{"gene":"NFXL1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2026,"finding":"NFXL1 is an ER-localized E3 ubiquitin ligase that mediates ubiquitylation of MHC-I, facilitating its capture by the TEX264-NBR1 autophagic complex and subsequent lysosomal degradation in pancreatic ductal adenocarcinoma cells.","method":"Genome-wide CRISPRi screen, ER exit synchronization assay, co-immunoprecipitation of MHC-I with TEX264-NBR1 complex, functional knockdown with MHC-I surface/total level readout","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide CRISPRi screen identifying NFXL1, functional rescue experiments, mechanistic pathway placement (ubiquitylation → autophagic capture), replicated across preprint (PMID:39554122) and peer-reviewed publication (PMID:42214332)","pmids":["42214332","39554122"],"is_preprint":false},{"year":2026,"finding":"NFXL1 is localized to the endoplasmic reticulum, where it physically associates with MHC-I; elevated NFXL1 correlates with reduced MHC-I protein expression at the plasma membrane in PDAC cells.","method":"CRISPRi knockdown with subcellular fractionation/ER exit assays and surface MHC-I quantification; binding assays between NFXL1 and MHC-I","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — ER localization and functional MHC-I interaction established by orthogonal methods (CRISPRi screen, ER exit assay, binding assay) replicated in two publications from the same group","pmids":["42214332","39554122"],"is_preprint":false},{"year":2010,"finding":"NFX1-like proteins (including NFXL1) contain a specific RING finger motif with a C4HC3 zinc ligand signature, suggesting they function as E3 ubiquitin ligases; NFX1-type zinc finger domains have been shown to mediate DNA binding.","method":"Manual sequence analysis, hidden Markov models, phylogenetic analysis","journal":"Plant biology (Stuttgart, Germany)","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/bioinformatic prediction only, no experimental validation of E3 ligase activity reported in this abstract","pmids":["20522174"],"is_preprint":false},{"year":2016,"finding":"NFXL1 protein shows cytoplasmic (not nuclear) localization in HEK and SH-SY5Y cells under standard conditions, suggesting nuclear translocation may require specific conditions for any transcriptional regulatory function.","method":"Immunofluorescence subcellular localization in HEK cells and SH-SY5Y cells","journal":"Journal of neurodevelopmental disorders","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single method (immunofluorescence), no functional consequence directly demonstrated","pmids":["27053962"],"is_preprint":false},{"year":2020,"finding":"TaNFXL1 (wheat ortholog of NFXL1) represses Fusarium graminearum resistance; virus-induced gene silencing and CRISPR-mediated knockout of TaNFXL1 both increased resistance to F. graminearum, and TaNFXL1 expression is induced by the mycotoxin deoxynivalenol (DON).","method":"Virus-induced gene silencing (VIGS), CRISPR/Cas9 genome editing, direct DON treatment with gene expression assays","journal":"Molecular plant-microbe interactions : MPMI","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal loss-of-function approaches (VIGS and CRISPR) with defined disease resistance phenotype; findings are in wheat ortholog, not human NFXL1","pmids":["31790345"],"is_preprint":false},{"year":2017,"finding":"Nfxl1 expression is down-regulated in Tbx6-deficient mice, indicating that Tbx6 transcription factor positively regulates Nfxl1 expression, potentially via LTR sequences of endogenous retroviruses containing Tbx6 binding motifs.","method":"Gene expression comparison between Tbx6+/- control and Tbx6-/- mice","journal":"Frontiers in chemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single gene expression comparison in knockout mice; no direct mechanistic experiment on NFXL1 protein function","pmids":["28664156"],"is_preprint":false}],"current_model":"NFXL1 is an ER-localized E3 ubiquitin ligase that ubiquitylates MHC-I, promoting its capture by the TEX264-NBR1 autophagic complex and subsequent lysosomal degradation in pancreatic cancer cells, thereby suppressing antigen presentation and immune surveillance; under basal conditions in non-cancer cells the protein shows cytoplasmic localization, and its RING finger domain structure is consistent with E3 ligase activity."