rare-disease-consult
A Claude Code plugin that runs a structured rare-disease diagnostic consultation. Claude does a guided interview about your symptoms, looks them up in two free medical databases (HPO and PubMed), and produces a ranked top-5 list of possible diagnoses with citations you can verify.
What it does
This plugin runs a single Claude session end-to-end on a rare-disease case, with access to two open public medical databases:
- HPO (Human Phenotype Ontology) — a standardized vocabulary of medical signs and symptoms
- PubMed — the NIH medical-literature database (~35 million articles)
Claude does a structured interview to gather your symptoms, history, and what's already been tried or ruled out, looks up which rare diseases match your symptoms, searches PubMed for similar published case reports, and produces a top-5 list with concrete citations.
Quick install
In a Claude Code session, paste this and press enter:
Please install the rare-disease-consult plugin from https://github.com/fryanpan/rare-disease-consult-plugin. Follow the instructions in its AGENT_INSTALL.md file.
Claude handles the safety disclaimer, prerequisite checks, clone, and registration. After restart, run /rare-disease-consult:consult.
Currently Claude Code only — Cowork support is planned. For the manual install or first-run troubleshooting, see Installation below.
How it works
There are four phases:
- Intake. Claude has an open-ended conversation to gather your symptoms, history, family history, and what's already been tried or ruled out.
- Summary. Claude composes a structured clinical summary and shows it to you to confirm before going further.
- Analysis. Claude looks up your symptoms in HPO, queries PubMed for similar published case reports, and synthesizes a top-5 list of candidate rare diseases. Each candidate is required to have concrete citations (HPO codes, PubMed IDs, or URLs); candidates without grounding are dropped. An average run makes ~23 tool calls per case.
- Output. A single document with three pieces:
- Top-5 summary table at the top — 10-second skim for you or a doctor.
- Per-diagnosis sections with what fits your picture, what doesn't, citations, and tests or specialists to discuss.
- Consolidated source list at the bottom so any single citation can be verified in one place.
Benchmark results
On a benchmark of 371 cases the model couldn't have memorized — published after Claude's training data was frozen, with safeguards against looking up the answer at runtime — this workflow scored about 76% Top-1 / 84% Top-5 (vs ~26% for a general physician at first visit). The improvement is statistically significant vs Claude without tools (47.7%) and Claude with thinking but no tools (54.9%).
One important caveat: agent runs vary run-to-run. A 25-case re-run under identical conditions agreed with itself on only 72% of cases. Read the tools number as "mid-to-high 70s," not as a precise 76%.
See Benchmark provenance below for the full methodology.
How to use this responsibly
This plugin helps with one step in a long medical journey — not the whole journey. If your symptoms have been hard to pin down, a structured differential from this tool can give you something concrete to walk into a doctor's office with. That's the use case. It isn't more than that.
What this tool is FOR
- A starting point for an informed conversation with your doctor. Walking in with "I've been wondering about Disease X — does that fit my picture?" is more productive than "I have these symptoms, what is it?"
- Help finding the right type of specialist to see. If the differential keeps surfacing immunology candidates, that's a signal to consider an immunologist over a general internist.
- A second-opinion-style sanity check when you've been told "we don't know" or "it's probably nothing" and your gut says otherwise.
What it is NOT
- Not medical advice. Only a physician can diagnose. Only a physician can prescribe, order tests, or rule things out responsibly.
- Not a substitute for urgent care. If you have red-flag symptoms (chest pain, stroke signs, sudden severe headache, sepsis features, etc.), go to the ER. The skill has a safety check that redirects, but don't rely on it as a triage layer.
- Not a treatment recommender. The skill never recommends starting, stopping, or changing medications. If it points at a condition, the next step is a doctor — not a supplement or off-label medication.
Risks worth taking seriously
Even when the tool surfaces a plausible-looking differential, several failure modes can hurt you:
