{"gene":"TMEM147","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2010,"finding":"TMEM147 is a novel core component of the Nicalin-NOMO protein complex. Mass spectrometry of affinity-purified complex preparations identified TMEM147 (~22 kDa) as a component. Overexpression and knockdown experiments in cultured cells confirmed close interdependence among TMEM147, Nicalin, and NOMO. Complex assembly is hierarchical: Nicalin-NOMO intermediate forms first, and Nicalin is the limiting factor that stabilizes the other two components. TMEM147 topology resembles APH-1 of the gamma-secretase complex. TMEM147 localizes to the endoplasmic reticulum.","method":"Affinity purification followed by mass spectrometry, overexpression and knockdown experiments in cultured cells, subcellular localization assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP/affinity purification + MS identification + gain- and loss-of-function validation, multiple orthogonal methods in one study","pmids":["20538592"],"is_preprint":false},{"year":2020,"finding":"TMEM147 localizes to both the ER and nuclear envelope in HeLa cells. TMEM147 physically interacts with lamin B receptor (LBR) and the C-terminus of LBR is essential for their functional interaction. Silencing TMEM147 drastically reduces LBR levels at the inner nuclear membrane and mislocalizes LBR to the ER. TMEM147 also physically interacts with sterol reductase DHCR7; TMEM147 downregulation causes sharp decline in DHCR7 protein levels and coordinate transcriptional decreases of LBR and DHCR7 expression. Lipidomic analysis upon TMEM147 silencing identified changes in cellular cholesterol levels, cholesteryl ester levels/profile, and cholesterol uptake.","method":"Co-immunoprecipitation, siRNA silencing, immunofluorescence/confocal microscopy, western blotting, lipidomic analysis","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP for two binding partners, siRNA KD with defined molecular phenotypes, lipidomics, multiple orthogonal methods in one study","pmids":["32694168"],"is_preprint":false},{"year":2021,"finding":"TMEM147 silencing causes increases in both curved-ER marker RTN4 and flat-ER marker CLIMP-63/CKAP4 area and intensity, with a profound shift toward flat ER areas, concurrent with reduction in DNA condensation. Protein network analyses identified TMEM147 function in ribosome binding, oxidoreductase activity, G protein-coupled receptor activity, and transmembrane transport.","method":"siRNA silencing, quantitative immunofluorescence of ER markers (RTN4, CLIMP63), protein network/pathway analysis of compiled TMEM147 interactors","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct ER morphology quantification upon KD with two orthogonal markers, single lab, network analysis is computational","pmids":["34638576"],"is_preprint":false},{"year":2022,"finding":"Bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability. Mechanistically, TMEM147 functions at the nuclear envelope to anchor LBR to the inner nuclear membrane and at the ER to facilitate translation of nascent polypeptides within the ribosome-bound TMCO1 translocon complex. In TMEM147-deficient cells: (1) LBR was mislocalized and nuclear segmentation was abnormal; (2) CKAP4 (CLIMP-63) and RTN4 (NOGO) were upregulated with ER reorientation; (3) missense variants were predicted to disrupt translocon complex assembly/function; (4) in vitro analyses showed accelerated protein degradation via the autophagy-lysosomal pathway.","method":"In silico structural modeling, in vitro protein degradation assays, patient fibroblast cell culture (immunofluorescence for LBR localization, ER marker expression), neutrophil morphology analysis, co-expression analysis","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (structural modeling, in vitro functional assay, primary patient cells with defined molecular phenotypes), independently confirmed across 23 individuals from 15 families","pmids":["36044892"],"is_preprint":false},{"year":2023,"finding":"TMEM147 interacts with DHCR7 (7-dehydrocholesterol reductase) in HCC cells, affecting cellular cholesterol homeostasis and increasing extracellular levels of 27-hydroxycholesterol (27HC). TMEM147 promotes DHCR7 expression by enhancing STAT2 transcriptional activity. Elevated 27HC upregulates glutathione peroxidase 4 (GPX4) in HCC cells, conferring ferroptosis resistance. HCC cell-derived 27HC increases lipid metabolism in macrophages and activates PPARγ signaling, driving M2 macrophage polarization.","method":"Immunoprecipitation, mass spectrometry, RNA-seq, lipidomic