{"gene":"TMEM126A","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2009,"finding":"TMEM126A encodes a transmembrane mitochondrial protein; mutations in TMEM126A cause autosomal-recessive nonsyndromic optic atrophy, establishing mitochondrial dysfunction as a pathogenic mechanism.","method":"Whole-genome homozygosity mapping, positional cloning, sequence analysis","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mapping and sequencing established disease gene identity; mitochondrial localization inferred but not yet directly experimentally validated in this paper","pmids":["19327736"],"is_preprint":false},{"year":2013,"finding":"TMEM126A protein localizes to the inner mitochondrial membrane (cristae compartment), its mRNA is enriched near mitochondria (mitochondria-localized mRNA), and the second transmembrane domain is required for mitochondrial localization.","method":"Cellular fractionation, mitochondrial sub-compartmentalization proteolysis assays, transmission electron microscopy, immunofluorescence confocal microscopy of truncated constructs, quantitative fluorescent in situ hybridization","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (fractionation, proteolysis protection assay, EM, confocal imaging of deletion constructs) in a single focused study establishing localization and domain requirement","pmids":["23500070"],"is_preprint":false},{"year":2021,"finding":"TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I; loss of TMEM126A causes isolated complex I deficiency, and TMEM126A associates with the newly synthesized mtDNA-encoded ND4 subunit during pulse-labeling, indicating a role in ND4 distal membrane module assembly. This function is distinct from its paralog TMEM126B, which acts in ND2-module assembly.","method":"Genome editing (knockout), co-immunoprecipitation/interaction studies, quantitative proteomics, pulse-labeling interaction studies","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interaction studies, pulse-labeling, quantitative proteomics, and genetic knockout with defined biochemical phenotype, replicated independently by a second lab (PMID:33882309)","pmids":["33879611"],"is_preprint":false},{"year":2021,"finding":"In the absence of NDUFS3, a small amount of functional complex I persists and the ND4 module remains stable and bound to TMEM126A, revealing TMEM126A as an assembly factor for the ND4-module intermediate of mitochondrial complex I.","method":"NDUFS3 ablation/depletion in mammalian cells, native PAGE, mass spectrometry, co-immunoprecipitation","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — independent replication of ND4-module assembly factor role using orthogonal genetic perturbation (NDUFS3 depletion) and biochemical fractionation; consistent with PMID:33879611","pmids":["33882309"],"is_preprint":false},{"year":2024,"finding":"TMEM126A physically interacts with the mitochondrial inner membrane insertase OXA1L, associates with mitochondrial ribosomes and translation products, and cooperates with OXA1L in co-translational insertion of mitochondria-encoded proteins into the inner membrane. Loss of TMEM126A destabilizes mitochondrial translation products, triggering their degradation by the iAAA protease; cargo-blocked OXA1L complexes are also cleared proteolytically by iAAA in the absence of TMEM126A.","method":"Co-immunoprecipitation/interaction proteomics, ribosome association assays, loss-of-function analysis, iAAA protease functional assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (interaction proteomics, ribosome association, protease dependency assays) in a single focused mechanistic study","pmids":["38199007"],"is_preprint":false},{"year":2018,"finding":"Loss of TMEM126A in breast cancer cells induces mitochondrial dysfunction, ROS production, and mitochondrial membrane potential depolarization, which in turn activates ECM remodeling and EMT via mitochondrial retrograde signaling; ROS scavengers reverse these effects, placing ROS downstream of TMEM126A loss.","method":"siRNA knockdown, overexpression, in vitro and in vivo metastasis assays, ROS measurement, mitochondrial membrane potential assay, RNA-sequencing, ROS scavenger rescue experiments","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — knockdown/OE with defined phenotypic readouts and pathway rescue, but no direct biochemical interaction or reconstitution; single lab","pmids":["30393159"],"is_preprint":false},{"year":2012,"finding":"TMEM126A physically associates and co-localizes with CD137L (4-1BBL) in macrophages (identified by yeast two-hybrid); knockdown of TMEM126A abolishes CD137L-induced tyrosine phosphorylation, upregulation of M-CSF, IL-1β, and TN-C, and CD137L-induced cell adherence, indicating TMEM126A couples CD137L reverse signaling in myeloid cells.","method":"Yeast two-hybrid, co-localization, siRNA knockdown, stable shRNA knockdown, tyrosine phosphorylation assay, cytokine expression