tooluniverse-variant-functional-annotation
This skill combines multiple authoritative databases to deliver protein-level variant annotation, mapping structural domains, conservation patterns, clinical classifications, and population allele frequencies. It's built for variant interpretation pipelines where you need functional evidence without full ACMG classification—use it to understand how a missense change affects protein structure and function.
tooluniverse-variant-functional-annotation annotates protein variants with structural impact, conservation, population frequency, and deleteriousness scoring.
AI-generated summary based on this skill's SKILL.md
Install
mims-harvard/ToolUniverse/tooluniverse-variant-functional-annotation · repository language: Python
git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-variant-functional-annotation ~/.claude/skills/tooluniverse-variant-functional-annotationFrequently asked questions
AI-generated answers based on this skill's SKILL.md and metadata
How do I annotate a protein variant like TP53 R175H with tooluniverse-variant-functional-annotation?
tooluniverse-variant-functional-annotation integrates ProtVar, ClinVar, gnomAD, and CADD to deliver comprehensive annotation. For TP53 R175H, the skill maps the amino acid change to structural domains, retrieves conservation scores, pulls population frequencies from gnomAD, and surfaces clinical classifications from ClinVar. You get functional context—domain location, predicted deleteriousness, and allele frequency—in a single output, ideal for understanding how the missense change affects protein structure and function.
What databases does tooluniverse-variant-functional-annotation use?
tooluniverse-variant-functional-annotation combines ClinVar for clinical significance, gnomAD for population allele frequencies, CADD for deleteriousness scoring, and ProtVar for protein-level structural and functional annotation. This multi-source integration lets you assess variant pathogenicity using conservation, location, frequency, and prediction data without needing to query each resource separately.
Can tooluniverse-variant-functional-annotation check if a variant is in a conserved domain?
Yes. tooluniverse-variant-functional-annotation annotates protein variants with structural and functional context, including whether the change falls within conserved domains. It combines conservation patterns with location data to help you understand the structural impact of missense variants and assess their likely functional consequence.
What's the functional impact of a missense variant according to this skill?
tooluniverse-variant-functional-annotation evaluates functional impact by combining multiple signals: conservation scores, domain location, CADD deleteriousness predictions, and clinical classifications from ClinVar. For missense variants, it maps the amino acid change to protein structure, shows whether it affects conserved regions, and retrieves population frequencies from gnomAD to contextualize rarity and predicted pathogenicity.
How does tooluniverse-variant-functional-annotation retrieve population frequencies?
tooluniverse-variant-functional-annotation queries gnomAD to retrieve population allele frequencies for your variant. These frequencies help assess variant rarity and are a key input for pathogenicity assessment—rare variants in conserved regions with high CADD scores are typically more likely to be deleterious than common variants.
Is tooluniverse-variant-functional-annotation a full ACMG classification tool?
No. tooluniverse-variant-functional-annotation is built for variant interpretation pipelines where you need functional evidence and structural context without full ACMG classification. It delivers protein-level annotation, conservation patterns, clinical classifications, and population frequencies—use it to understand how a missense change affects protein structure and function, then apply your own classification rules.
SKILL.md
rendered from the published skill — quoted content, verbatim
Protein Variant Functional Annotation
Comprehensive functional annotation of protein variants by combining ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies, CADD deleteriousness scoring, and ClinGen gene-disease validity.
Differentiation from tooluniverse-variant-interpretation: This skill focuses specifically on
protein-level functional evidence — structural mapping, residue context, protein domain impact,
and population allele frequencies. It does NOT produce full ACMG classifications or treatment
recommendations. Use tooluniverse-variant-interpretation for complete ACMG clinical classification.
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