analysis, ELISA for cholesterol and 27HC, ferroptosis assays, flow cytometry for macrophage phenotyping, immunofluorescence, in vitro and in vivo tumor models","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP + MS for interaction, lipidomics, in vitro/in vivo functional validation, but single lab; mechanistic chain is multi-step with some indirect links","pmids":["37891677"],"is_preprint":false},{"year":2016,"finding":"TMEM147 binds to Haemonchus contortus galectin (rHco-gal-m/f) as demonstrated by yeast two-hybrid screening and co-immunoprecipitation. In goat PBMC, TMEM147 localizes to the cell membrane. Knockdown of tmem147 by RNAi revealed that the galectin-TMEM147 interaction mediates cell proliferation, apoptosis, and transcription of IL-10 and TGF-β1. TMEM147 knockdown also affected galectin-regulated phagocytosis and nitric oxide production but did not affect galectin-regulated migration or IFN-γ transcription (negative finding for those functions).","method":"Yeast two-hybrid, co-immunoprecipitation, immunoblotting, RNAi knockdown, immunofluorescence/confocal microscopy, flow cytometry, functional cell assays","journal":"Parasites & vectors","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid confirmed by Co-IP, RNAi with defined functional readouts, but this is a parasite-host interaction study in a non-mammalian system (goat PBMC) and the binding partner is a parasitic protein","pmids":["27337943"],"is_preprint":false}],"current_model":"TMEM147 is a conserved multi-pass transmembrane protein resident at the ER and nuclear envelope that functions as a core component of the Nicalin-NOMO complex (modulating Nodal signaling), physically interacts with and stabilizes lamin B receptor (LBR) at the inner nuclear membrane and the sterol reductase DHCR7 at the ER to regulate cholesterol homeostasis, and participates in the TMCO1 ribosome-associated translocon complex to facilitate biogenesis of multipass membrane proteins; loss of TMEM147 mislocalizes LBR, disrupts ER architecture, impairs protein translation/stability, and causes syndromic intellectual disability in humans."},"narrative":{"mechanistic_narrative":"TMEM147 is a conserved multi-pass transmembrane protein resident at the endoplasmic reticulum and nuclear envelope that organizes membrane protein complexes governing ER architecture, sterol homeostasis, and nuclear envelope integrity [PMID:20538592, PMID:32694168]. It was first identified as a core subunit of the Nicalin-NOMO complex, where assembly is hierarchical and interdependent among the three components, with a topology resembling the gamma-secretase subunit APH-1 [PMID:20538592]. At the inner nuclear membrane TMEM147 physically interacts with and anchors lamin B receptor (LBR), and its loss reduces LBR levels and mislocalizes LBR to the ER with abnormal nuclear segmentation [PMID:32694168, PMID:36044892]. In parallel, TMEM147 binds and stabilizes the sterol reductase DHCR7 and coordinates LBR/DHCR7 expression, such that its depletion alters cellular cholesterol, cholesteryl ester profiles, and cholesterol uptake [PMID:32694168]. TMEM147 also functions within the ribosome-associated TMCO1 translocon complex to facilitate translation of nascent polypeptides, and its loss accelerates protein degradation through the autophagy-lysosomal pathway and remodels the ER toward flat-ER morphology (upregulation of CLIMP-63/CKAP4 and RTN4) [PMID:34638576, PMID:36044892]. Bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability in humans [PMID:36044892].","teleology":[{"year":2010,"claim":"Established TMEM147 as a bona fide protein rather than an orphan transmembrane ORF by placing it as an interdependent core subunit of the Nicalin-NOMO complex at the ER.","evidence":"Affinity purification/mass spectrometry plus overexpression and knockdown in cultured cells, with subcellular localization","pmids":["20538592"],"confidence":"High","gaps":["Did not define a catalytic or signaling output for the complex","APH-1-like topology was inferred, not structurally resolved","Role of the complex in Nodal signaling not directly tested here"]},{"year":2016,"claim":"Addressed whether TMEM147 has surface/immunomodulatory roles by showing it binds a parasite galectin and mediates proliferation, apoptosis, and cytokine transcription in immune cells.","evidence":"Yeast two-hybrid, Co-IP, RNAi and functional assays in goat PBMC (non-mammalian host-parasite system)","pmids":["27337943"],"confidence":"Medium","gaps":["Performed in a host-parasite context with a parasitic ligand, limiting generalization to