{"gene":"RNF170","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2011,"finding":"RNF170 is an ER membrane-localized RING domain ubiquitin E3 ligase that associates with activated IP3 receptors and mediates their ubiquitination and proteasomal degradation. RNF170 depletion by RNAi inhibited stimulus-induced IP3 receptor ubiquitination and degradation; overexpression of catalytically inactive RNF170 suppressed IP3 receptor processing. A substantial fraction of RNF170 constitutively associates with the erlin1/2 (SPFH1/2) complex, which recruits RNF170 to activated IP3 receptors (erlin1/2 depletion inhibited RNF170 binding to IP3 receptors, but RNF170 depletion did not affect erlin1/2 binding).","method":"Co-immunoprecipitation, RNAi knockdown, catalytically inactive mutant overexpression, subcellular fractionation/localization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, RNAi loss-of-function, dominant-negative mutant, multiple orthogonal methods in a focused mechanistic study, replicated by subsequent papers","pmids":["21610068"],"is_preprint":false},{"year":2015,"finding":"The ADSA-causing point mutation R199C in RNF170 destabilizes the protein by enhancing autoubiquitination and proteasomal degradation; ionic interactions between charged residues in the transmembrane domains are required for RNF170 stability. CRISPR/Cas9 deletion of RNF170 demonstrated that it mediates addition of all ubiquitin conjugates on activated IP3 receptors (monoubiquitin, K48- and K63-linked chains). ADSA lymphoblasts show impaired IP3-induced Ca2+ mobilization without changes in IP3 receptor levels or IP3 production, indicating a functional defect at the IP3 receptor locus.","method":"Site-directed mutagenesis, CRISPR/Cas9 knockout, Ca2+ mobilization assays, Western blot in patient-derived lymphoblasts","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis combined with CRISPR/Cas9 deletion and functional Ca2+ assays, patient-derived cell validation, multiple orthogonal methods in one focused study","pmids":["25882839"],"is_preprint":false},{"year":2019,"finding":"RNF170 functions as an E3 ubiquitin ligase that binds TLR3 and mediates K48-linked polyubiquitination at lysine 766 in the TIR domain of TLR3, promoting its proteasomal degradation. Genetic ablation of RNF170 selectively augmented TLR3-triggered innate immune responses (IRF3 and NF-κB signaling) both in vitro and in vivo, without affecting other TLR pathways.","method":"Co-immunoprecipitation (TLR3-binding protein identification), ubiquitination assay (K48-linkage, K766 site), RNF170 knockout, in vitro and in vivo innate immune response assays","journal":"Cellular & molecular immunology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, site-specific ubiquitination mapping, genetic ablation with defined immune phenotype in vitro and in vivo, single lab with multiple orthogonal methods","pmids":["31076723"],"is_preprint":false},{"year":2019,"finding":"Bi-allelic loss-of-function mutations in RNF170 cause autosomal recessive hereditary spastic paraplegia (HSP) by disrupting IP3 receptor degradation via the ER-associated degradation pathway. Functional evaluation in patient fibroblasts, mutant SH-SY5Y cells, and gene knockdown in zebrafish confirmed loss-of-function consequences.","method":"Patient fibroblast functional assays, mutant cell line analysis, zebrafish gene knockdown","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple model systems (patient cells, neuronal cell line, zebrafish), single lab, disease-gene linkage with functional validation","pmids":["31636353"],"is_preprint":false},{"year":2015,"finding":"Rnf170 knockout mice develop age-dependent gait abnormalities and reduced proprioception/thermal nociception, with significantly elevated Itpr1 (IP3 receptor type 1) protein levels in cerebellum and spinal cord but not cerebral cortex, confirming that Rnf170 mediates IP3 receptor degradation in vivo in a tissue-specific manner.","method":"Rnf170 knockout mouse model, gait analysis, protein blot (Western blot) for Itpr1 levels across brain regions","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean knockout mouse with defined phenotypic and biochemical readout, single lab","pmids":["26433933"],"is_preprint":false},{"year":2024,"finding":"ERLIN1/2 scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170. A conserved luminal N-terminal region in both TMUB1 and RNF170 is required for their interaction with the SPFH domain of adjacent ERLIN subunits at distinct interfaces. Protein variants that preclude these ERLIN interactions have been linked to hereditary spastic paraplegia.","method":"Protein interaction studies (co-IP/pulldown), 3D structural modelling, deletion/variant mapping of interaction domain, omics-based phenotypic characterization of