analysis","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid plus co-localization plus functional knockdown, but no reciprocal Co-IP or in vitro binding reconstitution; single lab","pmids":["22885069"],"is_preprint":false},{"year":2014,"finding":"TMEM126A couples TLR4 signaling in macrophages; TMEM126A-deficient macrophages show diminished upregulation of CD54, MHC II, CD86, and CD40 in response to TLR4 activation, and abolished LPS/TLR4-induced late-phase JNK/SAPK and IRF-3 phosphorylation.","method":"TMEM126A-deficient RAW264.7 cells, LPS stimulation, flow cytometry, phosphorylation assays","journal":"Molecular immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, loss-of-function with signaling readouts but no direct physical interaction demonstrated between TMEM126A and TLR4 components","pmids":["25549946"],"is_preprint":false},{"year":2024,"finding":"Integrative cross-linking mass spectrometry and coarse-grained molecular dynamics simulations, validated by super-resolution microscopy, localizes TMEM126A specifically to the cristae sub-compartment of the inner mitochondrial membrane.","method":"Cross-linking mass spectrometry (XL-MS), coarse-grained molecular dynamics simulation, super-resolution microscopy","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — super-resolution microscopy validates computational prediction; consistent with prior fractionation data (PMID:23500070); preprint, single lab","pmids":["bio_10.1101_2024.09.11.612425"],"is_preprint":true}],"current_model":"TMEM126A is an inner mitochondrial membrane (cristae) protein that functions as an assembly factor for the ND4-module of mitochondrial complex I by associating with the newly synthesized ND4 subunit during assembly; it also cooperates with the OXA1L insertase in co-translational insertion of mtDNA-encoded proteins, and its loss triggers iAAA protease-mediated quality control of both translation products and stalled OXA1L complexes, while disease-causing mutations disrupt complex I biogenesis leading to optic atrophy."},"narrative":{"mechanistic_narrative":"TMEM126A is an inner mitochondrial membrane protein localized to the cristae compartment that functions in the biogenesis of the oxidative phosphorylation machinery [PMID:23500070, PMID:33879611]. It acts as an assembly factor for the ND4 distal membrane module of mitochondrial complex I, associating with the newly synthesized mtDNA-encoded ND4 subunit during assembly and remaining bound to a stable ND4-module intermediate; this role is distinct from its paralog TMEM126B, which serves the ND2 module [PMID:33879611, PMID:33882309]. Mechanistically, TMEM126A cooperates with the inner-membrane insertase OXA1L and associates with mitochondrial ribosomes and nascent translation products to support co-translational insertion of mtDNA-encoded proteins; in its absence, translation products are destabilized and cleared by the iAAA protease, and cargo-blocked OXA1L complexes are likewise removed proteolytically [PMID:38199007]. Consistent with this biogenesis role, biallelic TMEM126A mutations cause autosomal-recessive nonsyndromic optic atrophy through mitochondrial dysfunction [PMID:19327736]. Loss of TMEM126A also produces isolated complex I deficiency [PMID:33879611].","teleology":[{"year":2009,"claim":"Established TMEM126A as a disease gene, linking it to mitochondrial dysfunction before any direct molecular role was known.","evidence":"whole-genome homozygosity mapping and positional cloning in optic atrophy families","pmids":["19327736"],"confidence":"Medium","gaps":["Mitochondrial localization inferred but not directly demonstrated","No molecular function assigned","Mechanism linking mutation to optic atrophy unresolved"]},{"year":2013,"claim":"Resolved where TMEM126A acts by placing it in the inner mitochondrial membrane cristae and showing a transmembrane domain dictates targeting.","evidence":"fractionation, proteolysis protection, EM, confocal imaging of deletion constructs, and mRNA FISH","pmids":["23500070"],"confidence":"High","gaps":["No molecular activity or interaction partners identified","Functional consequence of cristae localization not defined"]},{"year":2018,"claim":"Connected TMEM126A loss to downstream cellular phenotypes via ROS-driven mitochondrial retrograde signaling in cancer cells.","evidence":"siRNA/overexpression with ROS and membrane-potential assays, metastasis assays, and ROS-scavenger rescue in breast cancer cells","pmids":["30393159"],"confidence":"Medium","gaps":["No direct biochemical mechanism linking TMEM126A to ROS","Single lab without reconstitution","Relationship to complex I role not established at the time"]},{"year":2021,"claim":"Defined the core molecular function: TMEM126A is an assembly factor for the complex I ND4 distal membrane module that binds newly synthesized ND4.","evidence":"knockout, reciprocal interaction studies, pulse-labeling, and quantitative proteomics, independently