{"gene":"OAT","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":1988,"finding":"The OAT structural gene (ornithine aminotransferase) maps to human chromosome 10 (not the X chromosome, where related sequences also reside), and RFLP analysis demonstrates concordant segregation of the OAT locus with gyrate atrophy of the choroid and retina in a pedigree, with significant allelic disequilibrium between OAT haplotypes and gyrate atrophy chromosomes, providing genetic evidence that a defect in the OAT structural gene causes this autosomal recessive disorder.","method":"RFLP analysis using noncoding single-copy probes and cDNA subclones from the OAT gene; pedigree linkage analysis; chromosomal mapping","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal RFLP-based linkage and disequilibrium analysis in human pedigree, single study but multiple RFLP markers used; establishes gene-disease relationship but does not reconstitute enzymatic mechanism","pmids":["2893548"],"is_preprint":false}],"current_model":"OAT (ornithine aminotransferase) is a mitochondrial enzyme whose structural gene maps to human chromosome 10; loss-of-function mutations in OAT cause gyrate atrophy of the choroid and retina, established by genetic linkage and allelic disequilibrium analysis, though direct in vitro reconstitution or structural characterization of the human enzyme is not represented in the available literature."},"narrative":{"mechanistic_narrative":"OAT (ornithine aminotransferase) is the structural gene whose loss of function causes gyrate atrophy of the choroid and retina, an autosomal recessive disorder, as established by genetic linkage and allelic disequilibrium analysis in a human pedigree [PMID:2893548]. The gene maps to human chromosome 10, distinct from related sequences residing on the X chromosome [PMID:2893548]. Beyond this gene-disease mapping [PMID:2893548], the enzymatic mechanism, substrate specificity, and structural characterization of the human protein are not represented in the available corpus.","teleology":[{"year":1988,"claim":"Before this work it was unclear which locus harbored the causative defect for gyrate atrophy and whether the OAT structural gene resided on chromosome 10 or the X chromosome where related sequences also map; the study answered this by demonstrating co-segregation and allelic disequilibrium tying the chromosome 10 OAT gene to the disease.","evidence":"RFLP analysis with noncoding single-copy probes and cDNA subclones, pedigree linkage, and chromosomal mapping in human families","pmids":["2893548"],"confidence":"Medium","gaps":["Does not reconstitute or characterize OAT enzymatic activity in vitro","Does not identify the specific causative mutations or their effect on protein function","No structural model of the human enzyme established"]},{"year":null,"claim":"The catalytic mechanism, substrate specificity, subcellular handling, and structural basis of disease-causing mutations of human OAT remain uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct in vitro enzymatic reconstitution captured","No structural characterization of the human enzyme captured","Genotype-phenotype mechanism linking specific mutations to disease not resolved"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P04181","full_name":"Ornithine aminotransferase, mitochondrial","aliases":["Ornithine delta-aminotransferase","Ornithine--oxo-acid aminotransferase"],"length_aa":439,"mass_kda":48.5,"function":"Catalyzes the reversible interconversion of L-ornithine and 2-oxoglutarate to L-glutamate semialdehyde and L-glutamate","subcellular_location":"Mitochondrion 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drought responses in oat.","date":"2019","source":"Plant signaling & behavior","url":"https://pubmed.ncbi.nlm.nih.gov/31382811","citation_count":17,"is_preprint":false},{"pmid":"36230695","id":"PMC_36230695","title":"Organic Anion Transporters (OAT) and Other SLC22 Transporters in Progression of Renal Cell Carcinoma.","date":"2022","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/36230695","citation_count":16,"is_preprint":false},{"pmid":"32758805","id":"PMC_32758805","title":"Distributions of nutrients and avenanthramides within oat grain and effects on pearled kernel composition.","date":"2020","source":"Food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32758805","citation_count":16,"is_preprint":false},{"pmid":"35783977","id":"PMC_35783977","title":"Physiological and Proteomic Analysis Responsive Mechanisms for Salt Stress in Oat.","date":"2022","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/35783977","citation_count":16,"is_preprint":false},{"pmid":"20678822","id":"PMC_20678822","title":"Isolation and characterization of folate-producing bacteria from oat bran and rye flakes.","date":"2010","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20678822","citation_count":16,"is_preprint":false},{"pmid":"36958455","id":"PMC_36958455","title":"Enhancing the quality of steamed oat cake by partially gelatinized starch in oat flour and its molecular mechanism.","date":"2023","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/36958455","citation_count":16,"is_preprint":false},{"pmid":"34638062","id":"PMC_34638062","title":"Effect of processing on the solubility and molecular size of oat β-glucan and consequences for starch digestibility of oat-fortified noodles.","date":"2021","source":"Food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/34638062","citation_count":16,"is_preprint":false},{"pmid":"31631474","id":"PMC_31631474","title":"Characterising