{"gene":"TMEM94","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2024,"finding":"TMEM94 (ERMA) functions as a P-type ATPase transporter that mediates Mg2+ uptake into the endoplasmic reticulum. The protein contains cytosolic actuator, nucleotide, and phosphorylation domains analogous to P-type ATPases, and uniquely combines a P-type ATPase domain with a GMN motif. A conserved tyrosine residue was identified as critical for Mg2+ binding and catalytic activity, in a mechanism conserved with prokaryotic Mg2+ ATPases (mgtB and mgtA). The ER was established as a major intracellular Mg2+ compartment refilled by TMEM94.","method":"AlphaFold2 structural prediction, domain mutagenesis (tyrosine active-site mutation), Mg2+ transport assays in cells, loss-of-function experiments in mouse cardiomyocytes (Erma+/-) and human iPSC-cardiomyocytes (ERMA mRNA silencing), intracellular Mg2+ measurements","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site mutagenesis identifying critical tyrosine, functional transport assays, structural domain analysis, orthogonal cell-based loss-of-function models (mouse haploinsufficiency + human iPSC), multiple methods in one rigorous study","pmids":["38513662"],"is_preprint":false},{"year":2024,"finding":"TMEM94/ERMA haploinsufficiency in mice (Erma+/-) causes cardiac dysfunction and abnormal Ca2+ cycling in cardiomyocytes, establishing ERMA as an essential component of ER Mg2+ homeostasis required for normal cardiac function.","method":"Mouse Erma+/- haploinsufficiency model, cardiomyocyte Ca2+ cycling assays, cardiac function measurements","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean mouse haploinsufficiency model with defined cardiac phenotype and Ca2+ cycling readout, single lab but multiple orthogonal measurements","pmids":["38513662"],"is_preprint":false},{"year":2018,"finding":"TMEM94 encodes a transmembrane nuclear protein highly conserved across mammals. Bi-allelic truncating variants cause loss of TMEM94 expression. Loss of Tmem94 in a CRISPR/Cas9 mouse model is embryonic lethal and produces craniofacial and cardiac abnormalities and an abnormal neuronal migration pattern, placing TMEM94 as essential for craniofacial, cardiovascular, and nervous system development.","method":"CRISPR/Cas9 mouse knockout, RNA expression analysis (microarray and RNA sequencing) in patient-derived cells, gene expression analysis","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR/Cas9 KO mouse with defined developmental phenotype, transcriptome profiling in patient cells; single lab with multiple orthogonal readouts","pmids":["30526868"],"is_preprint":false},{"year":2025,"finding":"TUSC3 forms an ER-localized Mg2+ transport complex with ERMA (TMEM94). Loss of TUSC3 leads to ER Mg2+ depletion, demonstrating that ERMA-mediated ER Mg2+ uptake requires TUSC3 as a co-factor. TUSC3 knockout in mice causes ER Mg2+ depletion, PERK-eIF2α pathway activation, synaptic dysfunction, and ID-like cognitive phenotypes that are rescued by magnesium supplementation.","method":"TUSC3 knockout mouse model, ER Mg2+ measurements, co-complex analysis (TUSC3-ERMA interaction), PERK-eIF2α pathway activation assays, cognitive behavioral tests, fibroblast studies from TUSC3 mutant patients, magnesium supplementation rescue experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal complex formation between TUSC3 and ERMA, KO mouse with defined molecular and behavioral phenotypes, patient-derived fibroblast validation, pharmacological rescue; multiple orthogonal methods across mouse and human models","pmids":["41203647"],"is_preprint":false}],"current_model":"TMEM94 (ERMA) is an ER-localized multi-pass transmembrane P-type ATPase that mediates Mg2+ uptake into the endoplasmic reticulum using a mechanism requiring a conserved tyrosine for Mg2+ binding and a unique combination of P-type ATPase and GMN motif domains; it forms a functional transport complex with TUSC3, and its loss disrupts ER Mg2+ homeostasis, triggers ER stress (PERK-eIF2α), impairs synaptic function and cardiac Ca2+ cycling, and causes embryonic lethality in mice with craniofacial, cardiac, and neuronal migration defects."