Retrieve UniProt Natural Variants by Identifier

Retrieve natural variant annotations by UniProt accession, dbSNP identifier, or HGVS expression.

Usage

rba_uniprot_variation(
  id,
  id_type,
  source_type = NULL,
  consequence_type = NULL,
  wild_type = NULL,
  alternative_sequence = NULL,
  location = NULL,
  save_peff = FALSE,
  ...
)

Arguments

id

Character: A single identifier: either a UniProt primary or secondary accession, an NIH-NCBI dbSNP ID, or an HGVS expression.

id_type

Character: The type of supplied ID argument, one of: "uniprot", "dbsnp" or "hgvs".

source_type

Character: (optional) Variation's source type. You can choose up to two of: "uniprot", "large scale study", "mixed", "clinvar", "nci-tcga", "cosmic curated", "ensembl", "gnomad", "topmed", or "exac".

consequence_type

Character: (optional) Variation's consequence type. You can choose up to two of: "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.

save_peff

Logical or Character: (default = FALSE)

FALSE: Return the parsed JSON response.
TRUE: Save as PEFF file 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

If save_peff = FALSE, a list. For id_type = "uniprot", it represents the requested entry; for "dbsnp" or "hgvs", each element represents a matching entry and is named by accession when available. If PEFF output is requested, the response is written to disk and returned as a character string.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/{dbid}"
"GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/{hgvs}"
"GET https://www.ebi.ac.uk/proteins/api/variation/{accession}"

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(id = "rs121434451", id_type = "dbsnp")
# }
# \donttest{
rba_uniprot_variation(id = "NC_000008.11:g.22119227C>T", id_type = "hgvs")
# }
# \donttest{
rba_uniprot_variation(id = "O43593", id_type = "uniprot")
# }