{"gene":"TMEM41B","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":2018,"finding":"TMEM41B is a multispanning ER membrane protein required for autophagosome formation at an early step; its deletion causes accumulation of ATG proteins and small vesicles but not elongating autophagosome-like structures, and also causes lipid droplet accumulation.","method":"Genome-wide CRISPR screen with GFP-LC3-RFP reporter, TMEM41B-KO cell characterization, fluorescence microscopy","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — replicated independently across three labs in the same year with consistent phenotypes","pmids":["30093494"],"is_preprint":false},{"year":2018,"finding":"TMEM41B and VMP1 form a physical complex both in vivo (co-immunoprecipitation) and in vitro, and overexpression of VMP1 rescues autophagic flux in TMEM41B-KO cells, indicating they function together at an early step of autophagosome formation.","method":"Co-immunoprecipitation (in vivo), in vitro binding assay, autophagic flux rescue experiment","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — reciprocal Co-IP plus functional rescue, replicated across labs","pmids":["30093494","30773971"],"is_preprint":false},{"year":2018,"finding":"TMEM41B is required for autophagosome biogenesis; in its absence, LC3 accumulates at WIPI2- and DFCP1-positive isolation membranes, indicating a block at the phagophore stage. TMEM41B-KO cells also show enlarged lipid droplets and reduced mobilization and β-oxidation of fatty acids.","method":"Pooled CRISPR screens, quantitative microscopy, biochemical flux assays, interaction proteomics","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (CRISPR, microscopy, proteomics) in single study, corroborated by other labs","pmids":["30126924"],"is_preprint":false},{"year":2019,"finding":"TMEM41B is an integral ER membrane protein required for phagophore maturation; it is distantly related to VMP1 and plays related but not fully overlapping roles in autophagosome biogenesis.","method":"CRISPR screen with multiple autophagy reporters, quantitative microscopy, biochemical analyses","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 — multiple reporters and orthogonal methods, corroborating earlier reports","pmids":["30933966"],"is_preprint":false},{"year":2018,"finding":"Stasimon/TMEM41B localizes to mitochondria-associated ER membranes (MAM) and its interactome includes components of the ER, mitochondria, and COPI vesicle trafficking machinery; constitutive knockout in mice causes embryonic lethality.","method":"Immunoprecipitation-mass spectrometry (interactome), subcellular fractionation, super-resolution microscopy, knockout mouse characterization","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 — MS-validated interactome, fractionation, super-resolution imaging, and in vivo KO, all in one study","pmids":["30352685"],"is_preprint":false},{"year":2020,"finding":"TMEM41B is required for flavivirus (all Flaviviridae family members tested) and SARS-CoV-2 RNA replication; it is recruited to flavivirus RNA replication complexes and proposed to facilitate membrane curvature to create a protected replication environment. SNPs present at ~20% in East Asian populations reduce flavivirus infection.","method":"Full-genome CRISPR-Cas9 loss-of-function screens, mechanistic virology assays, SNP functional analysis","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 — genome-wide screen plus multiple mechanistic follow-up experiments replicated in preprint and final 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 replication; it contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate membrane expansion and curvature.","method":"Genome-wide CRISPR KO screen, viral lifecycle stage assays, lipid mobilization studies","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — replicated by multiple independent labs with mechanistic follow-up","pmids":["34043740","34871328"],"is_preprint":false},{"year":2022,"finding":"TMEM41B is required for DMV (double-membrane vesicle) formation during β-coronavirus infection; specifically, TMEM41B facilitates the nsp3-nsp4 interaction and ER zippering, whereas VMP1 is required for the subsequent closing of paired ER into DMVs, placing them at distinct steps.","method":"VMP1/TMEM41B KO cells, nsp3/4 expression and interaction assays, electron microscopy of DMV formation","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — KO cells with defined molecular phenotype, epistatic ordering of two proteins, replicated in companion Autophagy paper","pmids":["35536318","35900889"],"is_preprint":false},{"year":2022,"finding":"TMEM41B and VMP1 possess a DedA domain predicted to have two reentrant loops and have demonstrated lipid scrambling activity; both proteins function as lipid scramblases at the ER membrane.","method":"In vitro fluorescent liposome-based phospholipid scrambling assay, in vivo metabolic labeling with alkyne-choline","journal":"EMBO reports / STAR protocols","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro reconstitution of scramblase activity with biochemical assay","pmids":["35044051","35496801"],"is_preprint":false},{"year":2022,"finding":"TMEM41B and VMP1 modulate cellular lipid and energy metabolism (lipid mobilization, mitochondrial β-oxidation, and global metabolome/lipidome) to facilitate dengue virus replication; DENV inhibition in TMEM41B-deficient cells can be partially reversed by exogenous fatty acid supplementation, whereas VMP1 deficiency cannot, indicating distinct metabolic roles.","method":"TMEM41B/VMP1 KO cells, viral replication assays, fatty acid supplementation rescue, metabolomic