corroborated by NDUFS3 ablation with native PAGE and MS","pmids":["33879611","33882309"],"confidence":"High","gaps":["Structural basis of ND4 recognition not resolved","How TMEM126A is released from the intermediate unknown"]},{"year":2024,"claim":"Extended the mechanism to co-translational membrane insertion, showing TMEM126A partners with OXA1L and the mitoribosome and links to iAAA protease quality control.","evidence":"interaction proteomics, ribosome association assays, and iAAA protease dependency assays in loss-of-function cells","pmids":["38199007"],"confidence":"High","gaps":["Direct structural arrangement with OXA1L not defined","How insertion role and ND4-module assembly role are coordinated unclear"]},{"year":2024,"claim":"Refined sub-organellar localization to the cristae using integrative structural and imaging approaches.","evidence":"cross-linking MS and coarse-grained MD validated by super-resolution microscopy (preprint)","pmids":["bio_10.1101_2024.09.11.612425"],"confidence":"Medium","gaps":["Preprint, single lab","Does not address functional consequences of cristae positioning"]},{"year":null,"claim":"How the disease-causing mutations mechanistically disrupt ND4-module assembly or OXA1L cooperation to produce optic atrophy remains unresolved.","evidence":"no timeline finding directly connects mutant protein behavior to the assembly/insertion mechanism","pmids":[],"confidence":"Medium","gaps":["Mutation effect on ND4 binding untested","Tissue selectivity for optic neurons unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,4]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[1,8]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4]}],"complexes":["mitochondrial complex I ND4 module"],"partners":["OXA1L","ND4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H061","full_name":"Transmembrane protein 126A","aliases":[],"length_aa":195,"mass_kda":21.5,"function":"Protein required for the cotranslational protein quality control in the inner membrane of the mitochondria (PubMed:38199007). Associates with newly synthesized polypeptides and may act as a chaperone that cooperates with OXA1L for the insertion of newly synthesized mitochondrial proteins into the inner membrane (PubMed:38199007). Required for the assembly of the ND4 module of mitochondrial complex I (PubMed:33879611, PubMed:33882309)","subcellular_location":"Mitochondrion inner membrane","url":"https://www.uniprot.org/uniprotkb/Q9H061/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM126A","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TMEM126A","total_profiled":1310},"omim":[{"mim_id":"612989","title":"OPTIC ATROPHY 7 WITH OR WITHOUT AUDITORY NEUROPATHY; OPA7","url":"https://www.omim.org/entry/612989"},{"mim_id":"612988","title":"TRANSMEMBRANE PROTEIN 126A; TMEM126A","url":"https://www.omim.org/entry/612988"},{"mim_id":"165500","title":"OPTIC ATROPHY 1; OPA1","url":"https://www.omim.org/entry/165500"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMEM126A"},"hgnc":{"alias_symbol":["DKFZp586C1924","OPA7"],"prev_symbol":[]},"alphafold":{"accession":"Q9H061","domains":[{"cath_id":"-","chopping":"35-187","consensus_level":"medium","plddt":93.5639,"start":35,"end":187}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H061","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H061-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H061-F1-predicted_aligned_error_v6.png","plddt_mean":90.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM126A","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM126A"},"sequence":{"accession":"Q9H061","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H061.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H061/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H061"}},"corpus_meta":[{"pmid":"19327736","id":"PMC_19327736","title":"TMEM126A, encoding a mitochondrial protein, is mutated in autosomal-recessive nonsyndromic optic atrophy.","date":"2009","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19327736","citation_count":76,"is_preprint":false},{"pmid":"20405026","id":"PMC_20405026","title":"Nonsense mutation in TMEM126A causing autosomal recessive optic atrophy and auditory neuropathy.","date":"2010","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/20405026","citation_count":39,"is_preprint":false},{"pmid":"30393159","id":"PMC_30393159","title":"Loss of TMEM126A promotes extracellular matrix remodeling, epithelial-to-mesenchymal transition, and breast cancer metastasis by regulating mitochondrial retrograde signaling.","date":"2018","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/30393159","citation_count":29,"is_preprint":false},{"pmid":"33882309","id":"PMC_33882309","title":"NDUFS3 depletion permits complex I maturation and reveals TMEM126A/OPA7 as an assembly factor binding the ND4-module intermediate.