clinvar_variants: Fetch ClinVar variants for a gene and parse them into...

In rtemis.a3: Amino Acid Annotation (A3) Format

Fetch ClinVar variants for a gene and parse them into A3Variant objects

Description

Queries the NCBI ClinVar database via E-utilities for all variants associated with a gene, and returns those with protein-level amino acid changes as a named list of A3Variant objects.

Usage

clinvar_variants(
  gene,
  significance = c("pathogenic", "likely_pathogenic"),
  max_variants = 500L,
  esearch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
  esummary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi",
  batch_size = 500L,
  verbosity = 1L
)

Arguments

gene	Character scalar: HGNC gene symbol, e.g. "MAPT".
significance	Character vector: Clinical significance filter. Any combination of "pathogenic", "likely_pathogenic", "uncertain_significance", "likely_benign", "benign". Pass NULL to fetch all records regardless of significance.
max_variants	Integer scalar: Maximum number of ClinVar records to fetch after filtering. Defaults to 500L.
esearch_url	Character scalar: NCBI E-utilities esearch endpoint.
esummary_url	Character scalar: NCBI E-utilities esummary endpoint.
batch_size	Integer scalar: Number of UIDs per esummary request. NCBI recommends no more than 500 per request.
verbosity	Integer scalar: Verbosity level.

Details

Variants without a parseable protein change (intronic, regulatory, etc.) are silently skipped.

Value

Named list of A3Variant objects. Names use ⁠{from}{position}{to}⁠ notation (e.g. "R406W"), with a numeric suffix to disambiguate duplicates.

Author(s)

EDG

Examples

# Requires internet connection and fetches data from ClinVar.
## Not run: 
# Pathogenic and likely pathogenic variants (default)
mapt_variants <- clinvar_variants("MAPT")
# All variants regardless of significance
mapt_all <- clinvar_variants("MAPT", significance = NULL)

## End(Not run)

rtemis.a3 documentation built on April 29, 2026, 1:06 a.m.