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VEP in zebrafish

Resequencing of the genomic region of the zebrafish ATP synthase O subunit (atp5o) gene (ENSDARG00000001788) has revealed the following variants (alleles defined in the forward strand):

  • C/T at 9:33146126
  • A/G at 9:33147350
  • A/C at 9:33148752

Use the VEP tool in Ensembl to determine whether these variants result in a change in the proteins encoded by any of the Ensembl genes? Which transcripts? Have the variants already been found?

Go to www.ensembl.org and click on the Variant Effect Predictor link on the homepage. Click Launch VEP.

Choose zebrafish as the species. Enter the three variants as below:
9 33146126 . C T
9 33147350 . A G
9 33148752 . A C

Note: Variation data input can be done in a variety of formats. See more details here

Click Run. When your job is listed as Done, click View Results.

You will get a table with the consequence terms from the Sequence Ontology project (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. You can also upload the VEP results as a track and view them on Location pages in Ensembl.

All three variants affect the same three transcripts. The affected transcripts are: ENSDART00000141849, ENSDART00000143453, ENSDART00000005879.

Two variants are novel variants but one has previously been described (rs180140691) in dbSNP.