human biology","Reported plasma membrane localization conflicts with ER/nuclear envelope localization in mammalian cells","No mechanism linking galectin binding to downstream signaling defined"]},{"year":2020,"claim":"Identified the nuclear-envelope and sterol-regulatory functions of TMEM147 by demonstrating physical interactions with LBR and DHCR7 and their loss-of-function consequences.","evidence":"Reciprocal Co-IP, siRNA silencing, confocal microscopy, western blotting, and lipidomics in HeLa cells","pmids":["32694168"],"confidence":"High","gaps":["Did not resolve whether cholesterol changes are direct (stabilization) or transcriptional","Structural basis of the LBR C-terminus interaction not determined","No in vivo validation"]},{"year":2021,"claim":"Linked TMEM147 loss to a defined ER morphological shift, connecting its molecular interactions to organelle-scale architecture.","evidence":"siRNA silencing with quantitative immunofluorescence of ER markers RTN4 and CLIMP63 plus interactor network analysis","pmids":["34638576"],"confidence":"Medium","gaps":["Network functional assignments are computational, not experimentally tested","Causal link between ER reshaping and DNA condensation change unresolved","Single-lab observation"]},{"year":2022,"claim":"Established TMEM147 as a disease gene and integrated its roles by showing bi-allelic loss-of-function causes syndromic intellectual disability through LBR anchoring and TMCO1-translocon-dependent translation.","evidence":"Patient fibroblasts (LBR localization, ER markers), neutrophil morphology, in silico structural modeling, and in vitro protein degradation assays across 23 individuals from 15 families","pmids":["36044892"],"confidence":"High","gaps":["Translocon contribution inferred from modeling rather than direct biochemical reconstitution","Mechanism connecting molecular defects to neurodevelopmental phenotype not established","Substrate specificity of TMEM147 in the translocon not defined"]},{"year":2023,"claim":"Extended the DHCR7 axis to disease physiology by showing TMEM147 promotes DHCR7 via STAT2 and drives a 27-hydroxycholesterol-dependent program affecting ferroptosis resistance and macrophage polarization in hepatocellular carcinoma.","evidence":"Co-IP/MS, RNA-seq, lipidomics, ELISA, ferroptosis and macrophage phenotyping assays, in vitro and in vivo tumor models","pmids":["37891677"],"confidence":"Medium","gaps":["Multi-step mechanistic chain has indirect links (STAT2, 27HC, GPX4, PPARgamma)","Single-lab findings in a cancer context","Direct versus indirect control of DHCR7 transcription versus stability not disentangled"]},{"year":null,"claim":"How TMEM147 mechanistically couples its translocon role to substrate-specific biogenesis of multipass membrane proteins, and how this connects to the neurodevelopmental phenotype, remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No reconstituted structure of TMEM147 within the TMCO1 translocon","No defined substrate set whose biogenesis depends on TMEM147","Causal path from molecular defects to intellectual disability not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[1,3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1,4]}],"complexes":["Nicalin-NOMO complex","TMCO1 ribosome-associated translocon"],"partners":["NCLN","NOMO1","LBR","DHCR7","TMCO1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BVK8","full_name":"BOS complex subunit TMEM147","aliases":["Protein NIFIE 14","Transmembrane protein 147"],"length_aa":224,"mass_kda":25.3,"function":"Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes (PubMed:32820719, PubMed:36261522). The MPT complex takes over after the SEC61 complex: following membrane insertion of the first few transmembrane segments of proteins by the SEC61 complex, the MPT complex occludes the lateral gate of the SEC61 complex to promote insertion of subsequent transmembrane regions (PubMed:36261522). Also acts as a negative regulator of CHRM3 function, most likely by interfering with its trafficking to the cell membrane (PubMed:21056967). Negatively regulates CHRM3-mediated calcium mobilization and activation of RPS6KA1/p90RSK activity (PubMed:21056967). Regulates LBR localization to the nucleus inner membrane (PubMed:32694168)","subcellular_location":"Endoplasmic reticulum membrane; Nucleus membrane; Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9BVK8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM147","classification":"Not