CATVariant documentation
Read CATVariant documentation for AlphaMissense, REVEL, ClinVar, gnomAD, 3D protein structure, hotspot analysis, literature evidence, and API access.
Sequence variant analysis
CATVariant documents workflows for analyzing genetic variants and mutations in protein-coding genes. Start with a gene symbol, UniProt accession, protein sequence, PDB or mmCIF structure, or a custom list of variants.
Protein variant analysis
Guidance covers protein accessions, gene names, amino acid substitutions, full-protein analyses, and variant-level evidence summaries. Public reports connect sequence changes to protein structure and biological context.
Missense variant interpretation
Documentation names the computational predictors used for missense review, including AlphaMissense, REVEL, CADD, ESM1b, SIFT, PolyPhen-2, MetaLR, MetaSVM, MutPred, EVE, PhyloP, and splicing tools such as SpliceAI and Pangolin. The prioritization score is reported on a 0–1 scale and should be interpreted separately from clinical classifications.
Structure context
CATVariant maps variants to 3D protein structures and reports structural neighborhoods using an 8 Å distance rule. Hotspot analysis uses minimums of 5 residues and 10 variants, and interaction-network analysis adds residue-level context when available.
Population evidence
Guidance includes gnomAD population frequencies, ancestry and biological-sex context when available, and the distinction between population evidence and computational prediction scores.
Clinical evidence
Documentation summarizes ClinVar clinical annotations, disease and phenotype associations, and interpretation support. ClinVar classifications are kept distinct from AlphaMissense, REVEL, CADD, and other computational predictions; CATVariant is not a standalone clinical diagnosis.
Literature evidence
CATVariant includes published literature and citation context for variant and protein evidence review, alongside experimental measurements and MaveDB evidence when present.
API and programmatic access
Documentation covers public result endpoints and programmatic access to analysis outputs, including gene pages, variant pages, compact result indexes, evidence summaries, and links to the stable CATVariant URLs.