},"narrative":{"mechanistic_narrative":"TMEM94 (ERMA) is an endoplasmic reticulum-localized, multi-pass transmembrane P-type ATPase that mediates Mg2+ uptake into the ER, establishing the ER as a major intracellular Mg2+ store [PMID:38513662]. It carries cytosolic actuator, nucleotide, and phosphorylation domains characteristic of P-type ATPases, uniquely combined with a GMN motif, and uses a conserved active-site tyrosine for Mg2+ binding and catalysis in a manner shared with prokaryotic Mg2+ ATPases [PMID:38513662]. ERMA does not act alone: it forms an ER Mg2+ transport complex with TUSC3, which is required for ERMA-mediated Mg2+ uptake, and loss of either partner depletes ER Mg2+ and activates the PERK-eIF2α ER stress pathway, producing synaptic dysfunction and cognitive deficits that are rescued by magnesium supplementation [PMID:41203647]. Disruption of ERMA-dependent Mg2+ homeostasis impairs cardiomyocyte Ca2+ cycling and cardiac function [PMID:38513662], and complete loss is embryonic lethal in mice with craniofacial, cardiac, and neuronal migration defects, with bi-allelic truncating variants abolishing TMEM94 expression in patients [PMID:30526868].","teleology":[{"year":2018,"claim":"Before function was known, the question was whether TMEM94 was essential and disease-relevant; demonstrating embryonic lethality and human developmental phenotypes established it as a critical developmental gene.","evidence":"CRISPR/Cas9 mouse knockout with developmental phenotyping plus transcriptome profiling of patient-derived cells carrying bi-allelic truncating variants","pmids":["30526868"],"confidence":"Medium","gaps":["No molecular activity or transport function identified at this stage","Subcellular role described as nuclear, not yet resolved to the ER","Mechanism connecting gene loss to craniofacial/cardiac/neuronal defects unknown"]},{"year":2024,"claim":"The central mechanistic question — what TMEM94 actually does — was answered by showing it is an ER-resident P-type ATPase that pumps Mg2+ into the ER via a conserved active-site tyrosine, defining the ER as a refillable Mg2+ compartment.","evidence":"AlphaFold2 structural prediction, active-site tyrosine mutagenesis, cellular Mg2+ transport assays, and loss-of-function in mouse Erma+/- and human iPSC-cardiomyocytes","pmids":["38513662"],"confidence":"High","gaps":["No experimental high-resolution structure of the transporter","Stoichiometry and counter-ion/coupling of the transport cycle not defined","Co-factor requirement for transport not yet identified at this stage"]},{"year":2024,"claim":"Linking ER Mg2+ transport to organ physiology, ERMA haploinsufficiency was shown to disrupt cardiomyocyte Ca2+ cycling and cardiac function, connecting ER Mg2+ homeostasis to excitation-contraction coupling.","evidence":"Mouse Erma+/- haploinsufficiency model with cardiomyocyte Ca2+ cycling and cardiac function measurements","pmids":["38513662"],"confidence":"Medium","gaps":["Mechanistic link between ER Mg2+ and Ca2+ handling not molecularly resolved","Single lab, single phenotypic axis","Whether cardiac defect reflects transport loss specifically vs broader ER dysfunction unclear"]},{"year":2025,"claim":"The question of how ERMA achieves transport was advanced by identifying TUSC3 as an obligate ER complex partner, tying ERMA/TUSC3 Mg2+ depletion to PERK-eIF2α stress, synaptic and cognitive deficits reversible by Mg2+.","evidence":"TUSC3-ERMA co-complex analysis, TUSC3 knockout mouse, ER Mg2+ measurements, PERK-eIF2α assays, patient fibroblasts, and magnesium supplementation rescue","pmids":["41203647"],"confidence":"High","gaps":["Structural basis of the ERMA-TUSC3 interaction not defined","Whether TUSC3 modulates catalysis, targeting, or Mg2+ delivery unresolved","Direct binding interface and stoichiometry of the complex unknown"]},{"year":null,"claim":"How ER Mg2+ levels are sensed and how ERMA activity is regulated to coordinate cardiac, synaptic, and developmental demands remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No regulatory inputs or post-translational control of ERMA characterized","Mechanism connecting ER Mg2+ depletion to specific developmental defects unmapped","No experimental transporter structure or defined transport cycle"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0]},{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,3]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3]}],"complexes":["ERMA-TUSC3 ER Mg2+ transport complex"],"partners":["TUSC3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q12767","full_name":"Transmembrane protein 94","aliases":["Endoplasmic reticulum magnesium ATPase"],"length_aa":1356,"mass_kda":151.2,"function":"Could function in the uptake of Mg(2+) from the cytosol into the endoplasmic reticulum and regulate intracellular