Classified","n_dependent_lines":21,"n_total_lines":1208,"dependency_fraction":0.0173841059602649},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000105677","cell_line_id":"CID001797","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"KTN1","stoichiometry":10.0},{"gene":"RPL38","stoichiometry":10.0},{"gene":"NCLN","stoichiometry":10.0},{"gene":"SFT2D3","stoichiometry":0.2},{"gene":"RPS23","stoichiometry":0.2},{"gene":"RPS8","stoichiometry":0.2},{"gene":"SPCS3","stoichiometry":0.2},{"gene":"MARS","stoichiometry":0.2},{"gene":"CCDC47","stoichiometry":0.2},{"gene":"RPL32","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001797","total_profiled":1310},"omim":[{"mim_id":"620075","title":"NEURODEVELOPMENTAL DISORDER WITH FACIAL DYSMORPHISM, ABSENT LANGUAGE, AND PSEUDO-PELGER-HUET ANOMALY; NEDFLPH","url":"https://www.omim.org/entry/620075"},{"mim_id":"613585","title":"TRANSMEMBRANE PROTEIN 147; TMEM147","url":"https://www.omim.org/entry/613585"},{"mim_id":"609158","title":"NODAL MODULATOR 2; NOMO2","url":"https://www.omim.org/entry/609158"},{"mim_id":"609156","title":"NICALIN; NCLN","url":"https://www.omim.org/entry/609156"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMEM147"},"hgnc":{"alias_symbol":["NIFIE14","MGC1936"],"prev_symbol":[]},"alphafold":{"accession":"Q9BVK8","domains":[{"cath_id":"-","chopping":"4-223","consensus_level":"high","plddt":93.0062,"start":4,"end":223}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVK8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVK8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVK8-F1-predicted_aligned_error_v6.png","plddt_mean":92.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM147","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM147"},"sequence":{"accession":"Q9BVK8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BVK8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BVK8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVK8"}},"corpus_meta":[{"pmid":"37891677","id":"PMC_37891677","title":"TMEM147 aggravates the progression of HCC by modulating cholesterol homeostasis, suppressing ferroptosis, and promoting the M2 polarization of tumor-associated macrophages.","date":"2023","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/37891677","citation_count":70,"is_preprint":false},{"pmid":"20538592","id":"PMC_20538592","title":"Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20538592","citation_count":43,"is_preprint":false},{"pmid":"27337943","id":"PMC_27337943","title":"Transmembrane protein 147 (TMEM147): another partner protein of Haemonchus contortus galectin on the goat peripheral blood mononuclear cells (PBMC).","date":"2016","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/27337943","citation_count":27,"is_preprint":false},{"pmid":"37217070","id":"PMC_37217070","title":"The feedback loop of AURKA/DDX5/TMEM147-AS1/let-7 drives lipophagy to induce cisplatin resistance in epithelial ovarian cancer.","date":"2023","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/37217070","citation_count":21,"is_preprint":false},{"pmid":"32694168","id":"PMC_32694168","title":"TMEM147 interacts with lamin B receptor, regulates its localization and levels, and affects cholesterol homeostasis.","date":"2020","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/32694168","citation_count":15,"is_preprint":false},{"pmid":"36181243","id":"PMC_36181243","title":"The long non-sacoding RNA TMEM147-AS1/miR-133b/ZNF587 axis regulates the Warburg effect and promotes prostatic carcinoma invasion and proliferation.","date":"2022","source":"The journal of gene medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36181243","citation_count":12,"is_preprint":false},{"pmid":"36044892","id":"PMC_36044892","title":"Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huët anomaly.","date":"2022","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36044892","citation_count":8,"is_preprint":false},{"pmid":"34638576","id":"PMC_34638576","title":"Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34638576","citation_count":6,"is_preprint":false},{"pmid":"37303938","id":"PMC_37303938","title":"Long noncoding RNA TMEM147-AS1 serves as a microRNA-326 sponge to aggravate the malignancy of gastric cancer by upregulating SMAD5.","date":"2022","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/37303938","citation_count":6,"is_preprint":false},{"pmid":"39113102","id":"PMC_39113102","title":"Long non-coding RNA TMEM147 antisense RNA 1/microRNA-124/signal transducer and activator of transcription 3 axis in estrogen receptor-positive breast cancer.","date":"2024","source":"The journal of obstetrics and gynaecology