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tooluniverse-rare-disease-diagnosis

Map phenotypes to HPO terms and rank rare disease diagnoses.

Updated Apr 18, 2026
Search Tags:#rare-disease#variant-interpretation#phenotyping#hpo#gene-panel#orphanet
One-click install
npx skills add https://github.com/Centaurioun/osteogenesis_imperfecta --skill tooluniverse-rare-disease-diagnosis-centaurioun
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-rare-disease-diagnosis
Source: https://github.com/Centaurioun/osteogenesis_imperfecta/tree/main/.agents/skills/tooluniverse-rare-disease-diagnosis
Command: npx skills add https://github.com/Centaurioun/osteogenesis_imperfecta --skill tooluniverse-rare-disease-diagnosis-centaurioun

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Provides clinician-focused, evidence-graded diagnostic support for patients with suspected rare diseases by converting clinical descriptions into standardized phenotypes, matching those phenotypes to candidate diseases, prioritizing genes for testing, and interpreting genetic variants to produce actionable recommendations.

Core Features & Use Cases

  • Phenotype standardization: map free-text symptoms to HPO terms and classify core versus variable features.
  • Disease matching: search and cross-reference Orphanet and OMIM to generate a ranked differential diagnosis with ORPHA/OMIM identifiers.
  • Gene panel prioritization: extract and prioritize genes from candidate diseases using ClinGen validity, pLI/constraint scores, and expression evidence (GTEx, CELLxGENE).
  • Variant interpretation: aggregate ClinVar, gnomAD, CADD, AlphaMissense, EVE, SpliceAI and apply ACMG criteria with structured evidence.
  • Structure & literature analysis: optional AlphaFold2 structural assessment for VUS and PubMed/BioRxiv/OpenAlex searches to gather supporting studies.
  • Report-first workflow: produce a clinician-ready Markdown report, CSV gene panel, and variant interpretation table for handoff and documentation.

Quick Start

Generate a clinician-ready rare disease diagnostic report for a patient described as: 23-year-old with tall stature, long fingers, joint hypermobility, and aortic root dilation.

Frequently Asked Questions about tooluniverse-rare-disease-diagnosis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a differential diagnosis for a patient with suspected rare genetic diseases?▼

To generate a differential diagnosis for suspected rare diseases, map free-text clinical descriptions to standardized HPO terms, cross-reference Orphanet and OMIM databases, and produce a ranked list of candidate diseases with identifiers.

How do I prioritize genes for a rare disease testing panel using ClinGen and GTEx data?▼

Prioritize genes for a rare disease panel by extracting candidate genes from matched diseases, filtering by ClinGen validity, pLI constraint scores, and GTEx expression evidence to yield a structured CSV gene panel.

Can I use HPO phenotyping to interpret genetic variants according to ACMG criteria?▼

Yes, HPO phenotyping supports variant interpretation by aggregating ClinVar, gnomAD, CADD, AlphaMissense, EVE, and SpliceAI scores to apply ACMG criteria, producing a structured evidence table.

Does this rare disease diagnosis workflow integrate AlphaFold2 structure prediction for VUS analysis?▼

Yes, the rare disease diagnosis workflow integrates optional AlphaFold2 structural assessment for variants of uncertain significance (VUS) alongside PubMed, BioRxiv, and OpenAlex literature searches.

What is the best way to convert clinical descriptions into a clinician-ready rare disease diagnostic report?▼

The best way to convert clinical descriptions into a rare disease diagnostic report is through a report-first workflow that outputs clinician-ready Markdown reports, CSV gene panels, and variant interpretation tables for documentation.

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