ERLIN-knockout HeLa cells","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — interaction domain mapping with structural modelling and functional variant data, single lab with multiple approaches","pmids":["38782601"],"is_preprint":false},{"year":2025,"finding":"RNF170 (together with RNF149) mediates K48-linked polyubiquitination of DEK at lysine K349 within the DEK coding region (residues 270–350), promoting DEK proteasomal degradation; this suppresses the RIPK1-PANoptosis pathway in bronchial epithelial cells.","method":"Mass spectrometry (identifying RNF170 as DEK-binding E3), molecular docking, ubiquitination assay (K48, site K349), functional PANoptosis pathway assays","journal":"Phytomedicine","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — MS identification, site-specific ubiquitination mapping, single lab, limited independent validation of RNF170-specific contribution separate from RNF149","pmids":["40120540"],"is_preprint":false},{"year":2022,"finding":"A novel homozygous stop-gain variant (p.R64*) in RNF170 leads to significantly reduced mRNA and protein levels, confirming loss-of-function as the mechanism in RNF170-associated HSP.","method":"RT-qPCR, Western blot in patient-derived cells","journal":"Clinical genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single patient, two methods (RT-qPCR and Western blot) confirming loss-of-function but no new mechanistic pathway information","pmids":["36046950"],"is_preprint":false}],"current_model":"RNF170 is an ER membrane-resident RING-finger E3 ubiquitin ligase that is recruited by the ERLIN1/2 scaffold complex to activated IP3 receptors, where it mediates their ubiquitination (monoubiquitin, K48- and K63-linked chains) and proteasomal degradation to regulate intracellular Ca2+ signaling; it also targets TLR3 (via K48-linked ubiquitination at K766) for proteasomal degradation to suppress innate immune responses, and has been identified as a regulator of DEK degradation, with loss-of-function or destabilizing mutations causing hereditary spastic paraplegia or sensory ataxia in humans and model organisms."},"narrative":{"mechanistic_narrative":"RNF170 is an endoplasmic reticulum membrane-resident RING-domain E3 ubiquitin ligase that controls protein turnover at the ER and thereby shapes intracellular Ca2+ signaling and innate immune output [PMID:21610068, PMID:31076723]. Its founding function is the regulated degradation of activated IP3 receptors: a constitutive pool of RNF170 is bound to the ERLIN1/2 (SPFH1/2) scaffold complex, which recruits the ligase to stimulated IP3 receptors and enables their ubiquitination and proteasomal clearance [PMID:21610068]. RNF170 mediates the full repertoire of ubiquitin conjugates added to activated IP3 receptors, including monoubiquitin and K48- and K63-linked chains [PMID:25882839]. Protein stability is governed by ionic interactions between charged transmembrane residues and by a conserved luminal N-terminal region that docks onto the SPFH domain of adjacent ERLIN subunits, an interface also used by TMUB1 [PMID:25882839, PMID:38782601]. Beyond Ca2+ control, RNF170 binds TLR3 and catalyzes K48-linked polyubiquitination at K766 in the TIR domain to drive TLR3 proteasomal degradation, restraining TLR3-triggered IRF3 and NF-κB signaling [PMID:31076723], and it (with RNF149) ubiquitinates DEK at K349 to suppress the RIPK1-PANoptosis pathway [PMID:40120540]. Bi-allelic loss-of-function or destabilizing mutations in RNF170 cause autosomal recessive hereditary spastic paraplegia and sensory ataxia, with disease-associated alleles either enhancing RNF170 autoubiquitination/degradation or abolishing protein expression [PMID:25882839, PMID:31636353, PMID:36046950].","teleology":[{"year":2011,"claim":"Established RNF170 as the ER E3 ligase that ubiquitinates activated IP3 receptors and defined how it reaches its substrate, answering how stimulated IP3 receptors are targeted for degradation.","evidence":"Co-IP, RNAi knockdown, catalytically inactive mutant overexpression, and subcellular fractionation in cultured cells","pmids":["21610068"],"confidence":"High","gaps":["Did not define which ubiquitin linkage types RNF170 builds on the receptor","Mechanism by which ERLIN1/2 senses receptor activation to recruit RNF170 not resolved"]},{"year":2015,"claim":"Linked a disease mutation to RNF170 protein instability and showed RNF170 is responsible for all ubiquitin conjugate types on activated IP3 receptors, connecting ligase activity to a functional Ca2+ defect.","evidence":"Site-directed mutagenesis, CRISPR/Cas9 knockout, Ca2+ mobilization assays, and Western blot in ADSA patient-derived lymphoblasts","pmids":["25882839"],"confidence":"High","gaps":["How transmembrane ionic interactions structurally stabilize RNF170 not visualized","Link