Mg(2+) homeostasis","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q12767/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM94","classification":"Not Classified","n_dependent_lines":14,"n_total_lines":1208,"dependency_fraction":0.011589403973509934},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TMEM94","total_profiled":1310},"omim":[{"mim_id":"618316","title":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH CARDIAC DEFECTS AND DYSMORPHIC FACIES; IDDCDF","url":"https://www.omim.org/entry/618316"},{"mim_id":"618163","title":"TRANSMEMBRANE PROTEIN 94; TMEM94","url":"https://www.omim.org/entry/618163"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMEM94"},"hgnc":{"alias_symbol":["ERMA"],"prev_symbol":["KIAA0195"]},"alphafold":{"accession":"Q12767","domains":[{"cath_id":"-","chopping":"55-146_266-333_383-400","consensus_level":"medium","plddt":84.879,"start":55,"end":400},{"cath_id":"2.70.150,2.70.150","chopping":"154-220_233-262","consensus_level":"medium","plddt":87.1523,"start":154,"end":262},{"cath_id":"3.40.1110","chopping":"552-664_681-787_816-833","consensus_level":"high","plddt":83.1656,"start":552,"end":833}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12767","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q12767-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q12767-F1-predicted_aligned_error_v6.png","plddt_mean":72.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM94","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM94"},"sequence":{"accession":"Q12767","fasta_url":"https://rest.uniprot.org/uniprotkb/Q12767.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q12767/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12767"}},"corpus_meta":[{"pmid":"2985541","id":"PMC_2985541","title":"Nucleotide sequence of ermA, a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus.","date":"1985","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/2985541","citation_count":113,"is_preprint":false},{"pmid":"12936983","id":"PMC_12936983","title":"Presence of the tet(O) gene in erythromycin- and tetracycline-resistant strains of Streptococcus pyogenes and linkage with either the mef(A) or the erm(A) gene.","date":"2003","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/12936983","citation_count":87,"is_preprint":false},{"pmid":"2592348","id":"PMC_2592348","title":"Erythromycin-induced ribosome stall in the ermA leader: a barricade to 5'-to-3' nucleolytic cleavage of the ermA transcript.","date":"1989","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/2592348","citation_count":54,"is_preprint":false},{"pmid":"2463370","id":"PMC_2463370","title":"Erythromycin-induced stabilization of ermA messenger RNA in Staphylococcus aureus and Bacillus subtilis.","date":"1988","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/2463370","citation_count":52,"is_preprint":false},{"pmid":"11120994","id":"PMC_11120994","title":"Identification of an erm(A) erythromycin resistance methylase gene in Streptococcus pneumoniae isolated in Greece.","date":"2001","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/11120994","citation_count":51,"is_preprint":false},{"pmid":"29738416","id":"PMC_29738416","title":"Design and protocol of Estrogenic Regulation of Muscle Apoptosis (ERMA) study with 47 to 55-year-old women's cohort: novel results show menopause-related differences in blood count.","date":"2018","source":"Menopause (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/29738416","citation_count":49,"is_preprint":false},{"pmid":"22664438","id":"PMC_22664438","title":"ermA, ermC , tetM and tetK are essential for erythromycin and tetracycline resistance among methicillin-resistant Staphylococcus aureus strains isolated from a tertiary hospital in Malaysia.","date":"2012","source":"Indian journal of medical microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/22664438","citation_count":44,"is_preprint":false},{"pmid":"35498633","id":"PMC_35498633","title":"Newly Emerging MDR B. cereus in Mugil seheli as the First Report Commonly Harbor nhe, hbl, cytK, and pc-plc Virulence Genes and bla1, bla2, tetA, and ermA Resistance Genes.","date":"2022","source":"Infection and drug resistance","url":"https://pubmed.ncbi.nlm.nih.gov/35498633","citation_count":40,"is_preprint":false},{"pmid":"12161406","id":"PMC_12161406","title":"Conjugative transfer of the erm(A) gene from erythromycin-resistant Streptococcus pyogenes to macrolide-susceptible S. pyogenes, Enterococcus faecalis and Listeria innocua.","date":"2002","source":"The Journal of