Search UniProt Natural Variants

Search and retrieve natural variants annotated on protein sequences, including variants imported from supported large-scale studies.

Usage

rba_uniprot_variation_search(
  accession = NULL,
  source_type = NULL,
  consequence_type = NULL,
  wild_type = NULL,
  alternative_sequence = NULL,
  location = NULL,
  disease = NULL,
  omim = NULL,
  evidence = NULL,
  taxid = NULL,
  db_type = NULL,
  db_id = NULL,
  save_peff = FALSE,
  ...
)

Arguments

accession

Character: (optional) UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

source_type

Character: (optional) Up to two variant source types: "uniprot", "large scale study", "mixed", "clinvar", "nci-tcga", "cosmic curated", "ensembl", "gnomad", "topmed", or "exac".

consequence_type

Character: (optional) Up to two consequence types: "missense", "stop gained", or "stop lost".

wild_type

Character: (optional) Wild-type amino acid. Accepted values are IUPAC single-letter amino acid codes and "*" for a stop codon. You can supply up to 20 values.

alternative_sequence

Character: (optional) Alternative amino acid. Accepted values are IUPAC single-letter amino acid codes, "*" for a stop codon, and "-" for a deletion. You can supply up to 20 values.

location

Character: (optional) A valid amino acid range (e.g. 10-25) within the sequence where the variation occurs.

disease

Character: (optional) Human disease associated with a sequence variation. Accepted values are a disease name (e.g. Alzheimer disease 18), partial disease name (Alzheimer), or disease acronym (e.g. AD).

omim

Character or Numeric: (optional) OMIM ID that is associated with a variation. You can supply up to 20 values.

evidence

Character or Numeric: (optional) PubMed ID of a variation's citation. You can supply up to 20 values.

taxid

Numeric: (optional) NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

db_type

Character: (optional) Cross-reference database of the variation. You can supply up to two values. Examples include "dbSNP", "cosmic curated", and "ClinVar".

db_id

Character: (optional) Variation identifier in a cross-reference database. You can supply up to 20 values.

save_peff

Logical or Character: (default = FALSE)

FALSE: Return the parsed JSON response.
TRUE: Save the PEFF response to an automatically generated path.
Character string: A valid file path to save the PEFF file.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

With save_peff = FALSE, a list named by UniProt accession. Each element contains one matching entry and its variants. Otherwise, the PEFF response is written to disk and returned as a character string.

Details

At least one primary criterion is required: accession, disease, omim, evidence, taxid, db_type, or db_id. The other arguments refine those criteria.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/variation"

References

The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010
Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237
Proteins API Documentation
Citations note on UniProt website

Examples

# \donttest{
rba_uniprot_variation_search(accession = "P05067")
# }
# \donttest{
rba_uniprot_variation_search(disease = "alzheimer disease, 18")
# }
# \donttest{
rba_uniprot_variation_search(disease = "alzheimer",
    wild_type = "A", alternative_sequence = "T")
# }