profiling","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 — KO with defined phenotype and metabolomic profiling, single lab","pmids":["35939522"],"is_preprint":false},{"year":2023,"finding":"TMEM41B, as a lipid scramblase, is involved in ER-to-Golgi transport of GPI-anchored proteins and transmembrane proteins; loss of TMEM41B stabilizes PGAP1 (by slowing its ER-associated degradation) and delays ER-to-Golgi trafficking, thereby promoting GPI-AP processing.","method":"TMEM41B-KO cell lines, PI-PLC sensitivity assay, PGAP1 turnover/ERAD assay, GPI-AP trafficking assay","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — KO with multiple defined phenotypic readouts, single lab","pmids":["37279648"],"is_preprint":false},{"year":2025,"finding":"Purified recombinant TMEM41B forms a concentration-dependent Ca2+ release channel in single-channel electrophysiology assays; TMEM41B deficiency causes ER Ca2+ overload and overexpression depletes ER Ca2+, leading to upregulation of IL-2/IL-7 receptors, dysregulated JAK-STAT/AKT-mTOR/MAPK signaling, and a metabolically activated but immunologically naive T cell state with lowered activation threshold.","method":"Single-channel electrophysiology with purified recombinant protein, cellular Ca2+ measurements, T cell signaling and phenotyping assays","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro reconstitution (single-channel electrophysiology) plus cellular functional validation","pmids":["40038246"],"is_preprint":false},{"year":2024,"finding":"VMP1 and TMEM41B (lipid scramblases) are required for primitive endoderm specification in mouse ESCs by controlling the maturation, stability, and plasma membrane delivery of the WNT receptor FZD2; transgenic FZD2 re-expression rescues the XEN differentiation defect.","method":"ESC gene knockout, cell surface proteome profiling, differentiation assays, transgenic rescue","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 — KO with mechanistic rescue (FZD2 re-expression), cell surface proteomics, single lab","pmids":["39695329"],"is_preprint":false},{"year":2025,"finding":"TMEM41B stabilizes fatty acid synthase (FASN) in vascular smooth muscle cells by inhibiting FASN ubiquitination and degradation, driving lipid synthesis, intracellular lipid storage, and pro-inflammatory cytokine release; silencing TMEM41B in ApoE-/- mice reduces atherosclerotic plaque size.","method":"VSMC TMEM41B knockdown/overexpression, ubiquitination assay, in vivo ApoE-/- mouse model, lipidomics","journal":"Metabolism: clinical and experimental","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo KO with mechanistic ubiquitination assay, single lab","pmids":["41297878"],"is_preprint":false},{"year":2024,"finding":"CLCC1 partners with the phospholipid scramblase TMEM41B to recognize imbalanced ER bilayers and promote lipid scrambling, thereby licensing lipoprotein (VLDL) biogenesis; loss of either CLCC1 or TMEM41B leads to giant lumenal lipid droplets enclosed by imbalanced ER bilayers.","method":"Co-immunoprecipitation (CLCC1-TMEM41B interaction), KO mouse lipidomics, electron microscopy, lipoprotein secretion assay","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus KO phenotype with multiple readouts; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2024.06.07.596575"],"is_preprint":true},{"year":2025,"finding":"Hepatic loss of TMEM41B impairs VLDL secretion, reduces phosphatidylcholine and phosphatidylethanolamine levels, and increases neutral lipids; both TMEM41B and VMP1 localize to the MAM, and their loss reduces mitochondria-ER contact in hepatocytes. Restoring TMEM41B in VMP1-KO mice rescues both VLDL secretion and autophagy defects in a dose-dependent manner.","method":"Liver-specific KO and KI mice, lipidomics, metabolomics, electron microscopy, VLDL secretion assay, LC3-II/p62 biochemical assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — multiple in vivo genetic models with orthogonal biochemical readouts; preprint","pmids":["40291711"],"is_preprint":true},{"year":2024,"finding":"Postnatal ubiquitous depletion of Stasimon/TMEM41B in adult mice causes rapid weight loss, motor dysfunction, and death within ~3 weeks; TMEM41B depletion also severely impairs cell proliferation in mouse embryonic fibroblasts.","method":"Conditional KO mice with tamoxifen-inducible Cre, cell proliferation assays in MEFs","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo conditional KO with defined phenotype plus cellular proliferation assay, single lab","pmids":["38640735"],"is_preprint":false}],"current_model":"TMEM41B is an ER-resident multispanning membrane protein with a DedA/VTT domain that functions as a phospholipid scramblase (demonstrated by in vitro reconstitution) and a Ca2+ release channel (demonstrated by single-channel electrophysiology), forming a complex with VMP1 to regulate ER membrane curvature and bilayer lipid equilibration; these activities are required for autophagosome phagophore maturation, lipid droplet metabolism, VLDL lipoprotein biogenesis, GPI-anchored protein trafficking, and the formation of viral replication organelles (DMVs) for flaviviruses and coronaviruses, while also controlling ER Ca2+ homeostasis to maintain naive T cell quiescence."