antimicrobial chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/12161406","citation_count":33,"is_preprint":false},{"pmid":"16333132","id":"PMC_16333132","title":"Life-threatening invasive Helcococcus kunzii infections in intravenous-drug users and ermA-mediated erythromycin resistance.","date":"2005","source":"Journal of clinical microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/16333132","citation_count":30,"is_preprint":false},{"pmid":"12384375","id":"PMC_12384375","title":"Staphylococcus sciuri gene erm(33), encoding inducible resistance to macrolides, lincosamides, and streptogramin B antibiotics, is a product of recombination between erm(C) and erm(A).","date":"2002","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/12384375","citation_count":30,"is_preprint":false},{"pmid":"10508560","id":"PMC_10508560","title":"Simultaneous detection of erythromycin-resistant methylase genes ermA and ermC from Staphylococcus spp. by multiplex-PCR.","date":"1999","source":"Molecular and cellular probes","url":"https://pubmed.ncbi.nlm.nih.gov/10508560","citation_count":28,"is_preprint":false},{"pmid":"18077631","id":"PMC_18077631","title":"Differences in potential for selection of clindamycin-resistant mutants between inducible erm(A) and erm(C) Staphylococcus aureus genes.","date":"2007","source":"Journal of clinical microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/18077631","citation_count":28,"is_preprint":false},{"pmid":"11062198","id":"PMC_11062198","title":"Molecular analysis of the translational attenuator of a constitutively expressed erm(A) gene from Staphylococcus intermedius.","date":"2000","source":"The Journal of antimicrobial chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/11062198","citation_count":28,"is_preprint":false},{"pmid":"30526868","id":"PMC_30526868","title":"Bi-allelic TMEM94 Truncating Variants Are Associated with Neurodevelopmental Delay, Congenital Heart Defects, and Distinct Facial Dysmorphism.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30526868","citation_count":26,"is_preprint":false},{"pmid":"18952616","id":"PMC_18952616","title":"Unusual resistance patterns in macrolide-resistant Streptococcus pyogenes harbouring erm(A).","date":"2008","source":"The Journal of antimicrobial chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/18952616","citation_count":26,"is_preprint":false},{"pmid":"38513662","id":"PMC_38513662","title":"ERMA (TMEM94) is a P-type ATPase transporter for Mg2+ uptake in the endoplasmic reticulum.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38513662","citation_count":16,"is_preprint":false},{"pmid":"18409053","id":"PMC_18409053","title":"Molecular analysis of constitutive mutations in ermB and ermA selected in vitro from inducibly MLSB-resistant enterococci.","date":"2008","source":"Archives of pharmacal research","url":"https://pubmed.ncbi.nlm.nih.gov/18409053","citation_count":15,"is_preprint":false},{"pmid":"12356808","id":"PMC_12356808","title":"Prevalence of erm(A) and mef(B) erythromycin resistance determinants in isolates of Streptococcus pneumoniae from New Zealand.","date":"2002","source":"The Journal of antimicrobial chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/12356808","citation_count":15,"is_preprint":false},{"pmid":"27692714","id":"PMC_27692714","title":"Factors responsible for subclinical mastitis in cows caused by Staphylococcus chromogenes and its susceptibility to antibiotics based on bap, fnbA, eno, mecA, tetK, and ermA genes.","date":"2016","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/27692714","citation_count":14,"is_preprint":false},{"pmid":"15980403","id":"PMC_15980403","title":"Differences in the DNA sequences in the upstream attenuator region of erm(A) in clinical isolates of Streptococcus pyogenes and their correlation with macrolide/lincosamide resistance.","date":"2005","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/15980403","citation_count":14,"is_preprint":false},{"pmid":"2443127","id":"PMC_2443127","title":"Transformation of Arthrobacter and studies on the transcription of the Arthrobacter ermA gene in Streptomyces lividans and Escherichia coli.","date":"1987","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/2443127","citation_count":11,"is_preprint":false},{"pmid":"19996702","id":"PMC_19996702","title":"Development of TaqMan probe-based real-time PCR method for erm(A),erm(B), and erm(C), rapid detection of macrolide-lincosamide-streptogramin B resistance genes, from clinical