research","url":"https://pubmed.ncbi.nlm.nih.gov/39113102","citation_count":2,"is_preprint":false},{"pmid":"41055764","id":"PMC_41055764","title":"lncRNA TMEM147-AS1 promotes acute myeloid leukemia development by regulating miR-873-3p/ZFX axis.","date":"2025","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/41055764","citation_count":2,"is_preprint":false},{"pmid":"37668766","id":"PMC_37668766","title":"A biallelic loss-of-function variant in TMEM147 causes profound intellectual disability and spasticity.","date":"2023","source":"Neurogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/37668766","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9206,"output_tokens":2157,"usd":0.029986,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9183,"output_tokens":2656,"usd":0.056157,"stage2_stop_reason":"end_turn"},"total_usd":0.086143,"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\": 2010,\n      \"finding\": \"TMEM147 is a novel core component of the Nicalin-NOMO protein complex. Mass spectrometry of affinity-purified complex preparations identified TMEM147 (~22 kDa) as a component. Overexpression and knockdown experiments in cultured cells confirmed close interdependence among TMEM147, Nicalin, and NOMO. Complex assembly is hierarchical: Nicalin-NOMO intermediate forms first, and Nicalin is the limiting factor that stabilizes the other two components. TMEM147 topology resembles APH-1 of the gamma-secretase complex. TMEM147 localizes to the endoplasmic reticulum.\",\n      \"method\": \"Affinity purification followed by mass spectrometry, overexpression and knockdown experiments in cultured cells, subcellular localization assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP/affinity purification + MS identification + gain- and loss-of-function validation, multiple orthogonal methods in one study\",\n      \"pmids\": [\"20538592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TMEM147 localizes to both the ER and nuclear envelope in HeLa cells. TMEM147 physically interacts with lamin B receptor (LBR) and the C-terminus of LBR is essential for their functional interaction. Silencing TMEM147 drastically reduces LBR levels at the inner nuclear membrane and mislocalizes LBR to the ER. TMEM147 also physically interacts with sterol reductase DHCR7; TMEM147 downregulation causes sharp decline in DHCR7 protein levels and coordinate transcriptional decreases of LBR and DHCR7 expression. Lipidomic analysis upon TMEM147 silencing identified changes in cellular cholesterol levels, cholesteryl ester levels/profile, and cholesterol uptake.\",\n      \"method\": \"Co-immunoprecipitation, siRNA silencing, immunofluorescence/confocal microscopy, western blotting, lipidomic analysis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP for two binding partners, siRNA KD with defined molecular phenotypes, lipidomics, multiple orthogonal methods in one study\",\n      \"pmids\": [\"32694168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMEM147 silencing causes increases in both curved-ER marker RTN4 and flat-ER marker CLIMP-63/CKAP4 area and intensity, with a profound shift toward flat ER areas, concurrent with reduction in DNA condensation. Protein network analyses identified TMEM147 function in ribosome binding, oxidoreductase activity, G protein-coupled receptor activity, and transmembrane transport.\",\n      \"method\": \"siRNA silencing, quantitative immunofluorescence of ER markers (RTN4, CLIMP63), protein network/pathway analysis of compiled TMEM147 interactors\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct ER morphology quantification upon KD with two orthogonal markers, single lab, network analysis is computational\",\n      \"pmids\": [\"34638576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability. Mechanistically, TMEM147 functions at the nuclear envelope to anchor LBR to the inner nuclear membrane and at the ER to facilitate translation of nascent polypeptides within the ribosome-bound TMCO1 translocon complex. In TMEM147-deficient cells: (1) LBR was mislocalized and nuclear segmentation was abnormal; (2) CKAP4 (CLIMP-63) and RTN4 (NOGO) were upregulated with ER reorientation; (3) missense variants were predicted to disrupt translocon complex assembly/function; (4) in vitro analyses showed accelerated protein degradation via the autophagy-lysosomal pathway.