},"narrative":{"teleology":[{"year":2018,"claim":"Three independent CRISPR screens converged on TMEM41B as an ER membrane protein required at an early step of autophagosome formation, establishing it as a core autophagy factor and revealing an additional role in lipid droplet homeostasis.","evidence":"Genome-wide CRISPR screens with autophagy reporters, KO cell characterization, fluorescence and electron microscopy across multiple labs","pmids":["30093494","30126924"],"confidence":"High","gaps":["Molecular mechanism by which TMEM41B promotes phagophore elongation was unknown","Relationship to VMP1 was only partially characterized","Whether lipid droplet accumulation was a direct or indirect consequence was unclear"]},{"year":2018,"claim":"Discovery that TMEM41B and VMP1 physically interact and that VMP1 overexpression rescues TMEM41B-KO autophagy defects established them as a functional unit, while interactome analysis placed TMEM41B at mitochondria-associated ER membranes and showed that constitutive KO in mice is embryonic lethal.","evidence":"Reciprocal co-immunoprecipitation, in vitro binding, autophagic flux rescue, IP-MS interactome, subcellular fractionation, knockout mice","pmids":["30093494","30773971","30352685"],"confidence":"High","gaps":["Whether TMEM41B and VMP1 have identical or distinct biochemical activities was unknown","The enzymatic activity of the DedA domain had not been determined"]},{"year":2019,"claim":"Further reporter-based studies confirmed TMEM41B acts at the phagophore maturation stage and clarified that it plays related but not fully overlapping roles with VMP1 in autophagosome biogenesis.","evidence":"CRISPR screen with multiple autophagy reporters, quantitative microscopy, biochemical analyses","pmids":["30933966"],"confidence":"High","gaps":["The biochemical basis for the non-overlapping functions of TMEM41B and VMP1 remained undefined"]},{"year":2020,"claim":"Genome-wide screens for host dependency factors revealed TMEM41B as essential for flavivirus and SARS-CoV-2 replication, connecting its membrane-remodeling function to viral double-membrane vesicle formation and identifying population-level SNPs that reduce infection susceptibility.","evidence":"Full-genome CRISPR loss-of-function screens, virology stage-specific assays, SNP functional analysis","pmids":["33338421"],"confidence":"High","gaps":["Whether TMEM41B directly shapes membranes or acts indirectly through lipid composition changes was unresolved","Structural basis for membrane curvature activity was unknown"]},{"year":2021,"claim":"Mechanistic dissection showed TMEM41B acts at an early, post-entry stage of coronavirus replication by mobilizing cholesterol and lipids for membrane expansion, distinguishing its role from receptor-mediated viral entry.","evidence":"CRISPR KO screens, viral lifecycle stage assays, lipid mobilization studies","pmids":["34043740","34871328"],"confidence":"High","gaps":["Direct lipid transfer or scramblase activity had not yet been demonstrated biochemically"]},{"year":2022,"claim":"In vitro reconstitution demonstrated that TMEM41B (and VMP1) possess phospholipid scramblase activity, providing the first direct biochemical function for the DedA/VTT domain and explaining how it equilibrates ER bilayer leaflets.","evidence":"Fluorescent liposome-based phospholipid scrambling assay with purified protein, in vivo metabolic labeling","pmids":["35044051","35496801"],"confidence":"High","gaps":["Structural basis for scramblase activity was not resolved","Whether scramblase activity alone accounts for all membrane-remodeling phenotypes was unclear"]},{"year":2022,"claim":"Epistatic ordering of TMEM41B and VMP1 during β-coronavirus DMV biogenesis showed that TMEM41B facilitates nsp3–nsp4 interaction and ER zippering, while VMP1 is needed for subsequent DMV closure — placing them at sequential steps.","evidence":"KO cells expressing nsp3/4, interaction assays, electron microscopy of DMV intermediates","pmids":["35536318","35900889"],"confidence":"High","gaps":["Whether the same sequential relationship applies to autophagosome formation was not tested","Direct interaction between TMEM41B and viral nsps was not demonstrated"]},{"year":2022,"claim":"Metabolomic profiling revealed that TMEM41B and VMP1 have distinct effects on cellular lipid and energy metabolism during dengue virus replication, with TMEM41B deficiency uniquely rescuable by exogenous fatty acids.","evidence":"TMEM41B/VMP1 KO cells, viral replication assays, fatty acid supplementation, metabolomics","pmids":["35939522"],"confidence":"Medium","gaps":["The specific lipid species or metabolic pathway directly regulated by TMEM41B was not identified","Single-lab finding without independent replication"]},{"year":2023,"claim":"TMEM41B's scramblase activity was linked to ER-to-Golgi trafficking of GPI-anchored proteins: TMEM41B loss stabilized PGAP1 by slowing its ERAD and delayed cargo export, broadening the functional scope beyond autophagy.","evidence":"TMEM41B-KO cells, PI-PLC sensitivity assay, PGAP1 turnover assay, GPI-AP trafficking assay","pmids":["37279648"],"confidence":"Medium","gaps":["Whether TMEM41B directly scrambles specific phospholipids required for GPI-AP sorting was not shown","Single-lab study"]},{"year":2024,"claim":"Postnatal ubiquitous depletion of TMEM41B in adult mice caused rapid lethality within weeks, and MEFs showed severe proliferation defects, demonstrating that TMEM41B is essential not only during embryogenesis but throughout postnatal life.","evidence":"Tamoxifen-inducible conditional KO mice, cell proliferation assays in MEFs","pmids":["38640735"],"confidence":"Medium","gaps":["Which specific tissue(s) or cellular process failure causes postnatal lethality was not determined","Single-lab finding"]},{"year":2024,"claim":"VMP1 and TMEM41B scramblase activity was shown to control plasma membrane delivery of the WNT receptor FZD2, linking their function to primitive endoderm specification in mouse ESCs.","evidence":"ESC gene KO, cell surface proteomics, differentiation assays, transgenic FZD2 rescue","pmids":["39695329"],"confidence":"Medium","gaps":["Whether TMEM41B