isolates.","date":"2009","source":"Journal of microbiology and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/19996702","citation_count":11,"is_preprint":false},{"pmid":"17000084","id":"PMC_17000084","title":"Characterisation of the main clones of Streptococcus pyogenes carrying the ermA (subclass TR) gene in Spain.","date":"2006","source":"International journal of antimicrobial agents","url":"https://pubmed.ncbi.nlm.nih.gov/17000084","citation_count":9,"is_preprint":false},{"pmid":"16186169","id":"PMC_16186169","title":"Differences in the DNA sequence of the translational attenuator of several constitutively expressed erm(A) genes from clinical isolates of Streptococcus agalactiae.","date":"2005","source":"The Journal of antimicrobial chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/16186169","citation_count":8,"is_preprint":false},{"pmid":"17661294","id":"PMC_17661294","title":"Novel 10-bp deletion in the translational attenuator of a constitutively expressed erm(A) gene from Staphylococcus epidermidis.","date":"2007","source":"International microbiology : the official journal of the Spanish Society for Microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/17661294","citation_count":6,"is_preprint":false},{"pmid":"32825426","id":"PMC_32825426","title":"Fetal Anomalies Associated with Novel Pathogenic Variants in TMEM94.","date":"2020","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/32825426","citation_count":4,"is_preprint":false},{"pmid":"15924755","id":"PMC_15924755","title":"[Relation of pbp2B, ermB, ermA/B, mefA genes with resistance to penicillin and erythromycin among Streptococcus pneumoniae isolates from children].","date":"2005","source":"Zhonghua er ke za zhi = Chinese journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/15924755","citation_count":1,"is_preprint":false},{"pmid":"17340992","id":"PMC_17340992","title":"[The frequency of the occurrence of genes ermA, ermB, ermC and msrA/B among methicillin-resistant Staphylococcus aureus strains resistant to erythromycin].","date":"2006","source":"Medycyna doswiadczalna i mikrobiologia","url":"https://pubmed.ncbi.nlm.nih.gov/17340992","citation_count":1,"is_preprint":false},{"pmid":"41203647","id":"PMC_41203647","title":"TUSC3 regulates ERMA-mediated Mg2+ uptake for synaptic function and neurodevelopment.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41203647","citation_count":0,"is_preprint":false},{"pmid":"41011454","id":"PMC_41011454","title":"Dose-Dependent Effect of Tilmicosin Residues on ermA Rebound Mediated by IntI1 in Pig Manure Compost.","date":"2025","source":"Microorganisms","url":"https://pubmed.ncbi.nlm.nih.gov/41011454","citation_count":0,"is_preprint":false},{"pmid":"40058057","id":"PMC_40058057","title":"Characterization of the ribosomal RNA methylase gene erm(A) and its promoter mutation in Campylobacter coli from chicken cecum.","date":"2025","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/40058057","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.28.645872","title":"Antimicrobial susceptibility patterns of and biofilm formation by  <i>Staphylococcus aureus</i>  strains isolated from pediatric patients with atopic dermatitis","date":"2025-03-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.28.645872","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16499,"output_tokens":1675,"usd":0.037311,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8116,"output_tokens":2229,"usd":0.048153,"stage2_stop_reason":"end_turn"},"total_usd":0.085464,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking at the corpus, I need to identify papers about the human/mammalian gene TMEM94 (also known as ERMA, KIAA0195). The vast majority of papers (papers 1-14, 16-26, 28-29, 31-33) are about bacterial ermA/erm(A) genes — macrolide resistance methylase genes in Staphylococcus, Streptococcus, etc. These are clearly symbol collisions (bacterial antibiotic resistance genes, not the human TMEM94 protein). Paper 6 is about the ERMA study (Estrogenic Regulation of Muscle Apoptosis) — an epidemiological cohort, not the TMEM94 protein.