Protvar Tools#

Configuration File: protvar_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the protvar_tools.json configuration file.

Available Tools#

ProtVar_get_function (Type: ProtVarFunctionTool)#

Get the functional, structural, interaction, and predictive annotations returned by ProtVar at a …

ProtVar_get_function tool specification

Tool Information:

  • Name: ProtVar_get_function

  • Type: ProtVarFunctionTool

  • Description: Get the functional, structural, interaction, and predictive annotations returned by ProtVar at a specific amino acid position. Includes UniProt features/comments, gene and database references, predicted pockets and protein interactions, conservation/ESM/EVE/PopEVE scores, FoldX predictions, and M3D predictions when available. Example: P04637 position 175 returns DNA-binding annotations and structural/predictive context.

Parameters:

  • accession (string) (required) UniProt accession (e.g. ‘P04637’ for TP53).

  • position (integer) (required) Amino acid position in the protein (1-based).

  • variant_aa (string) (optional) Single-letter code for the variant amino acid (e.g. ‘H’ for histidine). Supply this to retrieve mutation-specific ESM, EVE, PopEVE, FoldX, and M3D predictions; without it ProtVar returns only position-level context.

Example Usage:

query = {
    "name": "ProtVar_get_function",
    "arguments": {
        "accession": "example_value",
        "position": 10
    }
}
result = tu.run(query)

ProtVar_get_population (Type: ProtVarPopulationTool)#

Get the known variants at a protein position from ProtVar’s population observations: one row per …

ProtVar_get_population tool specification

Tool Information:

  • Name: ProtVar_get_population

  • Type: ProtVarPopulationTool

  • Description: Get the known variants at a protein position from ProtVar’s population observations: one row per amino-acid change with its consequence, clinical significance (ClinVar/UniProt/Ensembl), population allele frequencies (gnomAD, ClinVar MAF), SIFT/PolyPhen predictions, associated diseases and cross-references. Only accession and position are needed.

Parameters:

  • accession (string) (required) UniProt accession (e.g. ‘P22304’ for IDS).

  • position (integer) (required) Amino acid position in the protein (1-based).

  • genomic_location (integer) (optional) Optional genomic coordinate (GRCh38); ProtVar answers for the whole protein position without it.

Example Usage:

query = {
    "name": "ProtVar_get_population",
    "arguments": {
        "accession": "example_value",
        "position": 10
    }
}
result = tu.run(query)

ProtVar_map_variant (Type: ProtVarTool)#

Map a human protein variant to genomic coordinates and retrieve computational variant-effect pred…

ProtVar_map_variant tool specification

Tool Information:

  • Name: ProtVar_map_variant

  • Type: ProtVarTool

  • Description: Map a human protein variant to genomic coordinates and retrieve computational variant-effect predictions. AlphaMissense/EVE/ESM/PopEVE/CADD outputs are explicitly labeled as model predictions, not clinical classifications, and AlphaMissense class thresholds are returned with each prediction.

Parameters:

  • variant (string) (required) Variant identifier in one of three formats: (1) ‘UniProtAccession SingleLetterChange’ e.g. ‘P04637 R175H’ (TP53 R175H); (2) dbSNP rsID e.g. ‘rs1799966’; (3) VCF genomic ‘chr17 43057065 . REF ALT’. Note: colon-separated ‘chr:pos:ref:alt’ is auto-converted to VCF format.

  • assembly (string) (optional) Genome assembly used for genomic input and output coordinates.

Example Usage:

query = {
    "name": "ProtVar_map_variant",
    "arguments": {
        "variant": "example_value"
    }
}
result = tu.run(query)