Mutation Overview

This tab shows a general overview of information available for the selected mutation. It describes the source of the mutation i.e gene name/sample name/tissue name with unique ID, and also shows the mutation syntax at the amino acid and nucleotide sequence level.


Substitutions involve the substitution of a single nucleotide and they are annotated 
using syntax derived from HGVS nomenclature recommendations 
[http://varnomen.hgvs.org/].

In COSMIC v70 (August 2014) we have applied filtering to the dataset. We have excluded 
data from any sample with over 15,000 mutations. In addition, we have flagged all 
known SNPs as defined by the 1000 genomes project, dbSNP and a panel of 378 normal (non-cancer) 
samples from Sanger CGP sequencing. Although all data are included in our download files, 
we have excluded flagged mutations from the website.

AA Mutation
The change that has occurred in the peptide sequence as a result of the mutation. 
Syntax 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
The change that has occurred in the nucleotide sequence as a result of the mutation. 
Syntax is identical to the method used for the peptide sequence.

The mutation type is used to describe the type of mutation that has occurred.

Mutation Types:


    Nonsense :      A substitution mutation resulting in a termination codon, 
                    foreshortening the translated peptide.

    Missense :      A substitution mutation resulting in an alternate codon, 
                    altering the amino acid at this position only.

    Coding silent : A synonymous substitution mutation which encodes the same 
                    amino acid as the wild type codon.

    Intronic :      A substitution mutation outside the coding domains. No interpretation is 
                    made as to its effect on splice sites or nearby regulatory regions.

    Complex :       A compound mutation which may involve multiple insertions, deletions 
                    and substitutions.

    Unknown :       A mutation with no detailed information available.      

Insertions and Deletions are annotated using syntax derived from HGVS nomenclature 
recommendations [http://varnomen.hgvs.org/].

Insertion
An insertion of novel sequence into the gene.

    In frame :   An insertion of nucleotides which does not affect the gene's translation frame, 
                 leaving the downstream peptide sequence intact.

    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.

    In frame :    A deletion of nucleotides which does not affect the gene's translation frame, 
                  leaving the downstream peptide sequence intact.

    Frameshift :  A deletion of nucleotides which alters the translation frame, changing the 
                  downstream peptide sequence (often resulting in premature termination).

Mutation Overview - Tissue Distribution

This tab shows a bar graph of the top 5 most common tissues in which this mutation has been identified. 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 on the X axis. Clicking on one of the bars links to the Cancer Browser (overview) page for the selected tissue.

Mutation Overview - Samples

This tab shows a table of samples associated with the selected mutation. This table also provides the ability to search, sort and export the table in csv and tsv format.

  1. Sample Name - The name of the sample that the mutation was found in, there could be multiple sample ids linked to the same sample name if we can not confirm whether the same sample name between different papers is indeed the same sample.
  2. Gene Name - The name of the gene this mutation was observed in. It links to Gene Analysis page with all the tissue/histology selections.
  3. Primary Tissue: The primary tissue from which the sample originated. It links to the Tissue Browser. More details on tissue classification can be found here
  4. Histology: The histological classification of the sample.
  5. Pubmed Id - The ID for the paper that the sample was noted in, linking to the cosmic reference overview page for more details of the publication.
  6. Zygosity: Information on whether the mutation was reported to be homozygous or heterozygous within the sample.
  7. Somatic Status: Information on whether the sample was reported to be Confirmed Somatic, Previously Reported or Variant of unknown origin.

Mutation Overview - Pathways Affected

This tab shows the biological pathways affected by the selected gene mutation. The source of the information is given in the first column (eg wikipathways) and there is a link in the second column to the source database.

Mutation Overview - References

This table lists all curated publications reporting this mutation. More details of the paper can be found by following the ‘COSMIC link’ or ‘Pubmed Link’. This table also provides the ability to search, sort and export the table in csv or tsv format.

  1. Reference Title - The abbreviated title of the article. Mouseover the title to see the full article title.
  2. Author – First author (s) of the publication, to see all authors of the publication please click the COSMIC or Pubmed link.
  3. Year - The publication year of the journal from which the article was taken.
  4. Journal - An abbreviated title of the journal the article was sourced from, followed by volume and page number.
  5. Status – There are currently three statuses:
    • Curated : The reference has been fully curated in to COSMIC.
    • Listed : The reference have been read, but the data has not been entered into COSMIC for one of many reasons.
    • Reviews : These references are reviews of mutation data from other references. They are not entered into COSMIC as the data has generally been entered via the original papers.
  6. COSMIC – Links to the more detailed page of reference listing all details from the selected publication including samples and gene analysed with or without mutation.
  7. Pubmed - Links to Pubmed for more details on this publication.

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