},"narrative":{"mechanistic_narrative":"NFXL1 is an endoplasmic reticulum-localized E3 ubiquitin ligase that restrains antigen presentation by targeting MHC-I for degradation in pancreatic ductal adenocarcinoma cells [PMID:42214332, PMID:39554122]. It physically associates with MHC-I at the ER and ubiquitylates it, channeling MHC-I into the TEX264-NBR1 autophagic complex for capture and subsequent lysosomal degradation; elevated NFXL1 correlates with reduced surface MHC-I, linking its activity to suppression of immune surveillance [PMID:42214332, PMID:39554122]. Under basal conditions in non-cancer cell lines NFXL1 shows cytoplasmic rather than nuclear localization [PMID:27053962]. Beyond these findings, the regulation and broader substrate range of human NFXL1 have not been characterized in the available corpus.","teleology":[{"year":2010,"claim":"Before any functional data, sequence analysis raised the question of what enzymatic activity NFX1-like proteins possess, predicting an E3 ubiquitin ligase role from a conserved RING motif.","evidence":"Manual sequence analysis, hidden Markov models, and phylogenetic analysis identifying a C4HC3 RING finger signature","pmids":["20522174"],"confidence":"Low","gaps":["No experimental validation of E3 ligase activity","No substrate identified","Prediction based on domain inference only"]},{"year":2016,"claim":"To address where NFXL1 acts, subcellular localization was tested, establishing a cytoplasmic distribution under standard conditions rather than constitutive nuclear residence.","evidence":"Immunofluorescence in HEK and SH-SY5Y cells","pmids":["27053962"],"confidence":"Medium","gaps":["Single method, single lab","No functional consequence demonstrated","Conditions driving any relocalization not defined"]},{"year":2017,"claim":"An upstream regulatory question was partially addressed by showing Tbx6 positively regulates Nfxl1 expression in mice.","evidence":"Gene expression comparison between Tbx6+/- and Tbx6-/- mice","pmids":["28664156"],"confidence":"Low","gaps":["Correlative expression change only","No direct evidence Tbx6 binds the Nfxl1 locus","No protein-level mechanism for NFXL1"]},{"year":2020,"claim":"Loss-of-function work on the wheat ortholog established a negative-regulatory role in pathogen defense, the first phenotypic evidence for an NFXL1-family gene.","evidence":"VIGS and CRISPR/Cas9 knockout of TaNFXL1 with Fusarium graminearum resistance and DON-induction assays","pmids":["31790345"],"confidence":"Medium","gaps":["Findings in wheat ortholog, not human NFXL1","Molecular mechanism of repression unresolved","No biochemical link to ubiquitylation"]},{"year":2026,"claim":"The central mechanistic question — what NFXL1 does at the protein level — was answered by placing it as an ER E3 ligase that ubiquitylates MHC-I and routes it through autophagic-lysosomal degradation, defining its role in immune evasion.","evidence":"Genome-wide CRISPRi screen, ER exit synchronization assays, co-immunoprecipitation of MHC-I with TEX264-NBR1, and functional knockdown with surface/total MHC-I readouts in PDAC cells","pmids":["42214332","39554122"],"confidence":"High","gaps":["Direct demonstration of NFXL1 catalytic transfer of ubiquitin to MHC-I not isolated from the pathway readout","Ubiquitin chain type and acceptor sites on MHC-I undefined","Whether the ER E3 role generalizes beyond PDAC unknown"]},{"year":null,"claim":"Whether the predicted RING-dependent catalytic activity directly drives MHC-I ubiquitylation, and what additional substrates NFXL1 acts on, remain open.","evidence":"","pmids":[],"confidence":"High","gaps":["No in vitro reconstitution of NFXL1 E3 activity","Substrate repertoire beyond MHC-I unknown","Regulation of NFXL1 in normal physiology uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0]}],"complexes":[],"partners":["MHC-I","TEX264","NBR1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6ZNB6","full_name":"NF-X1-type zinc finger protein NFXL1","aliases":["Ovarian zinc finger protein","hOZFP"],"length_aa":911,"mass_kda":101.3,"function":"","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/Q6ZNB6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NFXL1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CANX","stoichiometry":0.2},{"gene":"DDOST","stoichiometry":0.2},{"gene":"OST4","stoichiometry":0.2},{"gene":"RPN1","stoichiometry":0.2},{"gene":"RPN2","stoichiometry":0.2},{"gene":"CCDC47","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NFXL1","total_profiled":1310},"omim":[{"mim_id":"620488","title":"NUCLEAR TRANSCRIPTION FACTOR, X BOX-BINDING-LIKE 1; NFXL1","url":"https://www.omim.org/entry/620488"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NFXL1"},"hgnc":{"alias_symbol":["HOZFP"],"prev_symbol":[]},"alphafold":{"accession":"Q6ZNB6","domains":[{"cath_id":"3.30.40.10","chopping":"131-310","consensus_level":"high","plddt":83.4113,"start":131,"end":310},{"cath_id":"-","chopping":"733-779","consensus_level":"medium","plddt":76.3883,"start":733,"end":779},{"cath_id":"-","chopping":"795-832","consensus_level":"medium","plddt":71.5276,"start":795,"end":832}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZNB6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZNB6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZNB6-F1-predicted_aligned_error_v6.png","plddt_mean":73.