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Variation Table (Gene)

Short sequence variations are shown by consequence type in the Variation Table.

This view shows all the variant consequences in a gene. You can choose whether to have the information summarised in a table or a tree of Sequence Ontology (SO) consequence types. To switch between the two, use the link at the top right of the table/tree. Both the table and the tree are used to select a specific consequence type (e.g. missense, the stop gained, among others), using the "show" link, which then expands a table below.

Table by Consequence Type

The table for the specific consequence type (e.g. missense) contains all variants that fall within the gene have this particular consequence. If the same variant falls in several transcripts within the same gene, a new row will be displayed for each transcript. Therefore, this number reflects the number of variant consequence types across the transcripts. 

The variation sources shown in the page can be changed using the 'Configure this page' tool button at the left.

The SO term accession numbers (e.g. SO:0001792) are also available and linked to the Sequence Ontology Browser (MISO).

If you show a table for a variation consequence type, the columns will be as follows:

  • ID - The identifier of this particular genetic variation in an external database. Frequently, this will be an rs identifier, a reference SNP from NCBI dbSNP.
  • Chr:bp - Chromosome name and base pair co-ordinates
  • Alleles - Possible nucleotides at the position listed in the Chr:bp column. These are reported for the forward strand of the genome sequence
  • Global MAF - The global minor allele frequency is calculated using all 1000 Genomes Phase I data for this SNP, across populations
  • Class - For example, Single Nucleotide Polymorphism (SNP) and Insertion-Deletion (InDel)
  • Source - Original database/project from which the variation was imported
  • Evidence Data that support a variant and suggest how reliable the variant is. A summary of evidence status is available on our documentation on Variation data.
  • Clinical significance A term assigned by dbSNP and ClinVar that indicates pathogenicity or drug response. A list of clinical significance terms can be found on our documentation on Variation data.
  • Type - Consequence type based on SO (Sequence Ontology) terms. Click on Configure this page at the left to change the consequence types
  • Amino Acid - Possible amino acid(s) (if any) resulting from the allele(s) at the position of the variation. More than one amino acid will be listed for a non-synonymous variation
  • AA co-ordinate - The position of the amino acid (AA) within the protein sequence. The number refers to the position of the variation in the codon (1, 2, or 3).
  • SIFT - Prediction of variation effect on protein function by SIFT
  • PolyPhen - Prediction of variation effect on protein function by PolyPhen
  • Transcript - The specific Ensembl transcript for the gene of interest in which the variation shows the consequence type

Go to the Variation Image for a graphical view.

The Tree Display

The number in front of the consequence type reflects the number of the transcripts with that consequence type.  For example, if one variant (rsID) is found in three transcripts, it will contribute (3) to this number.

Some of the consequence types with subterms (or children terms) have hidden terms, and will show a larger count than is shown by the subterms displayed.  An example of this is "Coding sequence variant" in the image below. In cases such as this, the counts underneath the consequence type ('Synonymous variant' and 'Protein altering variant' subterms for 'Coding sequence variant' term) will not add up to the total count next to the type term.