\n\nPapers that are genuinely about human TMEM94:\n- Paper 15 (PMID:30526868): Clinical/genetic study + mouse KO model\n- Paper 17 (PMID:38513662): Mechanistic study of ERMA/TMEM94 as P-type ATPase Mg2+ transporter\n- Paper 27 (PMID:32825426): Clinical variants confirmation\n- Paper 30 (PMID:41203647): TUSC3-ERMA complex for ER Mg2+ transport\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2024,\n      \"finding\": \"TMEM94 (ERMA) functions as a P-type ATPase transporter that mediates Mg2+ uptake into the endoplasmic reticulum. The protein contains cytosolic actuator, nucleotide, and phosphorylation domains analogous to P-type ATPases, and uniquely combines a P-type ATPase domain with a GMN motif. A conserved tyrosine residue was identified as critical for Mg2+ binding and catalytic activity, in a mechanism conserved with prokaryotic Mg2+ ATPases (mgtB and mgtA). The ER was established as a major intracellular Mg2+ compartment refilled by TMEM94.\",\n      \"method\": \"AlphaFold2 structural prediction, domain mutagenesis (tyrosine active-site mutation), Mg2+ transport assays in cells, loss-of-function experiments in mouse cardiomyocytes (Erma+/-) and human iPSC-cardiomyocytes (ERMA mRNA silencing), intracellular Mg2+ measurements\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site mutagenesis identifying critical tyrosine, functional transport assays, structural domain analysis, orthogonal cell-based loss-of-function models (mouse haploinsufficiency + human iPSC), multiple methods in one rigorous study\",\n      \"pmids\": [\"38513662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TMEM94/ERMA haploinsufficiency in mice (Erma+/-) causes cardiac dysfunction and abnormal Ca2+ cycling in cardiomyocytes, establishing ERMA as an essential component of ER Mg2+ homeostasis required for normal cardiac function.\",\n      \"method\": \"Mouse Erma+/- haploinsufficiency model, cardiomyocyte Ca2+ cycling assays, cardiac function measurements\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean mouse haploinsufficiency model with defined cardiac phenotype and Ca2+ cycling readout, single lab but multiple orthogonal measurements\",\n      \"pmids\": [\"38513662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMEM94 encodes a transmembrane nuclear protein highly conserved across mammals. Bi-allelic truncating variants cause loss of TMEM94 expression. Loss of Tmem94 in a CRISPR/Cas9 mouse model is embryonic lethal and produces craniofacial and cardiac abnormalities and an abnormal neuronal migration pattern, placing TMEM94 as essential for craniofacial, cardiovascular, and nervous system development.\",\n      \"method\": \"CRISPR/Cas9 mouse knockout, RNA expression analysis (microarray and RNA sequencing) in patient-derived cells, gene expression analysis\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR/Cas9 KO mouse with defined developmental phenotype, transcriptome profiling in patient cells; single lab with multiple orthogonal readouts\",\n      \"pmids\": [\"30526868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TUSC3 forms an ER-localized Mg2+ transport complex with ERMA (TMEM94). Loss of TUSC3 leads to ER Mg2+ depletion, demonstrating that ERMA-mediated ER Mg2+ uptake requires TUSC3 as a co-factor. TUSC3 knockout in mice causes ER Mg2+ depletion, PERK-eIF2α pathway activation, synaptic dysfunction, and ID-like cognitive phenotypes that are rescued by magnesium supplementation.\",\n      \"method\": \"TUSC3 knockout mouse model, ER Mg2+ measurements, co-complex analysis (TUSC3-ERMA interaction), PERK-eIF2α pathway activation assays, cognitive behavioral tests, fibroblast studies from TUSC3 mutant patients, magnesium supplementation rescue experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal complex formation between TUSC3 and ERMA, KO mouse with defined molecular and behavioral phenotypes, patient-derived fibroblast validation, pharmacological rescue; multiple orthogonal methods across mouse and human models\",\n      \"pmids\": [\"41203647\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMEM94 (ERMA) is an ER-localized multi-pass transmembrane P-type ATPase that mediates Mg2+ uptake into the endoplasmic reticulum using a mechanism requiring a conserved tyrosine for Mg2+ binding and a unique combination of P-type ATPase and GMN motif domains; it forms a functional transport complex with TUSC3, and its loss disrupts ER Mg2+ homeostasis, triggers ER stress (PERK-eIF2α), impairs synaptic function and cardiac Ca2+ cycling, and causes embryonic lethality in mice with craniofacial, cardiac, and neuronal migration defects.