acts directly on FZD2 maturation or indirectly through global ER lipid remodeling was not resolved","Single-lab study in ESC model"]},{"year":2025,"claim":"Single-channel electrophysiology with purified recombinant TMEM41B demonstrated it forms a Ca²⁺-permeable channel, revealing a second intrinsic activity beyond scramblase function; TMEM41B deficiency caused ER Ca²⁺ overload that altered T cell signaling and maintained an aberrant naive-but-metabolically-activated state.","evidence":"Single-channel electrophysiology with purified protein, cellular Ca²⁺ imaging, T cell phenotyping and signaling assays","pmids":["40038246"],"confidence":"High","gaps":["Whether the Ca²⁺ channel and scramblase activities are structurally separable is unknown","Whether Ca²⁺ channel activity contributes to the autophagy or lipid metabolism phenotypes was not tested"]},{"year":2025,"claim":"TMEM41B was found to stabilize FASN by inhibiting its ubiquitination in vascular smooth muscle cells, promoting lipid synthesis and pro-inflammatory cytokine release; silencing TMEM41B reduced atherosclerotic plaques in ApoE⁻/⁻ mice.","evidence":"VSMC TMEM41B knockdown/overexpression, ubiquitination assay, in vivo ApoE⁻/⁻ mouse model","pmids":["41297878"],"confidence":"Medium","gaps":["Whether FASN stabilization is a direct interaction or secondary to altered ER lipid homeostasis is unclear","Single-lab finding"]},{"year":null,"claim":"Key unresolved questions include the high-resolution structure of TMEM41B, the structural relationship between its scramblase and Ca²⁺ channel activities, the identity of specific lipid substrates it scrambles in vivo, and whether its diverse cellular phenotypes (autophagy, lipid droplets, VLDL secretion, viral DMVs, T cell quiescence) all derive from a unified scramblase/channel mechanism or require additional activities.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of TMEM41B is available","Whether scramblase and Ca²⁺ channel represent one pore or two distinct activities is unknown","In vivo lipid substrate specificity has not been determined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[8,10,14]},{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[11]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[13]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,2,3,4,5,8,10,11]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[0,1,2,3]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,8,9,13]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[5,6,7]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[10,12]},{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[11]}],"complexes":["TMEM41B–VMP1 complex"],"partners":["VMP1","CLCC1","FASN"],"other_free_text":[]},"mechanistic_narrative":"TMEM41B is an ER-resident multispanning membrane protein containing a DedA/VTT domain that functions as both a phospholipid scramblase and a Ca²⁺ release channel, thereby maintaining ER bilayer lipid equilibrium and Ca²⁺ homeostasis [PMID:35044051, PMID:40038246]. It forms a physical complex with VMP1 and localizes to mitochondria-associated ER membranes, where it facilitates membrane curvature events essential for autophagosome phagophore maturation, lipid droplet metabolism, VLDL lipoprotein biogenesis, and GPI-anchored protein trafficking from the ER to the Golgi [PMID:30093494, PMID:30352685, PMID:37279648]. These same membrane-remodeling activities are co-opted by flaviviruses and coronaviruses, which require TMEM41B for the formation of double-membrane vesicle replication organelles [PMID:33338421, PMID:35536318]. Constitutive knockout causes embryonic lethality in mice, and postnatal depletion leads to rapid lethality and proliferation arrest, underscoring its essential role in cellular and organismal viability [PMID:30352685, PMID:38640735]."},"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":174,"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":165,"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":134,"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":121,"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":67,"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":54,"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":54,"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":43,"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":34,"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":"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":31,"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":14,"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":"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":"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":5,"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":"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":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 biology","url":"https://pubmed.ncbi.nlm.nih.gov/40291711","citation_count":2,"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":"40374896","id":"PMC_40374896","title":"Carrimycin exhibited broad spectrum inhibitory activities against coronaviruses replication through down-regulating host factor TMEM41B.","date":"2025","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40374896","citation_count":1,"is_preprint":false},{"pmid":"39709500","id":"PMC_39709500","title":"Inhibition of microRNA-660-5p decreases breast cancer progression through direct targeting of TMEM41B.","date":"2024","source":"Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/39709500","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},{"pmid":"41297878","id":"PMC_41297878","title":"TMEM41B contributes to atherosclerosis by promoting lipid synthesis