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The Sequence Types and Features Ontology (SO) is downloaded weekly from the SourceForge CVS repository at For more information about this ontology, see the Sequence Ontology Home Page at

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Accession:SO:0002008 term browser browse the term
Definition:A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid.
Comment:Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
Synonyms:exact_synonym: Jannovar:rare_amino_acid_variant;   rare amino acid variant;   snpEff:RARE_AMINO_ACID

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  SO ontology 0
    sequence_variant 0
      structural_variant 0
        feature_variant 0
          gene_variant 0
            transcript_variant 0
              coding_transcript_variant 0
                coding_sequence_variant 0
                  protein_altering_variant 0
                    inframe_variant 0
                      nonsynonymous_variant 0
                        missense_variant 0
                          non_conservative_missense_variant 0
                            rare_amino_acid_variant 0
                              pyrrolysine_loss 0
                              selenocysteine_loss 0
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