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NFXL1","jax_strain_url":"https://www.jax.org/strain/search?query=NFXL1"},"sequence":{"accession":"Q6ZNB6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6ZNB6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6ZNB6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZNB6"}},"corpus_meta":[{"pmid":"26410298","id":"PMC_26410298","title":"Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.","date":"2015","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/26410298","citation_count":119,"is_preprint":false},{"pmid":"28700604","id":"PMC_28700604","title":"Molecular characterization of the acquisition of longevity during seed maturation in soybean.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28700604","citation_count":53,"is_preprint":false},{"pmid":"31790345","id":"PMC_31790345","title":"Genome Editing of a Deoxynivalenol-Induced Transcription Factor Confers Resistance to Fusarium graminearum in Wheat.","date":"2020","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/31790345","citation_count":52,"is_preprint":false},{"pmid":"25781923","id":"PMC_25781923","title":"Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.","date":"2015","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25781923","citation_count":41,"is_preprint":false},{"pmid":"20522174","id":"PMC_20522174","title":"Structure and putative function of NFX1-like proteins in plants.","date":"2010","source":"Plant biology (Stuttgart, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/20522174","citation_count":20,"is_preprint":false},{"pmid":"27053962","id":"PMC_27053962","title":"An investigation of NFXL1, a gene implicated in a study of specific language impairment.","date":"2016","source":"Journal of neurodevelopmental disorders","url":"https://pubmed.ncbi.nlm.nih.gov/27053962","citation_count":8,"is_preprint":false},{"pmid":"34540591","id":"PMC_34540591","title":"Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment.","date":"2021","source":"Meta gene","url":"https://pubmed.ncbi.nlm.nih.gov/34540591","citation_count":8,"is_preprint":false},{"pmid":"39554122","id":"PMC_39554122","title":"A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39554122","citation_count":4,"is_preprint":false},{"pmid":"40132314","id":"PMC_40132314","title":"Exploring the functional variations of key candidate genes affecting egg production by hypothalamic-pituitary-ovarian axis in chickens.","date":"2025","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/40132314","citation_count":4,"is_preprint":false},{"pmid":"40430072","id":"PMC_40430072","title":"Rare Homozygous Variants in INSR and NFXL1 Are Associated with Severe Treatment-Resistant Psychosis.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40430072","citation_count":1,"is_preprint":false},{"pmid":"38003772","id":"PMC_38003772","title":"Expression of Genes Involved in Anthracnose Resistance in Chili (Capsicum baccatum) 'PBC80'-Derived Recombinant Inbred Lines.","date":"2023","source":"Pathogens (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/38003772","citation_count":1,"is_preprint":false},{"pmid":"28664156","id":"PMC_28664156","title":"LTRs of Endogenous Retroviruses as a Source of Tbx6 Binding Sites.","date":"2017","source":"Frontiers in chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28664156","citation_count":1,"is_preprint":false},{"pmid":"39334596","id":"PMC_39334596","title":"Genome-Wide Mapping of Consanguineous Families Confirms Previously Implicated Gene Loci and Suggests New Loci in Specific Language Impairment (SLI).","date":"2024","source":"Children (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/39334596","citation_count":1,"is_preprint":false},{"pmid":"42214332","id":"PMC_42214332","title":"A multi-subunit autophagic capture complex facilitates degradation of ER-stalled MHC class I in pancreatic cancer.","date":"2026","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/42214332","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8628,"output_tokens":1510,"usd":0.024267,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8193,"output_tokens":1947,"usd":0.04482,"stage2_stop_reason":"end_turn"},"total_usd":0.069087,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2026,\n      \"finding\": \"NFXL1 is an ER-localized E3 ubiquitin ligase that mediates ubiquitylation of MHC-I, facilitating its capture by the TEX264-NBR1 autophagic complex and subsequent lysosomal degradation in pancreatic ductal adenocarcinoma cells.