between impaired Ca2+ mobilization and neuronal degeneration not established"]},{"year":2015,"claim":"Demonstrated in vivo that loss of Rnf170 elevates IP3 receptor levels in a tissue-restricted manner and produces a neurological phenotype, validating the degradation function in the intact organism.","evidence":"Rnf170 knockout mouse with gait/proprioception analysis and Itpr1 Western blot across brain regions","pmids":["26433933"],"confidence":"Medium","gaps":["Why Itpr1 accumulation is cerebellar/spinal but not cortical is unexplained","Cell-autonomous basis of the neuronal phenotype not dissected"]},{"year":2019,"claim":"Expanded RNF170 substrate scope to innate immunity, showing it degrades TLR3 to restrain antiviral signaling, establishing a role beyond Ca2+ homeostasis.","evidence":"Co-IP, site-mapped K48-linked ubiquitination at K766, and RNF170 knockout with in vitro/in vivo immune response assays","pmids":["31076723"],"confidence":"High","gaps":["Whether ERLIN1/2 recruits RNF170 to TLR3 as it does for IP3 receptors not tested","Relationship between immune and neurological functions of RNF170 unknown"]},{"year":2019,"claim":"Confirmed bi-allelic loss-of-function RNF170 mutations cause autosomal recessive HSP through disrupted ERAD-mediated IP3 receptor degradation, cementing the gene-disease link.","evidence":"Patient fibroblast assays, mutant SH-SY5Y cells, and zebrafish gene knockdown","pmids":["31636353"],"confidence":"Medium","gaps":["Causal chain from IP3 receptor accumulation to motor neuron degeneration not delineated","Zebrafish knockdown not complemented by rescue in the same report"]},{"year":2022,"claim":"A nonsense variant reducing RNF170 mRNA and protein reinforced loss-of-function as the disease mechanism in HSP.","evidence":"RT-qPCR and Western blot in patient-derived cells","pmids":["36046950"],"confidence":"Low","gaps":["Single patient with no new pathway mechanism","No functional Ca2+ or substrate readout in this case"]},{"year":2024,"claim":"Defined the structural basis of RNF170 scaffolding, mapping conserved luminal N-terminal regions of RNF170 and TMUB1 onto distinct interfaces of the ERLIN SPFH domain, explaining how disease variants disrupt complex assembly.","evidence":"Co-IP/pulldown, 3D structural modelling, deletion/variant mapping, and omics of ERLIN-knockout HeLa cells","pmids":["38782601"],"confidence":"Medium","gaps":["No experimental high-resolution structure of the assembled complex","Functional role of TMUB1 within the RNF170-ERLIN module not defined"]},{"year":2025,"claim":"Identified DEK as an additional RNF170 substrate, with K48-linked ubiquitination at K349 suppressing RIPK1-PANoptosis, broadening the ligase's cell-death regulatory role.","evidence":"Mass spectrometry, molecular docking, site-mapped ubiquitination, and PANoptosis pathway assays in bronchial epithelial cells","pmids":["40120540"],"confidence":"Medium","gaps":["RNF170-specific contribution not cleanly separated from RNF149","Whether DEK targeting is ERLIN-dependent untested"]},{"year":null,"claim":"How RNF170 selects among its diverse substrates (IP3 receptors, TLR3, DEK) and whether ERLIN1/2 scaffolding operates for all of them remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying recruitment logic across the three substrate classes","Tissue-specific substrate preference and its relation to disease phenotype unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,6]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1]}],"complexes":["ERLIN1/2 (SPFH1/2) complex"],"partners":["ERLIN1","ERLIN2","ITPR1","TLR3","TMUB1","DEK","RNF149"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96K19","full_name":"E3 ubiquitin-protein ligase RNF170","aliases":["Putative LAG1-interacting protein","RING finger protein 170","RING-type E3 ubiquitin transferase RNF170"],"length_aa":258,"mass_kda":29.8,"function":"E3 ubiquitin-protein ligase that plays an essential role in stimulus-induced inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) ubiquitination and degradation via the endoplasmic reticulum-associated degradation (ERAD) pathway. Also involved in ITPR1 turnover in resting cells. Selectively inhibits the TLR3-triggered innate immune response by promoting the 'Lys-48'-linked polyubiquitination and degradation of TLR3 (PubMed:31076723)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q96K19/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RNF170","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RNF170","total_profiled":1310},"omim":[{"mim_id":"619686","title":"SPASTIC PARAPLEGIA 85, AUTOSOMAL RECESSIVE; SPG85","url":"https://www.omim.org/entry/619686"},{"mim_id":"614649","title":"RING FINGER PROTEIN 170; RNF170","url":"https://www.omim.org/entry/614649"},{"mim_id":"608984","title":"ATAXIA, SENSORY, 