Cortexa research tool·genomics·biothings

MyVariant Get Pathogenicity Scores

Get comprehensive pathogenicity prediction scores for a variant from dbNSFP. Returns REVEL, CADD, AlphaMissense, SIFT, PolyPhen-2, MetaRNN, GERP, PhyloP, and PhastCons scores in a single call. Use this when MyVariant_query_variants does not return dbnsfp data, or when you specifically need REVEL/AlphaMissense scores for ACMG PP3/BP4 classification.

Livelast probed 2026-04-30 23:07Z· 110msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 110ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "fields": {
      "default": "dbnsfp.revel.score,dbnsfp.cadd.phred,dbnsfp.alphamissense.score,dbnsfp.alphamissense.pred,dbnsfp.sift.score,dbnsfp.sift.pred,dbnsfp.polyphen2_hdiv.score,dbnsfp.polyphen2_hdiv.pred,dbnsfp.metarnn.score,dbnsfp.metarnn.pred,dbnsfp.gerp_rs,dbnsfp.phylop100way_vertebrate.rankscore,dbnsfp.phastcons100way_vertebrate.rankscore,dbnsfp.vest4.score,dbnsfp.mutationtaster.pred,clinvar.rcv.clinical_significance,dbsnp.rsid",
      "description": "Fields to return (pre-configured for pathogenicity scores)",
      "type": "string"
    },
    "variant_id": {
      "description": "Variant ID: rsID (e.g., rs45478192) or HGVS genomic (e.g., chr16:g.23635348A>C). Both formats work.",
      "type": "string"
    }
  },
  "required": [
    "variant_id"
  ],
  "type": "object"
}

Examples (1)

Default MyVariant Get Pathogenicity Scores call

public-safeinput

{
  "variant_id": ""
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_MyVariant_get_pathogenicity_scores
Tool name: MyVariant_get_pathogenicity_scores
Added: 2026-04-30 22:47Z
Tags: tooluniverse

MyVariant Get Pathogenicity Scores

Livelast probed 2026-04-30 23:07Z· 110msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "fields": { "default": "dbnsfp.revel.score,dbnsfp.cadd.phred,dbnsfp.alphamissense.score,dbnsfp.alphamissense.pred,dbnsfp.sift.score,dbnsfp.sift.pred,dbnsfp.polyphen2_hdiv.score,dbnsfp.polyphen2_hdiv.pred,dbnsfp.metarnn.score,dbnsfp.metarnn.pred,dbnsfp.gerp_rs,dbnsfp.phylop100way_vertebrate.rankscore,dbnsfp.phastcons100way_vertebrate.rankscore,dbnsfp.vest4.score,dbnsfp.mutationtaster.pred,clinvar.rcv.clinical_significance,dbsnp.rsid", "description": "Fields to return (pre-configured for pathogenicity scores)", "type": "string" }, "variant_id": { "description": "Variant ID: rsID (e.g., rs45478192) or HGVS genomic (e.g., chr16:g.23635348A>C). Both formats work.", "type": "string" } }, "required": [ "variant_id" ], "type": "object" }