Annotation resource/tool for 5'UTR variants
Contact: Sander Pajusalu sander.pajusalu@yale.edu
This tool is in active development
5utr is an VEP plugin aiming to provide different annotations relevant to 5' UTR (untranslated region) variants.
Current limitations
- Works only on single nucleotide substitutions (SNVs)
- Some annotations are available only for the nearest 100bp to CDS.
./vep -i variants.vcf.gz --cache --offline --assembly GRCh37 --dir_plugin /path/to/Sutr_dir --no_stats --plugin Sutr,/path/to/Sutr_resource_table_b37.tsv.gz,ALL -o out.file.txt
./vep -i variants.vcf.gz --cache --offline --assembly GRCh38 --dir_plugin /path/to/Sutr_dir --no_stats --plugin Sutr,/path/to/Sutr_resource_table_hg38.tsv.gz,ALL -o out.file.txt
Instaed of 'ALL' you can specify columns from Sutr.tsv.gz to be included in the annotation. See VEP manual for general usage instructions (e.g. using and downloading cache, additional annotations like gnomAD and ClinVar etc.)
The table is in nested format, meaning that if the same position is covered by multiple transcripts, the respective fields are comma-separated lists, where the values correspond to the respective transcripts marked in "transcript" field in the same order.
The annotations files can be accessed here, be sure to download right genome assembly matching with your vcf.
The following annotations are available:
chr, pos, REF, ALT - locus and allele
transcript
distance - distance from main start codon of CDS. -1 marks the nearest base in 5'UTR, +1 is the first base of CDS (start codon).
AUG_event - whether the variant creates a novel AUG (AUG_gain), removes the AUG in reference sequence (AUG_loss) or changes the position of AUG at the same locus (AUG_change)
var_frame, AUGgain_stop, var_kozak - these fields are relevant for AUG_gain and AUG_change (for the created AUG) - var_frame specifies if it is in-frame or out-of-frame with canonical start codon (CDS); AUGgain_stop indicates whether there is a stop before canonical start codon; var_kozak specifies the strength of kozak surrounding the novel AUG (weak, moderate, strong) ref_frame, AUGloss_stop, ref_kozak - the same as previous, but now these define properties for AUG in the reference sequence which was removed by the variant.
STOP_event, STOPgain_start, STOPloss_start - whether the variant creates a novel STOP codon (STOP_gain), removes the STOP in reference sequence (STOP_loss) or changes the position of STOP at the same locus (STOP_change). STOP_gain_start and STOPloss_start indicate whether there is a start codon somewhere upstream of the created/removed STOP, but located still in the same 5'UTR. Only the ones with_start should be biologically relevant.
kozak_strength, kozak_cat - kozak_strength specifiec whether the variant makes kozak sequence stronger or weaker or remains the same. kozak_cat higlights whether the kozak change affects main AUG (canonical start codon) or upstream AUG, and whether the affected nucleotide is at relative position -3 (m3) or +4 (p4).
TE_log2fold - change in predicted translational efficiency caused by the variant in log2fold scale. 0 indicates no change, -1 indicates 2-fold reduction of translation and +1 2-fold increase in translation. The predictions are calculated by the method and model published by Sample et al. in Nature Biotech 2019
Delta_dsRNA, Delta_G4 - change in minimum free energy (secondary structure) affecting double-stranded RNA or G4 quadruplex structures respectively. Negative values show that the RNA secondary structure has become more stable due to the variant, which is associated with reduced translation. The calculations were done for the nearest 100bps in 5'UTRs and follow the methods published by Murat et al, in Genome Biology 2018