1, AUTOSOMAL DOMINANT; SNAX1","url":"https://www.omim.org/entry/608984"},{"mim_id":"270800","title":"SPASTIC PARAPLEGIA 5A, AUTOSOMAL RECESSIVE; SPG5A","url":"https://www.omim.org/entry/270800"}],"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/RNF170"},"hgnc":{"alias_symbol":["DKFZP564A022","ADSA"],"prev_symbol":["SNAX1"]},"alphafold":{"accession":"Q96K19","domains":[{"cath_id":"3.30.40.10","chopping":"55-170","consensus_level":"high","plddt":84.0727,"start":55,"end":170},{"cath_id":"1.20.5","chopping":"22-50","consensus_level":"medium","plddt":78.8362,"start":22,"end":50},{"cath_id":"1.10.287","chopping":"191-258","consensus_level":"high","plddt":68.7565,"start":191,"end":258}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96K19","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96K19-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96K19-F1-predicted_aligned_error_v6.png","plddt_mean":78.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNF170","jax_strain_url":"https://www.jax.org/strain/search?query=RNF170"},"sequence":{"accession":"Q96K19","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96K19.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96K19/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96K19"}},"corpus_meta":[{"pmid":"11913691","id":"PMC_11913691","title":"ADSA Foundation Scholar Award. Formation and physical properties of milk protein gels.","date":"2002","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/11913691","citation_count":179,"is_preprint":false},{"pmid":"10913094","id":"PMC_10913094","title":"An A-factor-dependent extracytoplasmic function sigma factor (sigma(AdsA)) that is essential for morphological development in Streptomyces griseus.","date":"2000","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/10913094","citation_count":94,"is_preprint":false},{"pmid":"21610068","id":"PMC_21610068","title":"RNF170 protein, an endoplasmic reticulum membrane ubiquitin ligase, mediates inositol 1,4,5-trisphosphate receptor ubiquitination and degradation.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21610068","citation_count":83,"is_preprint":false},{"pmid":"18349221","id":"PMC_18349221","title":"ADSA Foundation Scholar Award: Possibilities and challenges of exopolysaccharide-producing lactic cultures in dairy foods.","date":"2008","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/18349221","citation_count":51,"is_preprint":false},{"pmid":"31636353","id":"PMC_31636353","title":"Bi-allelic variants in RNF170 are associated with hereditary spastic paraplegia.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31636353","citation_count":42,"is_preprint":false},{"pmid":"21115467","id":"PMC_21115467","title":"A mutation in the RNF170 gene causes autosomal dominant sensory ataxia.","date":"2010","source":"Brain : a journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/21115467","citation_count":34,"is_preprint":false},{"pmid":"34053756","id":"PMC_34053756","title":"ADSA Foundation Scholar Award: New frontiers in calf and heifer nutrition-From conception to puberty.","date":"2021","source":"Journal of dairy 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system.","date":"2003","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/12836921","citation_count":19,"is_preprint":false},{"pmid":"26433933","id":"PMC_26433933","title":"Age-dependent gait abnormalities in mice lacking the Rnf170 gene linked to human autosomal-dominant sensory ataxia.","date":"2015","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26433933","citation_count":12,"is_preprint":false},{"pmid":"33165979","id":"PMC_33165979","title":"RNF170-Related Hereditary Spastic Paraplegia: Confirmation by a Novel Mutation.","date":"2020","source":"Movement disorders : official journal of the Movement Disorder Society","url":"https://pubmed.ncbi.nlm.nih.gov/33165979","citation_count":9,"is_preprint":false},{"pmid":"34469621","id":"PMC_34469621","title":"RNF170 mutation causes autosomal dominant sensory ataxia with variable pyramidal involvement.","date":"2021","source":"European journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/34469621","citation_count":7,"is_preprint":false},{"pmid":"38782601","id":"PMC_38782601","title":"ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway.","date":"2024","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/38782601","citation_count":6,"is_preprint":false},{"pmid":"40120540","id":"PMC_40120540","title":"Eupalinolide B targets DEK and PANoptosis through E3 ubiquitin ligases RNF149 and RNF170 to negatively regulate asthma.","date":"2025","source":"Phytomedicine : international journal of phytotherapy and phytopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40120540","citation_count":6,"is_preprint":false},{"pmid":"35041108","id":"PMC_35041108","title":"A