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33882309","citation_count":24,"is_preprint":false},{"pmid":"38199007","id":"PMC_38199007","title":"Identification of TMEM126A as OXA1L-interacting protein reveals cotranslational quality control in mitochondria.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38199007","citation_count":21,"is_preprint":false},{"pmid":"23500070","id":"PMC_23500070","title":"TMEM126A is a mitochondrial located mRNA (MLR) protein of the mitochondrial inner membrane.","date":"2013","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/23500070","citation_count":21,"is_preprint":false},{"pmid":"33879611","id":"PMC_33879611","title":"Optic atrophy-associated TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/33879611","citation_count":21,"is_preprint":false},{"pmid":"22815638","id":"PMC_22815638","title":"TMEM126A mutation in a Moroccan family with autosomal recessive optic atrophy.","date":"2012","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/22815638","citation_count":18,"is_preprint":false},{"pmid":"22885069","id":"PMC_22885069","title":"Novel transmembrane protein 126A (TMEM126A) couples with CD137L reverse signals in myeloid cells.","date":"2012","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/22885069","citation_count":11,"is_preprint":false},{"pmid":"25549946","id":"PMC_25549946","title":"TMEM126A, a CD137 ligand binding protein, couples with the TLR4 signal transduction pathway in macrophages.","date":"2014","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25549946","citation_count":10,"is_preprint":false},{"pmid":"30961538","id":"PMC_30961538","title":"Novel likely pathogenic variants in TMEM126A identified in non-syndromic autosomal recessive optic atrophy: two case reports.","date":"2019","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30961538","citation_count":10,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.17.676758","title":"Proteomic and Kinetic Characterization of Prion Seeding in Distinct Human CJD Strains Unveils Early Diagnostic Biomarkers","date":"2025-09-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.17.676758","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.11.612425","title":"Integrative Molecular Dynamics Simulations Untangle Cross-Linking Data to Unveil Mitochondrial Protein Distributions","date":"2024-09-13","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.11.612425","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8452,"output_tokens":2294,"usd":0.029883,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9413,"output_tokens":2102,"usd":0.049807,"stage2_stop_reason":"end_turn"},"total_usd":0.07969,"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\": 2009,\n      \"finding\": \"TMEM126A encodes a transmembrane mitochondrial protein; mutations in TMEM126A cause autosomal-recessive nonsyndromic optic atrophy, establishing mitochondrial dysfunction as a pathogenic mechanism.\",\n      \"method\": \"Whole-genome homozygosity mapping, positional cloning, sequence analysis\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mapping and sequencing established disease gene identity; mitochondrial localization inferred but not yet directly experimentally validated in this paper\",\n      \"pmids\": [\"19327736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"TMEM126A protein localizes to the inner mitochondrial membrane (cristae compartment), its mRNA is enriched near mitochondria (mitochondria-localized mRNA), and the second transmembrane domain is required for mitochondrial localization.\",\n      \"method\": \"Cellular fractionation, mitochondrial sub-compartmentalization proteolysis assays, transmission electron microscopy, immunofluorescence confocal microscopy of truncated constructs, quantitative fluorescent in situ hybridization\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (fractionation, proteolysis protection assay, EM, confocal imaging of deletion constructs) in a single focused study establishing localization and domain requirement\",\n      \"pmids\": [\"23500070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I; loss of TMEM126A causes isolated complex I deficiency, and TMEM126A associates with the newly synthesized mtDNA-encoded ND4 subunit during pulse-labeling, indicating a role in ND4 distal membrane module assembly. This function is distinct from its paralog TMEM126B, which acts in ND2-module assembly.\",\n      \"method\": \"Genome editing (knockout), co-immunoprecipitation/interaction studies, quantitative proteomics, pulse-labeling interaction studies\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interaction studies, pulse-labeling, quantitative proteomics, and genetic knockout with defined biochemical phenotype, replicated independently by a second lab (PMID:33882309)\",\n      \"pmids\": [\"33879611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In the absence of NDUFS3, a small amount of functional complex I persists and the ND4 module remains stable and bound to TMEM126A, revealing TMEM126A as an assembly factor for the ND4-module intermediate of mitochondrial complex I.