\",\n      \"method\": \"In silico structural modeling, in vitro protein degradation assays, patient fibroblast cell culture (immunofluorescence for LBR localization, ER marker expression), neutrophil morphology analysis, co-expression analysis\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (structural modeling, in vitro functional assay, primary patient cells with defined molecular phenotypes), independently confirmed across 23 individuals from 15 families\",\n      \"pmids\": [\"36044892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM147 interacts with DHCR7 (7-dehydrocholesterol reductase) in HCC cells, affecting cellular cholesterol homeostasis and increasing extracellular levels of 27-hydroxycholesterol (27HC). TMEM147 promotes DHCR7 expression by enhancing STAT2 transcriptional activity. Elevated 27HC upregulates glutathione peroxidase 4 (GPX4) in HCC cells, conferring ferroptosis resistance. HCC cell-derived 27HC increases lipid metabolism in macrophages and activates PPARγ signaling, driving M2 macrophage polarization.\",\n      \"method\": \"Immunoprecipitation, mass spectrometry, RNA-seq, lipidomic analysis, ELISA for cholesterol and 27HC, ferroptosis assays, flow cytometry for macrophage phenotyping, immunofluorescence, in vitro and in vivo tumor models\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP + MS for interaction, lipidomics, in vitro/in vivo functional validation, but single lab; mechanistic chain is multi-step with some indirect links\",\n      \"pmids\": [\"37891677\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TMEM147 binds to Haemonchus contortus galectin (rHco-gal-m/f) as demonstrated by yeast two-hybrid screening and co-immunoprecipitation. In goat PBMC, TMEM147 localizes to the cell membrane. Knockdown of tmem147 by RNAi revealed that the galectin-TMEM147 interaction mediates cell proliferation, apoptosis, and transcription of IL-10 and TGF-β1. TMEM147 knockdown also affected galectin-regulated phagocytosis and nitric oxide production but did not affect galectin-regulated migration or IFN-γ transcription (negative finding for those functions).\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunoblotting, RNAi knockdown, immunofluorescence/confocal microscopy, flow cytometry, functional cell assays\",\n      \"journal\": \"Parasites & vectors\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid confirmed by Co-IP, RNAi with defined functional readouts, but this is a parasite-host interaction study in a non-mammalian system (goat PBMC) and the binding partner is a parasitic protein\",\n      \"pmids\": [\"27337943\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMEM147 is a conserved multi-pass transmembrane protein resident at the ER and nuclear envelope that functions as a core component of the Nicalin-NOMO complex (modulating Nodal signaling), physically interacts with and stabilizes lamin B receptor (LBR) at the inner nuclear membrane and the sterol reductase DHCR7 at the ER to regulate cholesterol homeostasis, and participates in the TMCO1 ribosome-associated translocon complex to facilitate biogenesis of multipass membrane proteins; loss of TMEM147 mislocalizes LBR, disrupts ER architecture, impairs protein translation/stability, and causes syndromic intellectual disability in humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMEM147 is a conserved multi-pass transmembrane protein resident at the endoplasmic reticulum and nuclear envelope that organizes membrane protein complexes governing ER architecture, sterol homeostasis, and nuclear envelope integrity [#0, #1]. It was first identified as a core subunit of the Nicalin-NOMO complex, where assembly is hierarchical and interdependent among the three components, with a topology resembling the gamma-secretase subunit APH-1 [#0]. At the inner nuclear membrane TMEM147 physically interacts with and anchors lamin B receptor (LBR), and its loss reduces LBR levels and mislocalizes LBR to the ER with abnormal nuclear segmentation [#1, #3]. In parallel, TMEM147 binds and stabilizes the sterol reductase DHCR7 and coordinates LBR/DHCR7 expression, such that its depletion alters cellular cholesterol, cholesteryl ester profiles, and cholesterol uptake [#1]. TMEM147 also functions within the ribosome-associated TMCO1 translocon complex to facilitate translation of nascent polypeptides, and its loss accelerates protein degradation through the autophagy-lysosomal pathway and remodels the ER toward flat-ER morphology (upregulation of CLIMP-63/CKAP4 and RTN4) [#2, #3]. Bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability in humans [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established TMEM147 as a bona fide protein rather than an orphan transmembrane ORF by placing it as an interdependent core subunit of the Nicalin-NOMO complex at the ER.