hinting at roles beyond autophagy.\",\n      \"evidence\": \"Subcellular fractionation, super-resolution microscopy, and IP-mass spectrometry interactome\",\n      \"pmids\": [\"30352685\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab interactome without functional validation\", \"Significance of MAM localization for autophagy not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed TMEM41B as a pan-viral host dependency factor required for Flaviviridae and SARS-CoV-2 infection, extending its membrane-remodeling role to viral replication.\",\n      \"evidence\": \"Genome-wide CRISPR screens, infection assays, and viral protein co-association with population SNP analysis\",\n      \"pmids\": [\"33338421\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TMEM41B acts directly at replication complexes not resolved\", \"Mechanism linking membrane curvature to viral RNA replication not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated that TMEM41B (and VMP1) possess intrinsic phospholipid scramblase activity, providing the biochemical activity underlying their membrane-shaping functions.\",\n      \"evidence\": \"In vitro liposome-based scrambling assays and in-cell alkyne-choline metabolic labeling; DedA-domain structural prediction\",\n      \"pmids\": [\"35496801\", \"35044051\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab reconstitution\", \"Substrate specificity and directionality of scrambling not fully mapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Dissected distinct mechanistic steps for TMEM41B versus VMP1 in coronavirus DMV biogenesis, clarifying their non-redundant contributions.\",\n      \"evidence\": \"KO cell analysis, nsp3/nsp4 expression and co-IP, EM of DMV formation\",\n      \"pmids\": [\"35536318\", \"35900889\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How scramblase activity mechanistically promotes ER zippering not resolved\", \"Direct role in physiological autophagosome zippering versus viral DMVs not disentangled\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected TMEM41B lipid function to secretory-pathway protein homeostasis, including GPI-anchored protein trafficking and PGAP1 stability.\",\n      \"evidence\": \"KO cell transport assays, PI-PLC sensitivity assays, and PGAP1 turnover assays\",\n      \"pmids\": [\"37279648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study\", \"Direct versus indirect effect of lipid scrambling on transport kinetics unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked TMEM41B/VMP1 scramblase activity to developmental WNT signaling through FZD2 receptor maturation and surface delivery.\",\n      \"evidence\": \"ESC knockouts, differentiation assays, cell-surface proteomics, and transgenic FZD2 rescue\",\n      \"pmids\": [\"39695329\", \"39968886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab system\", \"Whether FZD2 is a direct client of the scramblase or affected via general ER lipid changes unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified an unanticipated channel function: purified TMEM41B forms an ER Ca2+ release channel controlling naive T cell activation threshold.\",\n      \"evidence\": \"Single-channel electrophysiology with purified recombinant protein, ER Ca2+ measurements in loss/gain-of-function cells, T cell signaling analysis\",\n      \"pmids\": [\"40038246\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; reconciliation of channel activity with scramblase activity not addressed\", \"Structural basis of ion permeation unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended TMEM41B's lipid-handling role in vivo to hepatic VLDL secretion and to FASN stabilization driving lipid storage.\",\n      \"evidence\": \"Liver-specific KO/KI mouse models with lipidomics and EM (preprint); VSMC silencing/overexpression with ubiquitination and lipidomic assays\",\n      \"pmids\": [\"40291711\", \"41297878\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Hepatic study is a preprint\", \"Mechanism by which TMEM41B controls FASN ubiquitination not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Validated TMEM41B as a druggable antiviral target by showing carrimycin binds it and triggers its degradation to block DMV formation.\",\n      \"evidence\": \"Direct binding and K48-ubiquitination assays, overexpression rescue, and viral replication/DMV assays\",\n      \"pmids\": [\"40374896\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study\", \"Selectivity of carrimycin for TMEM41B versus off-targets not fully characterized\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single protein reconciles phospholipid scramblase activity with Ca2+ channel activity, and which structural features underlie each, remains unresolved.\",\n      \"evidence\": \"No experimental structure or unifying mechanistic model present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure reported\", \"Directionality/substrate range of scrambling incompletely defined\", \"Whether scramblase and channel activities are mechanistically coupled is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [9, 10]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [9, 10]},\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [3, 18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 18, 17]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [5, 7, 8]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [12, 14, 19]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"VMP1\", \"FZD2\", \"PGAP1\", \"FASN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}