the morphological characters and carbohydrate metabolism of oat culms and their association with lodging resistance.","date":"2019","source":"Plant biology (Stuttgart, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/31631474","citation_count":16,"is_preprint":false},{"pmid":"23147802","id":"PMC_23147802","title":"Supplementation with oat protein ameliorates exercise-induced fatigue in mice.","date":"2013","source":"Food & function","url":"https://pubmed.ncbi.nlm.nih.gov/23147802","citation_count":16,"is_preprint":false},{"pmid":"36756938","id":"PMC_36756938","title":"Effect of soluble oat fiber on intestinal microenvironment and TNBS-induced colitis.","date":"2023","source":"Food & function","url":"https://pubmed.ncbi.nlm.nih.gov/36756938","citation_count":15,"is_preprint":false},{"pmid":"24201466","id":"PMC_24201466","title":"Oat and wheat as contact allergens in personal care products.","date":"2013","source":"Dermatitis : contact, atopic, occupational, drug","url":"https://pubmed.ncbi.nlm.nih.gov/24201466","citation_count":15,"is_preprint":false},{"pmid":"29361693","id":"PMC_29361693","title":"Responses of Oat Grains to Fusarium poae and F. langsethiae Infections and Mycotoxin Contaminations.","date":"2018","source":"Toxins","url":"https://pubmed.ncbi.nlm.nih.gov/29361693","citation_count":15,"is_preprint":false},{"pmid":"24979232","id":"PMC_24979232","title":"Fermentation adaptability of three probiotic Lactobacillus strains to oat, germinated oat and malted oat substrates.","date":"2014","source":"Letters in applied microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/24979232","citation_count":15,"is_preprint":false},{"pmid":"31194741","id":"PMC_31194741","title":"A new identified suppressor of Cdc7p/SepH kinase, PomA, regulates fungal asexual reproduction via affecting phosphorylation of MAPK-HogA.","date":"2019","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31194741","citation_count":13,"is_preprint":false},{"pmid":"27636108","id":"PMC_27636108","title":"Characterization and Analysis of Protein Structures in Oat Bran.","date":"2016","source":"Journal of food science","url":"https://pubmed.ncbi.nlm.nih.gov/27636108","citation_count":13,"is_preprint":false},{"pmid":"33266331","id":"PMC_33266331","title":"Distinctive Features of Orbital Adipose Tissue (OAT) in Graves' Orbitopathy.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33266331","citation_count":12,"is_preprint":false},{"pmid":"16663046","id":"PMC_16663046","title":"Isolation and characterization of oat globulin messenger RNA.","date":"1983","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/16663046","citation_count":12,"is_preprint":false},{"pmid":"1541958","id":"PMC_1541958","title":"A clinical trial of oat bran and niacin in the treatment of hyperlipidemia.","date":"1992","source":"The Journal of family practice","url":"https://pubmed.ncbi.nlm.nih.gov/1541958","citation_count":12,"is_preprint":false},{"pmid":"36376030","id":"PMC_36376030","title":"The Potential Functions and Mechanisms of Oat on Cancer Prevention: A Review.","date":"2022","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36376030","citation_count":11,"is_preprint":false},{"pmid":"24471068","id":"PMC_24471068","title":"Hydration and Pasting Properties of Oat (Avena sativa) Flour.","date":"2012","source":"Preventive nutrition and food science","url":"https://pubmed.ncbi.nlm.nih.gov/24471068","citation_count":11,"is_preprint":false},{"pmid":"12964869","id":"PMC_12964869","title":"Integration, expression and inheritance of transgenes in hexaploid oat (Avena sativa L.).","date":"2003","source":"Journal of plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/12964869","citation_count":10,"is_preprint":false},{"pmid":"20555435","id":"PMC_20555435","title":"Development of oat-based markers from barley and wheat microsatellites.","date":"2010","source":"Genome","url":"https://pubmed.ncbi.nlm.nih.gov/20555435","citation_count":10,"is_preprint":false},{"pmid":"26455400","id":"PMC_26455400","title":"Identification of a new oat β-amylase by functional proteomics.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/26455400","citation_count":10,"is_preprint":false},{"pmid":"39059252","id":"PMC_39059252","title":"Ultrasonic extraction and antioxidant evaluation of oat saponins.","date":"2024","source":"Ultrasonics sonochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39059252","citation_count":9,"is_preprint":false},{"pmid":"36432463","id":"PMC_36432463","title":"Narrative Review on the Effects of Oat and Sprouted Oat Components on Blood Pressure.","date":"2022","source":"Nutrients","url":"https://pubmed.ncbi.nlm.nih.gov/36432463","citation_count":9,"is_preprint":false},{"pmid":"36483968","id":"PMC_36483968","title":"Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids.","date":"2022","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/36483968","citation_count":9,"is_preprint":false},{"pmid":"35892210","id":"PMC_35892210","title":"The inhibition of intestinal glucose absorption by oat-derived avenanthramides.","date":"2022","source":"Journal of food biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35892210","citation_count":9,"is_preprint":false},{"pmid":"28335393","id":"PMC_28335393","title":"Solvent Retention Capacities of Oat Flour.","date":"2017","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/28335393","citation_count":9,"is_preprint":false},{"pmid":"30263799","id":"PMC_30263799","title":"Physiochemical properties and probiotic survivability of symbiotic oat-based beverage.","date":"2017","source":"Food science and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/30263799","citation_count":9,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":46323,"output_tokens":890,"usd":0.07616,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6672,"output_tokens":781,"usd":0.026443,"stage2_stop_reason":"end_turn"},"total_usd":0.102603,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking through the abstracts, I need to identify papers about the canonical human/mammalian gene OAT (ornithine aminotransferase, also known as HOGA).