Rare disease patients wait 5 to 7 years for a diagnosis. Usually not because the answer is unknowable, but because the clues are scattered. The cardiologist sees a thick heart wall. The nephrologist sees protein in the urine. A rheumatologist sees joint pain and writes down fibromyalgia. Nobody puts them on the same page. Rare Agents reads a clinical note and does four things. Claude rewrites the symptoms in medical vocabulary, so "burning pain in his hands" becomes "acroparesthesia," because that's the word the databases actually know. Each term gets matched to an official HPO code. Those codes get scored against rare disease profiles. Then it says what to do: order this gene panel, watch for this, here are the trials recruiting now. The rule I built everything around is that Claude reads, but it never decides. Only the first step uses a model, and it's forbidden from naming a disease. The rest is lookups and arithmetic, so it can't invent a symptom, a disease, or a gene. I benchmarked it on 669 real published patients. Right answer first 72% of the time, top three 91%. A dumb baseline gets 44%. I also ran Abridge's 25 routine encounters through it, obesity and prediabetes and physicals, and got zero false alarms. That matters more, because a tool that cries wolf gets switched off in a week. Tools like Mendelian's MendelScan already scan health records for rare disease, but they read structured fields. "He's never really sweated" never becomes a billing code. It only exists in the note. So I read the conversation instead. It doesn't replace a geneticist. It gets the patient to one years earlier.
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