in vascular smooth muscle cells via fatty acid synthase stabilization.","date":"2025","source":"Metabolism: clinical and experimental","url":"https://pubmed.ncbi.nlm.nih.gov/41297878","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.07.596575","title":"CLCC1 Governs Bilayer Equilibration at the Endoplasmic Reticulum to Maintain Cellular and Systemic Lipid Homeostasis","date":"2024-06-08","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.07.596575","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14251,"output_tokens":3828,"usd":0.050086},"stage2":{"model":"claude-opus-4-6","input_tokens":7282,"output_tokens":3415,"usd":0.182677},"total_usd":0.232763,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B is a multispanning ER membrane protein required for autophagosome formation at an early step; its deletion causes accumulation of ATG proteins and small vesicles but not elongating autophagosome-like structures, and also causes lipid droplet accumulation.\",\n      \"method\": \"Genome-wide CRISPR screen with GFP-LC3-RFP reporter, TMEM41B-KO cell characterization, fluorescence microscopy\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated independently across three labs in the same year with consistent phenotypes\",\n      \"pmids\": [\"30093494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B and VMP1 form a physical complex both in vivo (co-immunoprecipitation) and in vitro, and overexpression of VMP1 rescues autophagic flux in TMEM41B-KO cells, indicating they function together at an early step of autophagosome formation.\",\n      \"method\": \"Co-immunoprecipitation (in vivo), in vitro binding assay, autophagic flux rescue experiment\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reciprocal Co-IP plus functional rescue, replicated across labs\",\n      \"pmids\": [\"30093494\", \"30773971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM41B is required for autophagosome biogenesis; in its absence, LC3 accumulates at WIPI2- and DFCP1-positive isolation membranes, indicating a block at the phagophore stage. TMEM41B-KO cells also show enlarged lipid droplets and reduced mobilization and β-oxidation of fatty acids.\",\n      \"method\": \"Pooled CRISPR screens, quantitative microscopy, biochemical flux assays, interaction proteomics\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (CRISPR, microscopy, proteomics) in single study, corroborated by other labs\",\n      \"pmids\": [\"30126924\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMEM41B is an integral ER membrane protein required for phagophore maturation; it is distantly related to VMP1 and plays related but not fully overlapping roles in autophagosome biogenesis.\",\n      \"method\": \"CRISPR screen with multiple autophagy reporters, quantitative microscopy, biochemical analyses\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple reporters and orthogonal methods, corroborating earlier reports\",\n      \"pmids\": [\"30933966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Stasimon/TMEM41B localizes to mitochondria-associated ER membranes (MAM) and its interactome includes components of the ER, mitochondria, and COPI vesicle trafficking machinery; constitutive knockout in mice causes embryonic lethality.\",\n      \"method\": \"Immunoprecipitation-mass spectrometry (interactome), subcellular fractionation, super-resolution microscopy, knockout mouse characterization\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — MS-validated interactome, fractionation, super-resolution imaging, and in vivo KO, all in one study\",\n      \"pmids\": [\"30352685\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TMEM41B is required for flavivirus (all Flaviviridae family members tested) and SARS-CoV-2 RNA replication; it is recruited to flavivirus RNA replication complexes and proposed to facilitate membrane curvature to create a protected replication environment. SNPs present at ~20% in East Asian populations reduce flavivirus infection.\",\n      \"method\": \"Full-genome CRISPR-Cas9 loss-of-function screens, mechanistic virology assays, SNP functional analysis\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide screen plus multiple mechanistic follow-up experiments replicated in preprint and final 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 replication; it contributes to viral replication complex formation via mobilization of cholesterol and other lipids to facilitate membrane expansion and curvature.\",\n      \"method\": \"Genome-wide CRISPR KO screen, viral lifecycle stage assays, lipid mobilization studies\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated by multiple independent labs with mechanistic follow-up\",\n      \"pmids\": [\"34043740\", \"34871328\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B is required for DMV (double-membrane vesicle) formation during β-coronavirus infection; specifically, TMEM41B facilitates the nsp3-nsp4 interaction and ER zippering, whereas VMP1 is required for the subsequent closing of paired ER into DMVs, placing them at distinct steps.\",\n      \"method\": \"VMP1/TMEM41B KO cells, nsp3/4 expression and interaction assays, electron microscopy of DMV formation\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO cells with defined molecular phenotype, epistatic ordering of two proteins, replicated in companion Autophagy paper\",\n      \"pmids\": [\"35536318\", \"35900889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B and VMP1 possess a DedA domain predicted to have two reentrant loops and have demonstrated lipid scrambling activity; both proteins function as lipid scramblases at the ER membrane.