get_variants_in_gene
Retrieve all genetic variants within a specific gene from the gnomAD database to analyze mutation patterns and population frequencies.
Instructions
Get all variants in a specific gene
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene_id | No | Ensembl gene ID | |
| gene_symbol | No | Gene symbol | |
| dataset | No | Dataset ID | gnomad_r4 |
| reference_genome | No | Reference genome | GRCh38 |
Implementation Reference
- src/index.ts:676-687 (handler)Handler logic for the 'get_variants_in_gene' tool: validates input, constructs GraphQL query parameters, executes the query via makeGraphQLRequest, and extracts variants from the response.
case "get_variants_in_gene": if (!args.gene_id && !args.gene_symbol) { throw new Error("Either gene_id or gene_symbol must be provided"); } result = await makeGraphQLRequest(QUERIES.getVariantsInGene, { geneId: (args.gene_id as string) || null, geneSymbol: (args.gene_symbol as string) || null, datasetId: parseDatasetId((args.dataset as string) || "gnomad_r4"), referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"), }); formattedResult = result.data?.gene?.variants || []; break; - src/index.ts:188-214 (schema)GraphQL query schema for fetching variants in a gene, defining the input parameters and output fields.
getVariantsInGene: ` query GetVariantsInGene($geneId: String, $geneSymbol: String, $datasetId: DatasetId!, $referenceGenome: ReferenceGenomeId!) { gene(gene_id: $geneId, gene_symbol: $geneSymbol, reference_genome: $referenceGenome) { variants(dataset: $datasetId) { variant_id pos rsids consequence hgvsc hgvsp lof exome { ac an af filters } genome { ac an af filters } } } } `, - src/index.ts:483-505 (schema)Input schema definition for the 'get_variants_in_gene' tool, specifying parameters and their types/descriptions.
inputSchema: { type: "object", properties: { gene_id: { type: "string", description: "Ensembl gene ID", }, gene_symbol: { type: "string", description: "Gene symbol", }, dataset: { type: "string", description: "Dataset ID", default: "gnomad_r4", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, }, - src/index.ts:480-506 (registration)Tool registration entry in the ListTools response, including name, description, and input schema.
{ name: "get_variants_in_gene", description: "Get all variants in a specific gene", inputSchema: { type: "object", properties: { gene_id: { type: "string", description: "Ensembl gene ID", }, gene_symbol: { type: "string", description: "Gene symbol", }, dataset: { type: "string", description: "Dataset ID", default: "gnomad_r4", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, }, },