\",\n      \"method\": \"NDUFS3 ablation/depletion in mammalian cells, native PAGE, mass spectrometry, co-immunoprecipitation\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — independent replication of ND4-module assembly factor role using orthogonal genetic perturbation (NDUFS3 depletion) and biochemical fractionation; consistent with PMID:33879611\",\n      \"pmids\": [\"33882309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TMEM126A physically interacts with the mitochondrial inner membrane insertase OXA1L, associates with mitochondrial ribosomes and translation products, and cooperates with OXA1L in co-translational insertion of mitochondria-encoded proteins into the inner membrane. Loss of TMEM126A destabilizes mitochondrial translation products, triggering their degradation by the iAAA protease; cargo-blocked OXA1L complexes are also cleared proteolytically by iAAA in the absence of TMEM126A.\",\n      \"method\": \"Co-immunoprecipitation/interaction proteomics, ribosome association assays, loss-of-function analysis, iAAA protease functional assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (interaction proteomics, ribosome association, protease dependency assays) in a single focused mechanistic study\",\n      \"pmids\": [\"38199007\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Loss of TMEM126A in breast cancer cells induces mitochondrial dysfunction, ROS production, and mitochondrial membrane potential depolarization, which in turn activates ECM remodeling and EMT via mitochondrial retrograde signaling; ROS scavengers reverse these effects, placing ROS downstream of TMEM126A loss.\",\n      \"method\": \"siRNA knockdown, overexpression, in vitro and in vivo metastasis assays, ROS measurement, mitochondrial membrane potential assay, RNA-sequencing, ROS scavenger rescue experiments\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — knockdown/OE with defined phenotypic readouts and pathway rescue, but no direct biochemical interaction or reconstitution; single lab\",\n      \"pmids\": [\"30393159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TMEM126A physically associates and co-localizes with CD137L (4-1BBL) in macrophages (identified by yeast two-hybrid); knockdown of TMEM126A abolishes CD137L-induced tyrosine phosphorylation, upregulation of M-CSF, IL-1β, and TN-C, and CD137L-induced cell adherence, indicating TMEM126A couples CD137L reverse signaling in myeloid cells.\",\n      \"method\": \"Yeast two-hybrid, co-localization, siRNA knockdown, stable shRNA knockdown, tyrosine phosphorylation assay, cytokine expression analysis\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid plus co-localization plus functional knockdown, but no reciprocal Co-IP or in vitro binding reconstitution; single lab\",\n      \"pmids\": [\"22885069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TMEM126A couples TLR4 signaling in macrophages; TMEM126A-deficient macrophages show diminished upregulation of CD54, MHC II, CD86, and CD40 in response to TLR4 activation, and abolished LPS/TLR4-induced late-phase JNK/SAPK and IRF-3 phosphorylation.\",\n      \"method\": \"TMEM126A-deficient RAW264.7 cells, LPS stimulation, flow cytometry, phosphorylation assays\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, loss-of-function with signaling readouts but no direct physical interaction demonstrated between TMEM126A and TLR4 components\",\n      \"pmids\": [\"25549946\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Integrative cross-linking mass spectrometry and coarse-grained molecular dynamics simulations, validated by super-resolution microscopy, localizes TMEM126A specifically to the cristae sub-compartment of the inner mitochondrial membrane.\",\n      \"method\": \"Cross-linking mass spectrometry (XL-MS), coarse-grained molecular dynamics simulation, super-resolution microscopy\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — super-resolution microscopy validates computational prediction; consistent with prior fractionation data (PMID:23500070); preprint, single lab\",\n      \"pmids\": [\"bio_10.1101_2024.09.11.612425\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TMEM126A is an inner mitochondrial membrane (cristae) protein that functions as an assembly factor for the ND4-module of mitochondrial complex I by associating with the newly synthesized ND4 subunit during assembly; it also cooperates with the OXA1L insertase in co-translational insertion of mtDNA-encoded proteins, and its loss triggers iAAA protease-mediated quality control of both translation products and stalled OXA1L complexes, while disease-causing mutations disrupt complex I biogenesis leading to optic atrophy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMEM126A is an inner mitochondrial membrane protein localized to the cristae compartment that functions