novel homozygous variant in RNF170 causes hereditary spastic paraplegia: a case report and review of the 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reports","url":"https://pubmed.ncbi.nlm.nih.gov/42052314","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12288,"output_tokens":2312,"usd":0.035772,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9363,"output_tokens":3052,"usd":0.061558,"stage2_stop_reason":"end_turn"},"total_usd":0.09733,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"RNF170 is an ER membrane-localized RING domain ubiquitin E3 ligase that associates with activated IP3 receptors and mediates their ubiquitination and proteasomal degradation. RNF170 depletion by RNAi inhibited stimulus-induced IP3 receptor ubiquitination and degradation; overexpression of catalytically inactive RNF170 suppressed IP3 receptor processing. A substantial fraction of RNF170 constitutively associates with the erlin1/2 (SPFH1/2) complex, which recruits RNF170 to activated IP3 receptors (erlin1/2 depletion inhibited RNF170 binding to IP3 receptors, but RNF170 depletion did not affect erlin1/2 binding).\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, catalytically inactive mutant overexpression, subcellular fractionation/localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, RNAi loss-of-function, dominant-negative mutant, multiple orthogonal methods in a focused mechanistic study, replicated by subsequent papers\",\n      \"pmids\": [\"21610068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The ADSA-causing point mutation R199C in RNF170 destabilizes the protein by enhancing autoubiquitination and proteasomal degradation; ionic interactions between charged residues in the transmembrane domains are required for RNF170 stability. CRISPR/Cas9 deletion of RNF170 demonstrated that it mediates addition of all ubiquitin conjugates on activated IP3 receptors (monoubiquitin, K48- and K63-linked chains). ADSA lymphoblasts show impaired IP3-induced Ca2+ mobilization without changes in IP3 receptor levels or IP3 production, indicating a functional defect at the IP3 receptor locus.\",\n      \"method\": \"Site-directed mutagenesis, CRISPR/Cas9 knockout, Ca2+ mobilization assays, Western blot in patient-derived lymphoblasts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis combined with CRISPR/Cas9 deletion and functional Ca2+ assays, patient-derived cell validation, multiple orthogonal methods in one focused study\",\n      \"pmids\": [\"25882839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RNF170 functions as an E3 ubiquitin ligase that binds TLR3 and mediates K48-linked polyubiquitination at lysine 766 in the TIR domain of TLR3, promoting its proteasomal degradation. Genetic ablation of RNF170 selectively augmented TLR3-triggered innate immune responses (IRF3 and NF-κB signaling) both in vitro and in vivo, without affecting other TLR pathways.\",\n      \"method\": \"Co-immunoprecipitation (TLR3-binding protein identification), ubiquitination assay (K48-linkage, K766 site), RNF170 knockout, in vitro and in vivo innate immune response assays\",\n      \"journal\": \"Cellular & molecular immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, site-specific ubiquitination mapping, genetic ablation with defined immune phenotype in vitro and in vivo, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"31076723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Bi-allelic loss-of-function mutations in RNF170 cause autosomal recessive hereditary spastic paraplegia (HSP) by disrupting IP3 receptor degradation via the ER-associated degradation pathway. Functional evaluation in patient fibroblasts, mutant SH-SY5Y cells, and gene knockdown in zebrafish confirmed loss-of-function consequences.\",\n      \"method\": \"Patient fibroblast functional assays, mutant cell line analysis, zebrafish gene knockdown\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple model systems (patient cells, neuronal cell line, zebrafish), single lab, disease-gene linkage with functional validation\",\n      \"pmids\": [\"31636353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rnf170 knockout mice develop age-dependent gait abnormalities and reduced proprioception/thermal nociception, with significantly elevated Itpr1 (IP3 receptor type 1) protein levels in cerebellum and spinal cord but not cerebral cortex, confirming that Rnf170 mediates IP3 receptor degradation in vivo in a tissue-specific manner.