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VEP analysis of FLG variants in human

Below, you will find a list of variants which have been reported in the FLG gene (ENSG00000143631), which codes for filaggrin. Mutations in the gene have been associated with atopic dermatitis.

  • C/A at 1: 152,302,797
  • G/A at 1: 152,307,085
  • C/T at 1: 152,310,208
  • G/A at 1: 152,308,234
  • C/T at 1: 152,313,454
  • C/T at 1: 152,309,920
  • A/G at 1: 152,309,268

Use the VEP tool in Ensembl and find out the following information:

  1. What consequences have been predicted for the variants?

  2. Are SIFT and PolyPhen predictions available for the variants? What are the scores?

  3. How many of these variants have been previously reported?

Go to the Ensembl homepage and click on the link VEP at the top of the page. Launch the VEP web interface. You will need to convert your variants into one of VEP’s supported input formats. We have converted the variants into the Ensembl default format below. Paste the variants into Input data:.

1  152302797 152302797 C/A
1  152307085 152307085 G/A
1  152310208 152310208 C/T
1  152308234 152308234 G/A
1  152313454 152313454 C/T
1  152309920 152309920 C/T
1  152309268 152309268 A/G

Enable SIFT and PolyPhen score predictions in the Predictions under Additional configurations and click Run. Once your job is done, click View results. You will retrieve a table of your VEP results. Note that there may be multiple entries in the table for each variant. VEP will give you all consequences for each feature the variant falls within.

  1. Filter your table to show variants affecting the FLG gene (ENSG00000143631) only. Under Filters select Gene from the drop-down menu and enter ENSG00000143631 in the text field. Click Add.

    Look for the Consequence column. This column will give you the sequence ontology (SO) terms (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc.) provided by VEP for the listed SNPs. You can read more about the Sequence Ontology project here. All 7 entries have been predicted to have missense consequences.

  2. Look for the SIFT and PolyPhen columns.

    Pathogenicty scores are available for all variants. Benign/tolerated scores are predicted for variants 1_152313454_C/T, 1_152310208_C/T and 1_152309920_C/T. For the other 4 variants, the SIFT and PolyPhen scores do not correspond.

  3. Look for the Existing variant column. If a variant has been previously described, a link will be available in this column.

    4 variants have been previously described: 1_152313454_C/T, 1_152308234_G/A, 1_152310208_C/T and 1_152309920_C/T. Variants 1_152302797_C/A, 1_152309268_A/G and 1_152307085_G/A are novel variants.