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Mutation Summary Page

  • Welcome to the mutation summary page. This page provides an overview of all the information, stored in COSMIC, associated with the selected mutation.
     
  • This page is divided into seven main sections.
     
Mutation Id
  • This id is used to identify a mutation within the COSMIC database and is assigned as the mutation is curated.
     
AA Mutation
  • This section details the change that has occurred in the peptide sequence as a result of the mutation. Formatting is based on the recommendations made by the Human Genome Variation Society. The mutation type is shown in brackets after the mutation string. A description of each type can be found below in the section entitled Mutation Type.
CDS Mutation
  • This section details the change that has occurred in the nucleotide sequence as a result of the mutation. Formatting is identical to the method used for the peptide sequence.
     
Mutation Type
  • The mutation type is used to describe the type of mutation that has occurred. :
    • Substitution : A mutation involving the substitution of a single nucleotide.
    • Substitution - Nonsense : A substitution mutation resulting in a termination codon, foreshortening the translated peptide.
    • Substitution - Missense : A substitution mutation resulting in an alternate codon, altering the amino acid at this position only.
    • Substitution - coding silent : A synonymous substitution mutation which encodes the same amino acid as the wild type codon.
    • Substitution - intronic : A substitution mutation outside the coding domains. No interpretation is made as to its effect on splice sites or nearby regulatory regions.
    • Insertion : An insertion of novel sequence into the gene.
    • Insertion - In frame : An insertion of nucleotides which does not affect the gene's translation frame, leaving the downstream peptide sequence intact.
    • Insertion - Frameshift : An insertion of novel sequence which alters the translation frame, changing the downstream peptide sequence (often resulting in premature termination).
    • Deletion : A deletion of a portion of the gene's sequence.
    • Deletion - In frame : A deletion of nucleotides which does not affect the gene's translation frame, leaving the downstream peptide sequence intact.
    • Deletion - Frameshift : A deletion of nucleotides which alters the translation frame, changing the downstream peptide sequence (often resulting in premature termination).
    • Complex : A compound mutation which may involve multiple insertions, deletions and substitutions.
    • Unknown : A mutation with no detailed information available.

     
Mutation Location
  • Here, an image displays the location of the mutation within the peptide sequence.

  • The grey bar at the top of this section shows the full length sequence. Below this can be found a red box, which indicates the area around the mutation. At the bottom of the image, the red box has been expanded and the peptide sequence around the mutation is shown. Here you will find a red triangle which indicates the starting point of the mutation. Clicking on the triangle will produce a pop-up window showing the mutation at both the peptide and nucleotide level.

  • Additionally there is a link, 'Show all mutations in area', to the main histogram page for the gene. This link will show the gene histogram zoomed into the area displayed on this page. This allows you to see any other mutations that have been identified in the surrounding area.
     
Contig View
  • This section contains links to the Ensembl Contig View website. The page will show the mutation in a window plus and minus 10 base pairs. More information about the COSMIC DAS sources is available in the Gene Summary help page (Additional Information section).


Genomic Co-ordinates
  • The genomic co-ordinates (most recent NCBI version in COSMIC) are displayed in this section for the selected mutation.


Gene
  • The name of the gene in which the mutation was found. Clicking on the gene name will link to the summary page for that gene.
     
Tissue Distribution (Top 5)
  • The top five tissues in which this mutation has been identified are described in the following bar chart.
     

  • Each bar represents the number of samples, for a specific tissue type, that have exhibited the selected mutation. A label indicating the name of the tissue type and the number of samples is located below each bar.
  • Clicking on one of the bars will take you to the tissue overview page for the selected tissue.
Associated Samples
  • A list showing all the samples, including their primary tissue types, that have the selected mutation. Clicking on a sample name will take you to the sample summary page for the selected sample. Clicking on the primary tissue type will take you to the tissue overview page.
     
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