\",\n      \"method\": \"In vitro fluorescent liposome-based phospholipid scrambling assay, in vivo metabolic labeling with alkyne-choline\",\n      \"journal\": \"EMBO reports / STAR protocols\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro reconstitution of scramblase activity with biochemical assay\",\n      \"pmids\": [\"35044051\", \"35496801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMEM41B and VMP1 modulate cellular lipid and energy metabolism (lipid mobilization, mitochondrial β-oxidation, and global metabolome/lipidome) to facilitate dengue virus replication; DENV inhibition in TMEM41B-deficient cells can be partially reversed by exogenous fatty acid supplementation, whereas VMP1 deficiency cannot, indicating distinct metabolic roles.\",\n      \"method\": \"TMEM41B/VMP1 KO cells, viral replication assays, fatty acid supplementation rescue, metabolomic profiling\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO with defined phenotype and metabolomic profiling, single lab\",\n      \"pmids\": [\"35939522\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM41B, as a lipid scramblase, is involved in ER-to-Golgi transport of GPI-anchored proteins and transmembrane proteins; loss of TMEM41B stabilizes PGAP1 (by slowing its ER-associated degradation) and delays ER-to-Golgi trafficking, thereby promoting GPI-AP processing.\",\n      \"method\": \"TMEM41B-KO cell lines, PI-PLC sensitivity assay, PGAP1 turnover/ERAD assay, GPI-AP trafficking assay\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO with multiple defined phenotypic readouts, single lab\",\n      \"pmids\": [\"37279648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Purified recombinant TMEM41B forms a concentration-dependent Ca2+ release channel in single-channel electrophysiology assays; TMEM41B deficiency causes ER Ca2+ overload and overexpression depletes ER Ca2+, leading to upregulation of IL-2/IL-7 receptors, dysregulated JAK-STAT/AKT-mTOR/MAPK signaling, and a metabolically activated but immunologically naive T cell state with lowered activation threshold.\",\n      \"method\": \"Single-channel electrophysiology with purified recombinant protein, cellular Ca2+ measurements, T cell signaling and phenotyping assays\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro reconstitution (single-channel electrophysiology) plus cellular functional validation\",\n      \"pmids\": [\"40038246\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VMP1 and TMEM41B (lipid scramblases) are required for primitive endoderm specification in mouse ESCs by controlling the maturation, stability, and plasma membrane delivery of the WNT receptor FZD2; transgenic FZD2 re-expression rescues the XEN differentiation defect.\",\n      \"method\": \"ESC gene knockout, cell surface proteome profiling, differentiation assays, transgenic rescue\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO with mechanistic rescue (FZD2 re-expression), cell surface proteomics, single lab\",\n      \"pmids\": [\"39695329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TMEM41B stabilizes fatty acid synthase (FASN) in vascular smooth muscle cells by inhibiting FASN ubiquitination and degradation, driving lipid synthesis, intracellular lipid storage, and pro-inflammatory cytokine release; silencing TMEM41B in ApoE-/- mice reduces atherosclerotic plaque size.\",\n      \"method\": \"VSMC TMEM41B knockdown/overexpression, ubiquitination assay, in vivo ApoE-/- mouse model, lipidomics\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo KO with mechanistic ubiquitination assay, single lab\",\n      \"pmids\": [\"41297878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CLCC1 partners with the phospholipid scramblase TMEM41B to recognize imbalanced ER bilayers and promote lipid scrambling, thereby licensing lipoprotein (VLDL) biogenesis; loss of either CLCC1 or TMEM41B leads to giant lumenal lipid droplets enclosed by imbalanced ER bilayers.\",\n      \"method\": \"Co-immunoprecipitation (CLCC1-TMEM41B interaction), KO mouse lipidomics, electron microscopy, lipoprotein secretion assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus KO phenotype with multiple readouts; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.06.07.596575\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Hepatic loss of TMEM41B impairs VLDL secretion, reduces phosphatidylcholine and phosphatidylethanolamine levels, and increases neutral lipids; both TMEM41B and VMP1 localize to the MAM, and their loss reduces mitochondria-ER contact in hepatocytes. Restoring TMEM41B in VMP1-KO mice rescues both VLDL secretion and autophagy defects in a dose-dependent manner.\",\n      \"method\": \"Liver-specific KO and KI mice, lipidomics, metabolomics, electron microscopy, VLDL secretion assay, LC3-II/p62 biochemical assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple in vivo genetic models with orthogonal biochemical readouts; preprint\",\n      \"pmids\": [\"40291711\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Postnatal ubiquitous depletion of Stasimon/TMEM41B in adult mice causes rapid weight loss, motor dysfunction, and death within ~3 weeks; TMEM41B depletion also severely impairs cell proliferation in mouse embryonic fibroblasts.