get_transcript
Retrieve detailed genetic information for a specific Ensembl transcript ID from the gnomAD database, including variant data and population genetics insights.
Instructions
Get information about a specific transcript
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| transcript_id | Yes | Ensembl transcript ID (e.g., ENST00000269305) | |
| reference_genome | No | Reference genome | GRCh38 |
Implementation Reference
- src/index.ts:689-695 (handler)The main handler function for the 'get_transcript' tool. It parses the input arguments, makes a GraphQL request using the predefined query, and formats the response.case "get_transcript": result = await makeGraphQLRequest(QUERIES.getTranscript, { transcriptId: args.transcript_id as string, referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"), }); formattedResult = result.data?.transcript || null; break;
- src/index.ts:216-252 (schema)GraphQL query schema definition for fetching transcript details including location, gene info, and gnomAD constraint metrics.getTranscript: ` query GetTranscript($transcriptId: String!, $referenceGenome: ReferenceGenomeId!) { transcript(transcript_id: $transcriptId, reference_genome: $referenceGenome) { transcript_id transcript_version reference_genome chrom start stop strand gene_id gene_symbol gene_version gnomad_constraint { exp_lof exp_mis exp_syn obs_lof obs_mis obs_syn oe_lof oe_lof_lower oe_lof_upper oe_mis oe_mis_lower oe_mis_upper oe_syn oe_syn_lower oe_syn_upper lof_z mis_z syn_z pLI } } } `,
- src/index.ts:507-525 (registration)Tool registration in the ListTools handler, defining name, description, and input schema for validation.{ name: "get_transcript", description: "Get information about a specific transcript", inputSchema: { type: "object", properties: { transcript_id: { type: "string", description: "Ensembl transcript ID (e.g., ENST00000269305)", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, required: ["transcript_id"], }, },
- src/index.ts:510-524 (schema)Input schema for the get_transcript tool, specifying required transcript_id and optional reference_genome.inputSchema: { type: "object", properties: { transcript_id: { type: "string", description: "Ensembl transcript ID (e.g., ENST00000269305)", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, required: ["transcript_id"], },