Mutation Annotations

For a more inclusive definition of mutations that may be of interest, we have grouped mutations into the following categories using the Variant_Classification column. The annotated category for each mutation has also been added to the maf file as the Variant_annotation column. The latest mutation data is available for download here.


  • Start_Codon_SNP
  • Start_Codon_Del
  • Start_Codon_Ins
  • Splice_Site
  • Frame_Shift_Del
  • Frame_Shift_Ins
  • Nonsense_Mutation
  • De_novo_Start_OutOfFrame

Other non-conserving

  • Missense_Mutation
  • In_Frame_Del
  • In_Frame_Ins
  • Nonstop_Mutation
  • Stop_Codon_Del
  • Stop_Codon_Ins

Other conserving

  • 5'Flank
  • Intron
  • IGR
  • 3'UTR
  • 5'UTR

Silent mutations are annotated in the Variant_annotation column as 'silent', but are not highlighted in the portal.

The portal colors mutations with the priority order of hotspot > damaging > other non-conserving > conserving. For instance, if a gene in a cell line has both hotspot and damaging mutations, it will be colored as hotspot. Hotspot mutations are defined as any mutation that is a hotspot in TCGA or COSMIC, and is not silent.