\",\n      \"method\": \"Conditional KO mice with tamoxifen-inducible Cre, cell proliferation assays in MEFs\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo conditional KO with defined phenotype plus cellular proliferation assay, single lab\",\n      \"pmids\": [\"38640735\"],\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 phospholipid scramblase (demonstrated by in vitro reconstitution) and a Ca2+ release channel (demonstrated by single-channel electrophysiology), forming a complex with VMP1 to regulate ER membrane curvature and bilayer lipid equilibration; these activities are required for autophagosome phagophore maturation, lipid droplet metabolism, VLDL lipoprotein biogenesis, GPI-anchored protein trafficking, and the formation of viral replication organelles (DMVs) for flaviviruses and coronaviruses, while also controlling ER Ca2+ homeostasis to maintain naive T cell quiescence.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TMEM41B is an ER-resident multispanning membrane protein containing a DedA/VTT domain that functions as both a phospholipid scramblase and a Ca²⁺ release channel, thereby maintaining ER bilayer lipid equilibrium and Ca²⁺ homeostasis [PMID:35044051, PMID:40038246]. It forms a physical complex with VMP1 and localizes to mitochondria-associated ER membranes, where it facilitates membrane curvature events essential for autophagosome phagophore maturation, lipid droplet metabolism, VLDL lipoprotein biogenesis, and GPI-anchored protein trafficking from the ER to the Golgi [PMID:30093494, PMID:30352685, PMID:37279648]. These same membrane-remodeling activities are co-opted by flaviviruses and coronaviruses, which require TMEM41B for the formation of double-membrane vesicle replication organelles [PMID:33338421, PMID:35536318]. Constitutive knockout causes embryonic lethality in mice, and postnatal depletion leads to rapid lethality and proliferation arrest, underscoring its essential role in cellular and organismal viability [PMID:30352685, PMID:38640735].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Three independent CRISPR screens converged on TMEM41B as an ER membrane protein required at an early step of autophagosome formation, establishing it as a core autophagy factor and revealing an additional role in lipid droplet homeostasis.\",\n      \"evidence\": \"Genome-wide CRISPR screens with autophagy reporters, KO cell characterization, fluorescence and electron microscopy across multiple labs\",\n      \"pmids\": [\"30093494\", \"30126924\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism by which TMEM41B promotes phagophore elongation was unknown\",\n        \"Relationship to VMP1 was only partially characterized\",\n        \"Whether lipid droplet accumulation was a direct or indirect consequence was unclear\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Discovery that TMEM41B and VMP1 physically interact and that VMP1 overexpression rescues TMEM41B-KO autophagy defects established them as a functional unit, while interactome analysis placed TMEM41B at mitochondria-associated ER membranes and showed that constitutive KO in mice is embryonic lethal.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, in vitro binding, autophagic flux rescue, IP-MS interactome, subcellular fractionation, knockout mice\",\n      \"pmids\": [\"30093494\", \"30773971\", \"30352685\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TMEM41B and VMP1 have identical or distinct biochemical activities was unknown\",\n        \"The enzymatic activity of the DedA domain had not been determined\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Further reporter-based studies confirmed TMEM41B acts at the phagophore maturation stage and clarified that it plays related but not fully overlapping roles with VMP1 in autophagosome biogenesis.\",\n      \"evidence\": \"CRISPR screen with multiple autophagy reporters, quantitative microscopy, biochemical analyses\",\n      \"pmids\": [\"30933966\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The biochemical basis for the non-overlapping functions of TMEM41B and VMP1 remained undefined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Genome-wide screens for host dependency factors revealed TMEM41B as essential for flavivirus and SARS-CoV-2 replication, connecting its membrane-remodeling function to viral double-membrane vesicle formation and identifying population-level SNPs that reduce infection susceptibility.\",\n      \"evidence\": \"Full-genome CRISPR loss-of-function screens, virology stage-specific assays, SNP functional analysis\",\n      \"pmids\": [\"33338421\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TMEM41B directly shapes membranes or acts indirectly through lipid composition changes was unresolved\",\n        \"Structural basis for membrane curvature activity was unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Mechanistic dissection showed TMEM41B acts at an early, post-entry stage of coronavirus replication by mobilizing cholesterol and lipids for membrane expansion, distinguishing its role from receptor-mediated viral entry.\",\n      \"evidence\": \"CRISPR KO screens, viral lifecycle stage assays, lipid mobilization studies\",\n      \"pmids\": [\"34043740\", \"34871328\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct lipid transfer or scramblase activity had not yet been demonstrated biochemically\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"In vitro reconstitution demonstrated that TMEM41B (and VMP1) possess phospholipid scramblase activity, providing the first direct biochemical function for the DedA/VTT domain and explaining how it equilibrates ER bilayer leaflets.\",\n      \"evidence\": \"Fluorescent liposome-based phospholipid scrambling assay with purified protein, in vivo metabolic labeling\",\n      \"pmids\": [\"35044051\", \"35496801\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for scramblase activity was not resolved\",\n        \"Whether scramblase activity alone accounts for all membrane-remodeling phenotypes was unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Epistatic ordering of TMEM41B and VMP1 during β-coronavirus DMV biogenesis showed that TMEM41B facilitates nsp3–nsp4 interaction and ER zippering, while VMP1 is needed for subsequent DMV closure — placing them at sequential steps.