Genes and Regulation

For the top panel describing variation details such as source and class, see this help page.

Three tables are shown.

The Gene and Transcript consequences table shows the position and effect of the variation on specific genes and transcripts.

Columns in the table are as follows:

Gene - The Ensembl Gene ID. Click for more information about the gene.
Transcript (strand) - The Ensembl Transcript ID and chromosomal strand (+ indicates the forward strand, - indicates the reverse strand). Click on the ID for more information about the transcript.
Allele (transcript allele) - The alternate allele (not the allele in the reference genome) is shown for the forward strand, along with the allele found in the transcript (in parentheses). Note, the transcript allele may be on the reverse strand.
Type - The consequence type. Note this is transcript dependent (the variation consequence may vary between transcripts). For variation types, see this article.
Position in transcript - Nucleotide position in the transcript, counting from the transcript start.
Position in CDS - Nucleotide position in the CoDing Sequence (CDS), counting from the start of the coding sequence (ATG).
Position in protein - Amino acid position in the protein sequence.
Amino Acid - Possible amino acids(s) (if any) resulting form the allele(s) at the position of the variation. More than one amino acid will be listed for a missense variant.
Codons - The location of the variation within a codon is indicated in bold.
SIFT - Prediction of variation effect on protein function by SIFT. A score and a qualitative prediction (either tolerated or deleterious) are provided. Scores nearer 0 are more likely to be deleterious and are coloured in red. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated' (coloured in green).
PolyPhen-2 - Prediction of variation effect on protein function by PolyPhen-2. A score and a qualitative prediction (probably damaging, possibly damaging, benign or unknown) are provided. The PolyPhen-2 score represents the probability that a substitution is damaging, so values nearer 1 are more confidently predicted to be deleterious (note that this the opposite to SIFT).
CADD - Prediction of variant effect on protein function by CADD. A score and a qualitative prediction (likely deleterious and likely benign) are provided. Scores range from 0 (likely benign) to 100 (likely deleterious).
REVEL - Prediction of variant effect on protein function by REVEL. A score and a qualitative prediction (likely disease causing and likely benign) are provided. Scores range from 0 (likely benign) to 1 (likely disease causing).
MetaLR - Prediction of variant effect on protein function by MetaLR. A score and a qualitative prediction (damaging and tolerated) are provided. Scores range from 0 (tolerated) to 1 (damaging).
MutationAssessor - Prediction of variant effect on protein function by MutationAssessor. A score and a qualitative prediction (high, medium, low or neutral) of the impact on the protein function are provided. Scores range from 0 (neutral) to 1 (high).
Detail - For a quick allele report on one specific transcript, click 'Show'.

The Gene expression correlations table shows GTEx eQTL data, which identifies the influence of variants on tissue-specific gene expression.

Columns in the table are as follows:

Gene - The gene(s) (Ensembl stable gene ID) found to have altered expression associated with the variant of interest.
P-value (-log₁₀) - Nominal p-values of the individual variant-gene pair.
Effect size - Effect of the alternative allele relative to the reference allele
Tissue - The tissue in which gene expression was found to be associated with the variant of interest.

The Regulatory consequences table shows Ensembl regulatory features and motifs at the variant position that may be involved in gene regulation from the Regulatory Build.

Columns in the table are as follows:

Feature - The Ensembl stable ID is shown for regulatory features (ENSR#). An ID from the relevant source (e.g. JASPAR) is shown for motifs, specifically binding motifs or Position Weight Matrices. The Ensembl ID associated with the motif is shown under the motif name.
Feature type - This is either an Ensembl regulatory feature, or a motif.
Allele - The alternate allele (not the reference allele) is shown. For the reference allele, see the information at the top of the view.
Consequence type - The consequence type of the variant ('regulatory region' is the most generic value here).
Motif name - For motifs, this is the name from the relevant source.
Motif position - This is the position of the variant within the motif, in base pair coordinates, from the start of the motif.
High information position - The variation position appears to be important to the motif.
Motif score change - This lets you know if the alternate allele increases or decreases the motif score. For example, if the allele increases the score, it means the sequence around and including the variant matches the known motif consensus sequence much better.

Note: Use the Show/hide columns button to turn unwanted columns off (or on). Expore the table using the 'CSV' button at the top right of each table. The Filter box provides a search.