get_protein_variants

Retrieve disease-associated variants and mutations for a protein using its UniProt accession number to analyze genetic variations.

Instructions

Disease-associated variants and mutations

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1261-1301 (handler)

The main handler function for the 'get_protein_variants' tool. Fetches protein data from UniProt API and extracts variant information including natural variants, mutagenesis sites, disease-associated variants, and polymorphisms.

private async handleGetProteinVariants(args: any) {
  if (!isValidProteinInfoArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid protein variants arguments');
  }

  try {
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format: 'json' },
    });

    const protein = response.data;
    const variantInfo = {
      accession: protein.primaryAccession,
      naturalVariants: protein.features?.filter((f: any) => f.type === 'Natural variant') || [],
      mutagenesisFeatures: protein.features?.filter((f: any) => f.type === 'Mutagenesis') || [],
      diseaseVariants: protein.features?.filter((f: any) =>
        f.type === 'Natural variant' && f.association?.disease
      ) || [],
      polymorphisms: protein.comments?.filter((c: any) => c.commentType === 'POLYMORPHISM') || [],
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(variantInfo, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching protein variants: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:536-544 (registration)

Tool registration in the ListToolsRequestSchema handler, including name, description, and input schema.

name: 'get_protein_variants',
description: 'Disease-associated variants and mutations',
inputSchema: {
  type: 'object',
  properties: {
    accession: { type: 'string', description: 'UniProt accession number' },
  },
  required: ['accession'],
},

src/index.ts:752-753 (registration)
Dispatch case in the CallToolRequestSchema switch statement that routes calls to the handler.
```
case 'get_protein_variants':
  return this.handleGetProteinVariants(args);
```

src/index.ts:79-89 (helper)

Input validation helper function used by get_protein_variants and other protein info tools.

const isValidProteinInfoArgs = (
  args: any
): args is { accession: string; format?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.accession === 'string' &&
    args.accession.length > 0 &&
    (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format))
  );
};

UniProt MCP Server