in the biogenesis of the oxidative phosphorylation machinery [#1, #2]. It acts as an assembly factor for the ND4 distal membrane module of mitochondrial complex I, associating with the newly synthesized mtDNA-encoded ND4 subunit during assembly and remaining bound to a stable ND4-module intermediate; this role is distinct from its paralog TMEM126B, which serves the ND2 module [#2, #3]. Mechanistically, TMEM126A cooperates with the inner-membrane insertase OXA1L and associates with mitochondrial ribosomes and nascent translation products to support co-translational insertion of mtDNA-encoded proteins; in its absence, translation products are destabilized and cleared by the iAAA protease, and cargo-blocked OXA1L complexes are likewise removed proteolytically [#4]. Consistent with this biogenesis role, biallelic TMEM126A mutations cause autosomal-recessive nonsyndromic optic atrophy through mitochondrial dysfunction [#0]. Loss of TMEM126A also produces isolated complex I deficiency [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established TMEM126A as a disease gene, linking it to mitochondrial dysfunction before any direct molecular role was known.\",\n      \"evidence\": \"whole-genome homozygosity mapping and positional cloning in optic atrophy families\",\n      \"pmids\": [\"19327736\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mitochondrial localization inferred but not directly demonstrated\", \"No molecular function assigned\", \"Mechanism linking mutation to optic atrophy unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved where TMEM126A acts by placing it in the inner mitochondrial membrane cristae and showing a transmembrane domain dictates targeting.\",\n      \"evidence\": \"fractionation, proteolysis protection, EM, confocal imaging of deletion constructs, and mRNA FISH\",\n      \"pmids\": [\"23500070\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No molecular activity or interaction partners identified\", \"Functional consequence of cristae localization not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connected TMEM126A loss to downstream cellular phenotypes via ROS-driven mitochondrial retrograde signaling in cancer cells.\",\n      \"evidence\": \"siRNA/overexpression with ROS and membrane-potential assays, metastasis assays, and ROS-scavenger rescue in breast cancer cells\",\n      \"pmids\": [\"30393159\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical mechanism linking TMEM126A to ROS\", \"Single lab without reconstitution\", \"Relationship to complex I role not established at the time\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the core molecular function: TMEM126A is an assembly factor for the complex I ND4 distal membrane module that binds newly synthesized ND4.\",\n      \"evidence\": \"knockout, reciprocal interaction studies, pulse-labeling, and quantitative proteomics, independently corroborated by NDUFS3 ablation with native PAGE and MS\",\n      \"pmids\": [\"33879611\", \"33882309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ND4 recognition not resolved\", \"How TMEM126A is released from the intermediate unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the mechanism to co-translational membrane insertion, showing TMEM126A partners with OXA1L and the mitoribosome and links to iAAA protease quality control.\",\n      \"evidence\": \"interaction proteomics, ribosome association assays, and iAAA protease dependency assays in loss-of-function cells\",\n      \"pmids\": [\"38199007\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct structural arrangement with OXA1L not defined\", \"How insertion role and ND4-module assembly role are coordinated unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Refined sub-organellar localization to the cristae using integrative structural and imaging approaches.\",\n      \"evidence\": \"cross-linking MS and coarse-grained MD validated by super-resolution microscopy (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.09.11.612425\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab\", \"Does not address functional consequences of cristae positioning\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the disease-causing mutations mechanistically disrupt ND4-module assembly or OXA1L cooperation to produce optic atrophy remains unresolved.\",\n      \"evidence\": \"no timeline finding directly connects mutant protein behavior to the assembly/insertion mechanism\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mutation effect on ND4 binding untested\", \"Tissue selectivity for optic neurons unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005743\", \"supporting_discovery_ids\": [1, 8]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [1, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\"mitochondrial complex I ND4 module\"],\n    \"partners\": [\"OXA1L\", \"ND4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}