\",\n      \"method\": \"Genome-wide CRISPRi screen, ER exit synchronization assay, co-immunoprecipitation of MHC-I with TEX264-NBR1 complex, functional knockdown with MHC-I surface/total level readout\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide CRISPRi screen identifying NFXL1, functional rescue experiments, mechanistic pathway placement (ubiquitylation → autophagic capture), replicated across preprint (PMID:39554122) and peer-reviewed publication (PMID:42214332)\",\n      \"pmids\": [\"42214332\", \"39554122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NFXL1 is localized to the endoplasmic reticulum, where it physically associates with MHC-I; elevated NFXL1 correlates with reduced MHC-I protein expression at the plasma membrane in PDAC cells.\",\n      \"method\": \"CRISPRi knockdown with subcellular fractionation/ER exit assays and surface MHC-I quantification; binding assays between NFXL1 and MHC-I\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ER localization and functional MHC-I interaction established by orthogonal methods (CRISPRi screen, ER exit assay, binding assay) replicated in two publications from the same group\",\n      \"pmids\": [\"42214332\", \"39554122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NFX1-like proteins (including NFXL1) contain a specific RING finger motif with a C4HC3 zinc ligand signature, suggesting they function as E3 ubiquitin ligases; NFX1-type zinc finger domains have been shown to mediate DNA binding.\",\n      \"method\": \"Manual sequence analysis, hidden Markov models, phylogenetic analysis\",\n      \"journal\": \"Plant biology (Stuttgart, Germany)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/bioinformatic prediction only, no experimental validation of E3 ligase activity reported in this abstract\",\n      \"pmids\": [\"20522174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NFXL1 protein shows cytoplasmic (not nuclear) localization in HEK and SH-SY5Y cells under standard conditions, suggesting nuclear translocation may require specific conditions for any transcriptional regulatory function.\",\n      \"method\": \"Immunofluorescence subcellular localization in HEK cells and SH-SY5Y cells\",\n      \"journal\": \"Journal of neurodevelopmental disorders\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (immunofluorescence), no functional consequence directly demonstrated\",\n      \"pmids\": [\"27053962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TaNFXL1 (wheat ortholog of NFXL1) represses Fusarium graminearum resistance; virus-induced gene silencing and CRISPR-mediated knockout of TaNFXL1 both increased resistance to F. graminearum, and TaNFXL1 expression is induced by the mycotoxin deoxynivalenol (DON).\",\n      \"method\": \"Virus-induced gene silencing (VIGS), CRISPR/Cas9 genome editing, direct DON treatment with gene expression assays\",\n      \"journal\": \"Molecular plant-microbe interactions : MPMI\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal loss-of-function approaches (VIGS and CRISPR) with defined disease resistance phenotype; findings are in wheat ortholog, not human NFXL1\",\n      \"pmids\": [\"31790345\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Nfxl1 expression is down-regulated in Tbx6-deficient mice, indicating that Tbx6 transcription factor positively regulates Nfxl1 expression, potentially via LTR sequences of endogenous retroviruses containing Tbx6 binding motifs.