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",
      },
    },
  },
},

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