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Mutation Summary Page

The Mutation Summary Page contains information about one somatic mutation and how it affects the associated gene. Each mutation is identified by its chromosomal position and nucleotide-level change.

Summary

Mutation Summary

  • ID: A unique identifier (UUID) for this mutation
  • DNA Change: Denotes the chromosome number, position, and nucleotide change of the mutation
  • Type: A broad categorization of the mutation
  • Reference Genome Assembly: The reference genome in which the chromosomal position refers to
  • Allele in the Reference Assembly: The nucleotide(s) that compose the site in the reference assembly
  • Functional Impact: A subjective classification of the severity of the variant consequence. The categories are:
  • HIGH: The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay
  • MODERATE: A non-disruptive variant that might change protein effectiveness
  • LOW: Assumed to be mostly harmless or unlikely to change protein behavior

External References

A separate panel contains links to databases that contain information about the specific mutation. These include dbSNP, COSMIC, and CIViC.

Consequences

Mutation Consequences

The consequences of the mutation are displayed in a table. The fields that detail each mutation are listed below:

  • Gene: The symbol for the affected gene
  • AA Change: Details on the amino acid change, including compounds and position, if applicable
  • Consequence: The biological consequence of each mutation
  • Coding DNA Change: The specific nucleotide change and position of the mutation within the gene
  • Strand: If the gene is located on the forward (+) or reverse (-) strand
  • Transcript(s): The transcript(s) affected by the mutation. Each contains a link to the Ensembl entry for the transcript

Cancer Distribution

Mutation Distribution

The Cancer Distribution table contains information about how the mutation affects each project, which can be exported as a JSON object. The table contains the following fields:

  • Project ID: The ID for a specific project
  • Disease Type: The disease associated with the project
  • Site: The anatomical site affected by the disease
  • # Affected Cases: The number of affected cases and total number of cases displayed as a fraction and percentage

Protein Viewer

Mutation Protein Graph

The protein viewer displays a plot representing the position of mutations along the polypeptide chain associated with the mutation. The y-axis represents the number of cases that exhibit each mutation, whereas the x-axis represents the polypeptide chain sequence. Pfam domains that were identified along the polypeptide chain are identified with colored rectangles labeled with pfam IDs. See the Gene Summary Page for additional details about the protein viewer.