predict_splice_impact
Analyzes genetic variants to predict their impact on splicing, including splice sites and junctions, for investigating splicing alterations in genomic data.
Instructions
Focus on splicing-specific effects only.
Analyzes splice sites, splice site usage, and splice junctions.
Perfect for: investigating splicing variants, understanding splice alterations.
Example: "Analyze splicing impact of chr6:41129252C>T"
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chromosome | Yes | ||
| position | Yes | ||
| ref | Yes | ||
| alt | Yes | ||
| tissue_type | No |
Implementation Reference
- src/index.ts:168-174 (handler)MCP CallTool request handler for 'predict_splice_impact': validates input using variantPredictionSchema, calls AlphaGenomeClient.predictSpliceImpact(), and returns JSON-formatted result as text content.
case 'predict_splice_impact': { const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams; const result = await getClient().predictSpliceImpact(params); return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }], }; } - src/tools.ts:290-310 (schema)Tool schema definition for 'predict_splice_impact' including name, description, and inputSchema with properties for chromosome, position, ref, alt, and optional tissue_type.
export const PREDICT_SPLICE_IMPACT_TOOL: Tool = { name: 'predict_splice_impact', description: `Focus on splicing-specific effects only. Analyzes splice sites, splice site usage, and splice junctions. Perfect for: investigating splicing variants, understanding splice alterations. Example: "Analyze splicing impact of chr6:41129252C>T"`, inputSchema: { type: 'object', properties: { chromosome: { type: 'string', pattern: '^chr([1-9]|1[0-9]|2[0-2]|X|Y)$' }, position: { type: 'number', minimum: 1 }, ref: { type: 'string', pattern: '^[ATGCatgc]+$' }, alt: { type: 'string', pattern: '^[ATGCatgc]+$' }, tissue_type: { type: 'string' }, }, required: ['chromosome', 'position', 'ref', 'alt'], }, }; - src/index.ts:99-101 (registration)MCP ListTools request handler that returns ALL_TOOLS array containing PREDICT_SPLICE_IMPACT_TOOL.
server.setRequestHandler(ListToolsRequestSchema, async () => { return { tools: ALL_TOOLS }; }); - src/tools.ts:709-730 (registration)ALL_TOOLS array includes PREDICT_SPLICE_IMPACT_TOOL at position 6 (line 715), used for tool listing.
export const ALL_TOOLS: Tool[] = [ PREDICT_VARIANT_TOOL, BATCH_SCORE_TOOL, ASSESS_PATHOGENICITY_TOOL, PREDICT_TISSUE_SPECIFIC_TOOL, COMPARE_VARIANTS_TOOL, PREDICT_SPLICE_IMPACT_TOOL, PREDICT_EXPRESSION_IMPACT_TOOL, ANALYZE_GWAS_LOCUS_TOOL, COMPARE_ALLELES_TOOL, BATCH_TISSUE_COMPARISON_TOOL, PREDICT_TF_BINDING_IMPACT_TOOL, PREDICT_CHROMATIN_IMPACT_TOOL, COMPARE_PROTECTIVE_RISK_TOOL, BATCH_PATHOGENICITY_FILTER_TOOL, COMPARE_VARIANTS_SAME_GENE_TOOL, PREDICT_ALLELE_SPECIFIC_EFFECTS_TOOL, ANNOTATE_REGULATORY_CONTEXT_TOOL, BATCH_MODALITY_SCREEN_TOOL, GENERATE_VARIANT_REPORT_TOOL, EXPLAIN_VARIANT_IMPACT_TOOL, ]; - src/alphagenome-client.ts:280-292 (helper)AlphaGenomeClient method predictSpliceImpact that bridges to Python by calling callPythonBridge with action 'predict_splice_impact' and variant parameters.
async predictSpliceImpact(params: VariantPredictionParams): Promise<any> { try { return await this.callPythonBridge('predict_splice_impact', { chromosome: params.chromosome, position: params.position, ref: params.ref, alt: params.alt, tissue_type: params.tissue_type, }); } catch (error) { if (error instanceof ApiError) throw error; throw new ApiError(`Splice impact prediction failed: ${error}`, 500); }