\",\n      \"method\": \"Gene expression comparison between Tbx6+/- control and Tbx6-/- mice\",\n      \"journal\": \"Frontiers in chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single gene expression comparison in knockout mice; no direct mechanistic experiment on NFXL1 protein function\",\n      \"pmids\": [\"28664156\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NFXL1 is an ER-localized E3 ubiquitin ligase that ubiquitylates MHC-I, promoting its capture by the TEX264-NBR1 autophagic complex and subsequent lysosomal degradation in pancreatic cancer cells, thereby suppressing antigen presentation and immune surveillance; under basal conditions in non-cancer cells the protein shows cytoplasmic localization, and its RING finger domain structure is consistent with E3 ligase activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NFXL1 is an endoplasmic reticulum-localized E3 ubiquitin ligase that restrains antigen presentation by targeting MHC-I for degradation in pancreatic ductal adenocarcinoma cells [#0, #1]. It physically associates with MHC-I at the ER and ubiquitylates it, channeling MHC-I into the TEX264-NBR1 autophagic complex for capture and subsequent lysosomal degradation; elevated NFXL1 correlates with reduced surface MHC-I, linking its activity to suppression of immune surveillance [#0, #1]. Under basal conditions in non-cancer cell lines NFXL1 shows cytoplasmic rather than nuclear localization [#3]. Beyond these findings, the regulation and broader substrate range of human NFXL1 have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Before any functional data, sequence analysis raised the question of what enzymatic activity NFX1-like proteins possess, predicting an E3 ubiquitin ligase role from a conserved RING motif.\",\n      \"evidence\": \"Manual sequence analysis, hidden Markov models, and phylogenetic analysis identifying a C4HC3 RING finger signature\",\n      \"pmids\": [\"20522174\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No experimental validation of E3 ligase activity\", \"No substrate identified\", \"Prediction based on domain inference only\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"To address where NFXL1 acts, subcellular localization was tested, establishing a cytoplasmic distribution under standard conditions rather than constitutive nuclear residence.\",\n      \"evidence\": \"Immunofluorescence in HEK and SH-SY5Y cells\",\n      \"pmids\": [\"27053962\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single method, single lab\", \"No functional consequence demonstrated\", \"Conditions driving any relocalization not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"An upstream regulatory question was partially addressed by showing Tbx6 positively regulates Nfxl1 expression in mice.\",\n      \"evidence\": \"Gene expression comparison between Tbx6+/- and Tbx6-/- mice\",\n      \"pmids\": [\"28664156\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Correlative expression change only\", \"No direct evidence Tbx6 binds the Nfxl1 locus\", \"No protein-level mechanism for NFXL1\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Loss-of-function work on the wheat ortholog established a negative-regulatory role in pathogen defense, the first phenotypic evidence for an NFXL1-family gene.\",\n      \"evidence\": \"VIGS and CRISPR/Cas9 knockout of TaNFXL1 with Fusarium graminearum resistance and DON-induction assays\",\n      \"pmids\": [\"31790345\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Findings in wheat ortholog, not human NFXL1\", \"Molecular mechanism of repression unresolved\", \"No biochemical link to ubiquitylation\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The central mechanistic question — what NFXL1 does at the protein level — was answered by placing it as an ER E3 ligase that ubiquitylates MHC-I and routes it through autophagic-lysosomal degradation, defining its role in immune evasion.\",\n      \"evidence\": \"Genome-wide CRISPRi screen, ER exit synchronization assays, co-immunoprecipitation of MHC-I with TEX264-NBR1, and functional knockdown with surface/total MHC-I readouts in PDAC cells\",\n      \"pmids\": [\"42214332\", \"39554122\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct demonstration of NFXL1 catalytic transfer of ubiquitin to MHC-I not isolated from the pathway readout\", \"Ubiquitin chain type and acceptor sites on MHC-I undefined\", \"Whether the ER E3 role generalizes beyond PDAC unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the predicted RING-dependent catalytic activity directly drives MHC-I ubiquitylation, and what additional substrates NFXL1 acts on, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No in vitro reconstitution of NFXL1 E3 activity\", \"Substrate repertoire beyond MHC-I unknown\", \"Regulation of NFXL1 in normal physiology uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"MHC-I\", \"TEX264\", \"NBR1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":3,"faith_pct":100.0}}