\",\n      \"method\": \"Rnf170 knockout mouse model, gait analysis, protein blot (Western blot) for Itpr1 levels across brain regions\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean knockout mouse with defined phenotypic and biochemical readout, single lab\",\n      \"pmids\": [\"26433933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ERLIN1/2 scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170. A conserved luminal N-terminal region in both TMUB1 and RNF170 is required for their interaction with the SPFH domain of adjacent ERLIN subunits at distinct interfaces. Protein variants that preclude these ERLIN interactions have been linked to hereditary spastic paraplegia.\",\n      \"method\": \"Protein interaction studies (co-IP/pulldown), 3D structural modelling, deletion/variant mapping of interaction domain, omics-based phenotypic characterization of ERLIN-knockout HeLa cells\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — interaction domain mapping with structural modelling and functional variant data, single lab with multiple approaches\",\n      \"pmids\": [\"38782601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF170 (together with RNF149) mediates K48-linked polyubiquitination of DEK at lysine K349 within the DEK coding region (residues 270–350), promoting DEK proteasomal degradation; this suppresses the RIPK1-PANoptosis pathway in bronchial epithelial cells.\",\n      \"method\": \"Mass spectrometry (identifying RNF170 as DEK-binding E3), molecular docking, ubiquitination assay (K48, site K349), functional PANoptosis pathway assays\",\n      \"journal\": \"Phytomedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — MS identification, site-specific ubiquitination mapping, single lab, limited independent validation of RNF170-specific contribution separate from RNF149\",\n      \"pmids\": [\"40120540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A novel homozygous stop-gain variant (p.R64*) in RNF170 leads to significantly reduced mRNA and protein levels, confirming loss-of-function as the mechanism in RNF170-associated HSP.\",\n      \"method\": \"RT-qPCR, Western blot in patient-derived cells\",\n      \"journal\": \"Clinical genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single patient, two methods (RT-qPCR and Western blot) confirming loss-of-function but no new mechanistic pathway information\",\n      \"pmids\": [\"36046950\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RNF170 is an ER membrane-resident RING-finger E3 ubiquitin ligase that is recruited by the ERLIN1/2 scaffold complex to activated IP3 receptors, where it mediates their ubiquitination (monoubiquitin, K48- and K63-linked chains) and proteasomal degradation to regulate intracellular Ca2+ signaling; it also targets TLR3 (via K48-linked ubiquitination at K766) for proteasomal degradation to suppress innate immune responses, and has been identified as a regulator of DEK degradation, with loss-of-function or destabilizing mutations causing hereditary spastic paraplegia or sensory ataxia in humans and model organisms.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RNF170 is an endoplasmic reticulum membrane-resident RING-domain E3 ubiquitin ligase that controls protein turnover at the ER and thereby shapes intracellular Ca2+ signaling and innate immune output [#0, #2]. Its founding function is the regulated degradation of activated IP3 receptors: a constitutive pool of RNF170 is bound to the ERLIN1/2 (SPFH1/2) scaffold complex, which recruits the ligase to stimulated IP3 receptors and enables their ubiquitination and proteasomal clearance [#0]. RNF170 mediates the full repertoire of ubiquitin conjugates added to activated IP3 receptors, including monoubiquitin and K48- and K63-linked chains [#1]. Protein stability is governed by ionic interactions between charged transmembrane residues and by a conserved luminal N-terminal region that docks onto the SPFH domain of adjacent ERLIN subunits, an interface also used by TMUB1 [#1, #5]. Beyond Ca2+ control, RNF170 binds TLR3 and catalyzes K48-linked polyubiquitination at K766 in the TIR domain to drive TLR3 proteasomal degradation, restraining TLR3-triggered IRF3 and NF-\\u03baB signaling [#2], and it (with RNF149) ubiquitinates DEK at K349 to suppress the RIPK1-PANoptosis pathway [#6]. Bi-allelic loss-of-function or destabilizing mutations in RNF170 cause autosomal recessive hereditary spastic paraplegia and sensory ataxia, with disease-associated alleles either enhancing RNF170 autoubiquitination/degradation or abolishing protein expression [#1, #3, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established RNF170 as the ER E3 ligase that ubiquitinates activated IP3 receptors and defined how it reaches its substrate, answering how stimulated IP3 receptors are targeted for degradation.