\",\n      \"evidence\": \"Affinity purification/mass spectrometry plus overexpression and knockdown in cultured cells, with subcellular localization\",\n      \"pmids\": [\"20538592\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define a catalytic or signaling output for the complex\", \"APH-1-like topology was inferred, not structurally resolved\", \"Role of the complex in Nodal signaling not directly tested here\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Addressed whether TMEM147 has surface/immunomodulatory roles by showing it binds a parasite galectin and mediates proliferation, apoptosis, and cytokine transcription in immune cells.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, RNAi and functional assays in goat PBMC (non-mammalian host-parasite system)\",\n      \"pmids\": [\"27337943\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Performed in a host-parasite context with a parasitic ligand, limiting generalization to human biology\", \"Reported plasma membrane localization conflicts with ER/nuclear envelope localization in mammalian cells\", \"No mechanism linking galectin binding to downstream signaling defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified the nuclear-envelope and sterol-regulatory functions of TMEM147 by demonstrating physical interactions with LBR and DHCR7 and their loss-of-function consequences.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA silencing, confocal microscopy, western blotting, and lipidomics in HeLa cells\",\n      \"pmids\": [\"32694168\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether cholesterol changes are direct (stabilization) or transcriptional\", \"Structural basis of the LBR C-terminus interaction not determined\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked TMEM147 loss to a defined ER morphological shift, connecting its molecular interactions to organelle-scale architecture.\",\n      \"evidence\": \"siRNA silencing with quantitative immunofluorescence of ER markers RTN4 and CLIMP63 plus interactor network analysis\",\n      \"pmids\": [\"34638576\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Network functional assignments are computational, not experimentally tested\", \"Causal link between ER reshaping and DNA condensation change unresolved\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established TMEM147 as a disease gene and integrated its roles by showing bi-allelic loss-of-function causes syndromic intellectual disability through LBR anchoring and TMCO1-translocon-dependent translation.\",\n      \"evidence\": \"Patient fibroblasts (LBR localization, ER markers), neutrophil morphology, in silico structural modeling, and in vitro protein degradation assays across 23 individuals from 15 families\",\n      \"pmids\": [\"36044892\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Translocon contribution inferred from modeling rather than direct biochemical reconstitution\", \"Mechanism connecting molecular defects to neurodevelopmental phenotype not established\", \"Substrate specificity of TMEM147 in the translocon not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended the DHCR7 axis to disease physiology by showing TMEM147 promotes DHCR7 via STAT2 and drives a 27-hydroxycholesterol-dependent program affecting ferroptosis resistance and macrophage polarization in hepatocellular carcinoma.\",\n      \"evidence\": \"Co-IP/MS, RNA-seq, lipidomics, ELISA, ferroptosis and macrophage phenotyping assays, in vitro and in vivo tumor models\",\n      \"pmids\": [\"37891677\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Multi-step mechanistic chain has indirect links (STAT2, 27HC, GPX4, PPARgamma)\", \"Single-lab findings in a cancer context\", \"Direct versus indirect control of DHCR7 transcription versus stability not disentangled\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TMEM147 mechanistically couples its translocon role to substrate-specific biogenesis of multipass membrane proteins, and how this connects to the neurodevelopmental phenotype, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No reconstituted structure of TMEM147 within the TMCO1 translocon\", \"No defined substrate set whose biogenesis depends on TMEM147\", \"Causal path from molecular defects to intellectual disability not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"complexes\": [\"Nicalin-NOMO complex\", \"TMCO1 ribosome-associated translocon\"],\n    \"partners\": [\"NCLN\", \"NOMO1\", \"LBR\", \"DHCR7\", \"TMCO1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}