\n\nMost papers are about:\n- Oat (Avena sativa) cereal grain biology\n- Organic Anion Transporters (SLC22 family)\n- Oat cell carcinoma (histological tumor type)\n- Fungal HogA/SakA MAPK pathways\n\nThe query gene is **OAT = ornithine aminotransferase** (HGNC symbol OAT, alias HOGA). Let me search for papers specifically about this enzyme.\n\n**Paper [51]** — \"The ornithine aminotransferase (OAT) locus: analysis of RFLPs in gyrate atrophy\" (PMID: 2893548) — This is directly about the human OAT gene (ornithine aminotransferase). It discusses the structural gene mapped to chromosome 10, RFLPs, and linkage to gyrate atrophy. This is genetic mapping/linkage, not mechanistic biochemistry, but it does confirm OAT deficiency causes gyrate atrophy.\n\n**Paper [25]** — \"Biological Roles of Ornithine Aminotransferase (OAT) in Plant Stress Tolerance\" (PMID: 30469329) — This is about plant OAT (ornithine aminotransferase), which is an ortholog. It describes OAT as producing pyrroline-5-carboxylate (P5C) from ornithine in mitochondria, functioning in an alternative proline metabolic pathway. This is a review, but contains mechanistic claims about the enzyme's biochemistry.\n\nOnly paper [51] is clearly about the human OAT gene with experimental data. Paper [25] is a review about plant OAT orthologs.\n\nThe mechanistic content from [51] is primarily genetic (RFLP mapping, linkage to disease), not direct biochemical mechanism experiments.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1988,\n      \"finding\": \"The OAT structural gene (ornithine aminotransferase) maps to human chromosome 10 (not the X chromosome, where related sequences also reside), and RFLP analysis demonstrates concordant segregation of the OAT locus with gyrate atrophy of the choroid and retina in a pedigree, with significant allelic disequilibrium between OAT haplotypes and gyrate atrophy chromosomes, providing genetic evidence that a defect in the OAT structural gene causes this autosomal recessive disorder.\",\n      \"method\": \"RFLP analysis using noncoding single-copy probes and cDNA subclones from the OAT gene; pedigree linkage analysis; chromosomal mapping\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal RFLP-based linkage and disequilibrium analysis in human pedigree, single study but multiple RFLP markers used; establishes gene-disease relationship but does not reconstitute enzymatic mechanism\",\n      \"pmids\": [\"2893548\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"OAT (ornithine aminotransferase) is a mitochondrial enzyme whose structural gene maps to human chromosome 10; loss-of-function mutations in OAT cause gyrate atrophy of the choroid and retina, established by genetic linkage and allelic disequilibrium analysis, though direct in vitro reconstitution or structural characterization of the human enzyme is not represented in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"OAT (ornithine aminotransferase) is the structural gene whose loss of function causes gyrate atrophy of the choroid and retina, an autosomal recessive disorder, as established by genetic linkage and allelic disequilibrium analysis in a human pedigree [#0]. The gene maps to human chromosome 10, distinct from related sequences residing on the X chromosome [#0]. Beyond this gene-disease mapping [#0], the enzymatic mechanism, substrate specificity, and structural characterization of the human protein are not represented in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1988,\n      \"claim\": \"Before this work it was unclear which locus harbored the causative defect for gyrate atrophy and whether the OAT structural gene resided on chromosome 10 or the X chromosome where related sequences also map; the study answered this by demonstrating co-segregation and allelic disequilibrium tying the chromosome 10 OAT gene to the disease.\",\n      \"evidence\": \"RFLP analysis with noncoding single-copy probes and cDNA subclones, pedigree linkage, and chromosomal mapping in human families\",\n      \"pmids\": [\"2893548\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not reconstitute or characterize OAT enzymatic activity in vitro\",\n        \"Does not identify the specific causative mutations or their effect on protein function\",\n        \"No structural model of the human enzyme established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The catalytic mechanism, substrate specificity, subcellular handling, and structural basis of disease-causing mutations of human OAT remain uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct in vitro enzymatic reconstitution captured\",\n        \"No structural characterization of the human enzyme captured\",\n        \"Genotype-phenotype mechanism linking specific mutations to disease not resolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"loss","faith_supported":2,"faith_total":3,"faith_pct":66.66666666666667}}