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMEM94 (ERMA) is an endoplasmic reticulum-localized, multi-pass transmembrane P-type ATPase that mediates Mg2+ uptake into the ER, establishing the ER as a major intracellular Mg2+ store [#0]. It carries cytosolic actuator, nucleotide, and phosphorylation domains characteristic of P-type ATPases, uniquely combined with a GMN motif, and uses a conserved active-site tyrosine for Mg2+ binding and catalysis in a manner shared with prokaryotic Mg2+ ATPases [#0]. ERMA does not act alone: it forms an ER Mg2+ transport complex with TUSC3, which is required for ERMA-mediated Mg2+ uptake, and loss of either partner depletes ER Mg2+ and activates the PERK-eIF2\\u03b1 ER stress pathway, producing synaptic dysfunction and cognitive deficits that are rescued by magnesium supplementation [#3]. Disruption of ERMA-dependent Mg2+ homeostasis impairs cardiomyocyte Ca2+ cycling and cardiac function [#1], and complete loss is embryonic lethal in mice with craniofacial, cardiac, and neuronal migration defects, with bi-allelic truncating variants abolishing TMEM94 expression in patients [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Before function was known, the question was whether TMEM94 was essential and disease-relevant; demonstrating embryonic lethality and human developmental phenotypes established it as a critical developmental gene.\",\n      \"evidence\": \"CRISPR/Cas9 mouse knockout with developmental phenotyping plus transcriptome profiling of patient-derived cells carrying bi-allelic truncating variants\",\n      \"pmids\": [\"30526868\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No molecular activity or transport function identified at this stage\",\n        \"Subcellular role described as nuclear, not yet resolved to the ER\",\n        \"Mechanism connecting gene loss to craniofacial/cardiac/neuronal defects unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The central mechanistic question — what TMEM94 actually does — was answered by showing it is an ER-resident P-type ATPase that pumps Mg2+ into the ER via a conserved active-site tyrosine, defining the ER as a refillable Mg2+ compartment.\",\n      \"evidence\": \"AlphaFold2 structural prediction, active-site tyrosine mutagenesis, cellular Mg2+ transport assays, and loss-of-function in mouse Erma+/- and human iPSC-cardiomyocytes\",\n      \"pmids\": [\"38513662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No experimental high-resolution structure of the transporter\",\n        \"Stoichiometry and counter-ion/coupling of the transport cycle not defined\",\n        \"Co-factor requirement for transport not yet identified at this stage\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linking ER Mg2+ transport to organ physiology, ERMA haploinsufficiency was shown to disrupt cardiomyocyte Ca2+ cycling and cardiac function, connecting ER Mg2+ homeostasis to excitation-contraction coupling.\",\n      \"evidence\": \"Mouse Erma+/- haploinsufficiency model with cardiomyocyte Ca2+ cycling and cardiac function measurements\",\n      \"pmids\": [\"38513662\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanistic link between ER Mg2+ and Ca2+ handling not molecularly resolved\",\n        \"Single lab, single phenotypic axis\",\n        \"Whether cardiac defect reflects transport loss specifically vs broader ER dysfunction unclear\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The question of how ERMA achieves transport was advanced by identifying TUSC3 as an obligate ER complex partner, tying ERMA/TUSC3 Mg2+ depletion to PERK-eIF2\\u03b1 stress, synaptic and cognitive deficits reversible by Mg2+.\",\n      \"evidence\": \"TUSC3-ERMA co-complex analysis, TUSC3 knockout mouse, ER Mg2+ measurements, PERK-eIF2\\u03b1 assays, patient fibroblasts, and magnesium supplementation rescue\",\n      \"pmids\": [\"41203647\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the ERMA-TUSC3 interaction not defined\",\n        \"Whether TUSC3 modulates catalysis, targeting, or Mg2+ delivery unresolved\",\n        \"Direct binding interface and stoichiometry of the complex unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ER Mg2+ levels are sensed and how ERMA activity is regulated to coordinate cardiac, synaptic, and developmental demands remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No regulatory inputs or post-translational control of ERMA characterized\",\n        \"Mechanism connecting ER Mg2+ depletion to specific developmental defects unmapped\",\n        \"No experimental transporter structure or defined transport cycle\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"ERMA-TUSC3 ER Mg2+ transport complex\"],\n    \"partners\": [\"TUSC3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}