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 functional annotations at a specific amino acid position from ProtVar. Returns annotated UniP…

ProtVar_get_function tool specification

Tool Information:

  • Name: ProtVar_get_function

  • Type: ProtVarFunctionTool

  • Description: Get functional annotations at a specific amino acid position from ProtVar. Returns annotated UniProt features overlapping that position (domains, active sites, binding sites, PTMs), the protein’s function description, and structural context. Use to understand the biological importance of a variant site before interpreting pathogenicity scores. Example: P04637 position 175 returns DNA-binding domain overlap and TP53 tumor suppressor function.

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). Optional but recommended.

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 get pathogenicity predictions (AlphaMissen…

ProtVar_map_variant tool specification

Tool Information:

  • Name: ProtVar_map_variant

  • Type: ProtVarTool

  • Description: Map a human protein variant to genomic coordinates and get pathogenicity predictions (AlphaMissense, EVE, ESM, conservation). Accepts three input formats: (1) protein ‘ACCESSION CHANGE’ e.g. ‘P04637 R175H’; (2) dbSNP rsID e.g. ‘rs1799966’; (3) VCF-style genomic ‘chr17 43057065 . T G’. Returns isoform mappings, consequence type, and variant effect scores.

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.

Example Usage:

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