variant_searcher

Instructions

Search MyVariant.info for genetic variant DATABASE RECORDS.

⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy!

Important: This searches for variant DATABASE RECORDS (frequency, significance, etc.),
NOT articles about variants. For articles about variants, use article_searcher.

Searches the comprehensive variant database including:
- Population frequencies (gnomAD, 1000 Genomes, etc.)
- Clinical significance (ClinVar)
- Functional predictions (SIFT, PolyPhen, CADD)
- Gene and protein consequences

Search by various identifiers or filter by clinical/functional criteria.

Input Schema

Name	Required	Description
`cadd_score_min`	No	Minimum CADD score for pathogenicity
`consequence`	No	Variant consequence (e.g., 'missense_variant')
`frequency_max`	No	Maximum allele frequency
`frequency_min`	No	Minimum allele frequency
`gene`	No	Gene symbol (e.g., 'BRAF', 'TP53')
`hgvs`	No	HGVS notation (genomic, coding, or protein)
`hgvsc`	No	Coding sequence change (e.g., 'c.1799T>A')
`hgvsp`	No	Protein change in HGVS format (e.g., 'p.V600E')
`include_cbioportal`	No	Include cBioPortal cancer genomics summary when searching by gene
`page`	No	Page number (1-based)
`page_size`	No	Results per page
`polyphen_prediction`	No	PolyPhen-2 functional prediction
`region`	No	Genomic region (e.g., 'chr7:140753336-140753337')
`rsid`	No	dbSNP rsID (e.g., 'rs113488022')
`sift_prediction`	No	SIFT functional prediction
`significance`	No	Clinical significance filter

Input Schema (JSON Schema)

{
  "properties": {
    "cadd_score_min": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Minimum CADD score for pathogenicity",
      "title": "Cadd Score Min"
    },
    "consequence": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Variant consequence (e.g., 'missense_variant')",
      "title": "Consequence"
    },
    "frequency_max": {
      "anyOf": [
        {
          "maximum": 1,
          "minimum": 0,
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Maximum allele frequency",
      "title": "Frequency Max"
    },
    "frequency_min": {
      "anyOf": [
        {
          "maximum": 1,
          "minimum": 0,
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Minimum allele frequency",
      "title": "Frequency Min"
    },
    "gene": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Gene symbol (e.g., 'BRAF', 'TP53')",
      "title": "Gene"
    },
    "hgvs": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGVS notation (genomic, coding, or protein)",
      "title": "Hgvs"
    },
    "hgvsc": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Coding sequence change (e.g., 'c.1799T>A')",
      "title": "Hgvsc"
    },
    "hgvsp": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Protein change in HGVS format (e.g., 'p.V600E')",
      "title": "Hgvsp"
    },
    "include_cbioportal": {
      "default": true,
      "description": "Include cBioPortal cancer genomics summary when searching by gene",
      "title": "Include Cbioportal",
      "type": "boolean"
    },
    "page": {
      "default": 1,
      "description": "Page number (1-based)",
      "minimum": 1,
      "title": "Page",
      "type": "integer"
    },
    "page_size": {
      "default": 10,
      "description": "Results per page",
      "maximum": 100,
      "minimum": 1,
      "title": "Page Size",
      "type": "integer"
    },
    "polyphen_prediction": {
      "anyOf": [
        {
          "enum": [
            "probably_damaging",
            "possibly_damaging",
            "benign"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "PolyPhen-2 functional prediction",
      "title": "Polyphen Prediction"
    },
    "region": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region (e.g., 'chr7:140753336-140753337')",
      "title": "Region"
    },
    "rsid": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "dbSNP rsID (e.g., 'rs113488022')",
      "title": "Rsid"
    },
    "sift_prediction": {
      "anyOf": [
        {
          "enum": [
            "deleterious",
            "tolerated"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "SIFT functional prediction",
      "title": "Sift Prediction"
    },
    "significance": {
      "anyOf": [
        {
          "enum": [
            "pathogenic",
            "likely_pathogenic",
            "uncertain_significance",
            "likely_benign",
            "benign",
            "conflicting"
          ],
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Clinical significance filter",
      "title": "Significance"
    }
  },
  "title": "variant_searcherArguments",
  "type": "object"
}

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Input Schema

Input Schema (JSON Schema)

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