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);
  }

AlphaGenome MCP Server