\",\n      \"evidence\": \"Co-IP, RNAi knockdown, catalytically inactive mutant overexpression, and subcellular fractionation in cultured cells\",\n      \"pmids\": [\"21610068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which ubiquitin linkage types RNF170 builds on the receptor\", \"Mechanism by which ERLIN1/2 senses receptor activation to recruit RNF170 not resolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked a disease mutation to RNF170 protein instability and showed RNF170 is responsible for all ubiquitin conjugate types on activated IP3 receptors, connecting ligase activity to a functional Ca2+ defect.\",\n      \"evidence\": \"Site-directed mutagenesis, CRISPR/Cas9 knockout, Ca2+ mobilization assays, and Western blot in ADSA patient-derived lymphoblasts\",\n      \"pmids\": [\"25882839\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How transmembrane ionic interactions structurally stabilize RNF170 not visualized\", \"Link between impaired Ca2+ mobilization and neuronal degeneration not established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated in vivo that loss of Rnf170 elevates IP3 receptor levels in a tissue-restricted manner and produces a neurological phenotype, validating the degradation function in the intact organism.\",\n      \"evidence\": \"Rnf170 knockout mouse with gait/proprioception analysis and Itpr1 Western blot across brain regions\",\n      \"pmids\": [\"26433933\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Why Itpr1 accumulation is cerebellar/spinal but not cortical is unexplained\", \"Cell-autonomous basis of the neuronal phenotype not dissected\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Expanded RNF170 substrate scope to innate immunity, showing it degrades TLR3 to restrain antiviral signaling, establishing a role beyond Ca2+ homeostasis.\",\n      \"evidence\": \"Co-IP, site-mapped K48-linked ubiquitination at K766, and RNF170 knockout with in vitro/in vivo immune response assays\",\n      \"pmids\": [\"31076723\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ERLIN1/2 recruits RNF170 to TLR3 as it does for IP3 receptors not tested\", \"Relationship between immune and neurological functions of RNF170 unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Confirmed bi-allelic loss-of-function RNF170 mutations cause autosomal recessive HSP through disrupted ERAD-mediated IP3 receptor degradation, cementing the gene-disease link.\",\n      \"evidence\": \"Patient fibroblast assays, mutant SH-SY5Y cells, and zebrafish gene knockdown\",\n      \"pmids\": [\"31636353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal chain from IP3 receptor accumulation to motor neuron degeneration not delineated\", \"Zebrafish knockdown not complemented by rescue in the same report\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A nonsense variant reducing RNF170 mRNA and protein reinforced loss-of-function as the disease mechanism in HSP.\",\n      \"evidence\": \"RT-qPCR and Western blot in patient-derived cells\",\n      \"pmids\": [\"36046950\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single patient with no new pathway mechanism\", \"No functional Ca2+ or substrate readout in this case\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined the structural basis of RNF170 scaffolding, mapping conserved luminal N-terminal regions of RNF170 and TMUB1 onto distinct interfaces of the ERLIN SPFH domain, explaining how disease variants disrupt complex assembly.\",\n      \"evidence\": \"Co-IP/pulldown, 3D structural modelling, deletion/variant mapping, and omics of ERLIN-knockout HeLa cells\",\n      \"pmids\": [\"38782601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No experimental high-resolution structure of the assembled complex\", \"Functional role of TMUB1 within the RNF170-ERLIN module not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified DEK as an additional RNF170 substrate, with K48-linked ubiquitination at K349 suppressing RIPK1-PANoptosis, broadening the ligase's cell-death regulatory role.\",\n      \"evidence\": \"Mass spectrometry, molecular docking, site-mapped ubiquitination, and PANoptosis pathway assays in bronchial epithelial cells\",\n      \"pmids\": [\"40120540\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RNF170-specific contribution not cleanly separated from RNF149\", \"Whether DEK targeting is ERLIN-dependent untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RNF170 selects among its diverse substrates (IP3 receptors, TLR3, DEK) and whether ERLIN1/2 scaffolding operates for all of them remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying recruitment logic across the three substrate classes\", \"Tissue-specific substrate preference and its relation to disease phenotype unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 6]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"ERLIN1/2 (SPFH1/2) complex\"],\n    \"partners\": [\"ERLIN1\", \"ERLIN2\", \"ITPR1\", \"TLR3\", \"TMUB1\", \"DEK\", \"RNF149\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}