\",\n      \"evidence\": \"KO cells expressing nsp3/4, interaction assays, electron microscopy of DMV intermediates\",\n      \"pmids\": [\"35536318\", \"35900889\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether the same sequential relationship applies to autophagosome formation was not tested\",\n        \"Direct interaction between TMEM41B and viral nsps was not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Metabolomic profiling revealed that TMEM41B and VMP1 have distinct effects on cellular lipid and energy metabolism during dengue virus replication, with TMEM41B deficiency uniquely rescuable by exogenous fatty acids.\",\n      \"evidence\": \"TMEM41B/VMP1 KO cells, viral replication assays, fatty acid supplementation, metabolomics\",\n      \"pmids\": [\"35939522\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific lipid species or metabolic pathway directly regulated by TMEM41B was not identified\",\n        \"Single-lab finding without independent replication\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"TMEM41B's scramblase activity was linked to ER-to-Golgi trafficking of GPI-anchored proteins: TMEM41B loss stabilized PGAP1 by slowing its ERAD and delayed cargo export, broadening the functional scope beyond autophagy.\",\n      \"evidence\": \"TMEM41B-KO cells, PI-PLC sensitivity assay, PGAP1 turnover assay, GPI-AP trafficking assay\",\n      \"pmids\": [\"37279648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether TMEM41B directly scrambles specific phospholipids required for GPI-AP sorting was not shown\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Postnatal ubiquitous depletion of TMEM41B in adult mice caused rapid lethality within weeks, and MEFs showed severe proliferation defects, demonstrating that TMEM41B is essential not only during embryogenesis but throughout postnatal life.\",\n      \"evidence\": \"Tamoxifen-inducible conditional KO mice, cell proliferation assays in MEFs\",\n      \"pmids\": [\"38640735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which specific tissue(s) or cellular process failure causes postnatal lethality was not determined\",\n        \"Single-lab finding\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"VMP1 and TMEM41B scramblase activity was shown to control plasma membrane delivery of the WNT receptor FZD2, linking their function to primitive endoderm specification in mouse ESCs.\",\n      \"evidence\": \"ESC gene KO, cell surface proteomics, differentiation assays, transgenic FZD2 rescue\",\n      \"pmids\": [\"39695329\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether TMEM41B acts directly on FZD2 maturation or indirectly through global ER lipid remodeling was not resolved\",\n        \"Single-lab study in ESC model\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Single-channel electrophysiology with purified recombinant TMEM41B demonstrated it forms a Ca²⁺-permeable channel, revealing a second intrinsic activity beyond scramblase function; TMEM41B deficiency caused ER Ca²⁺ overload that altered T cell signaling and maintained an aberrant naive-but-metabolically-activated state.\",\n      \"evidence\": \"Single-channel electrophysiology with purified protein, cellular Ca²⁺ imaging, T cell phenotyping and signaling assays\",\n      \"pmids\": [\"40038246\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether the Ca²⁺ channel and scramblase activities are structurally separable is unknown\",\n        \"Whether Ca²⁺ channel activity contributes to the autophagy or lipid metabolism phenotypes was not tested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"TMEM41B was found to stabilize FASN by inhibiting its ubiquitination in vascular smooth muscle cells, promoting lipid synthesis and pro-inflammatory cytokine release; silencing TMEM41B reduced atherosclerotic plaques in ApoE⁻/⁻ mice.\",\n      \"evidence\": \"VSMC TMEM41B knockdown/overexpression, ubiquitination assay, in vivo ApoE⁻/⁻ mouse model\",\n      \"pmids\": [\"41297878\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether FASN stabilization is a direct interaction or secondary to altered ER lipid homeostasis is unclear\",\n        \"Single-lab finding\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the high-resolution structure of TMEM41B, the structural relationship between its scramblase and Ca²⁺ channel activities, the identity of specific lipid substrates it scrambles in vivo, and whether its diverse cellular phenotypes (autophagy, lipid droplets, VLDL secretion, viral DMVs, T cell quiescence) all derive from a unified scramblase/channel mechanism or require additional activities.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of TMEM41B is available\",\n        \"Whether scramblase and Ca²⁺ channel represent one pore or two distinct activities is unknown\",\n        \"In vivo lipid substrate specificity has not been determined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [8, 10, 14]},\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 2, 3, 4, 5, 8, 10, 11]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 8, 9, 13]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [5, 6, 7]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [10, 12]},\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [\n      \"TMEM41B–VMP1 complex\"\n    ],\n    \"partners\": [\n      \"VMP1\",\n      \"CLCC1\",\n      \"FASN\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}