functional variation

1. FANS Functional Analysis for Novel SNPs and Mutations Biomedical IT National Genotyping Center 05/29/09 http://fans.ngc.sinica.edu.tw

5. Risk Analysis Flow VERY HIGHT VERY LOW RISK LEVEL HIGH MEDIUM No Splice-site? Yes Risk : High Splice site No SNPs in intron and untranslated region are not analyzed Non-synonymous? Risk : Very High Non-sense? Coding? Risk : High ESE or ESS Motif Diminished? Risk : Medium Non-sense Mis-sense (non-conservative change) Risk : High Mis-sense (protein domain abolished) Mis-sense (conservative change) Protein Structure Affection? ESE or ESS Motif Diminished? Protein Domain Abolished? Risk : High Splicing regulation (protein domain abolished) Protein Domain Abolished? Risk : Medium Splicing regulation Risk : Very Low Sense Variations in Transcripts Yes Yes Yes Yes Yes Yes Yes Yes No No No No No No No

11. Part 4 : Analysis Flow

12. Risk Types & Risk Levels High Alters GT-AG splice site Splice site Non-coding Very Low Does not change amino acid and disrupt exon splicing regulation Sense Medium Disrupts exon splicing regulation, make the same protein domain Splicing regulation High Disrupts exon splicing regulation, make protein domain abolished Splicing regulation (protein domain abolished) Medium Does not change ESE, ESS and known protein domain and results in analogous protein structure Mis-sense (conservative change) High Changes ESE, ESS and known protein domain and results in protein structure abolished Mis-sense (protein domain abolished) High Predicts to affect protein structure Mis-sense (non-conservative change) Very High Causes premature stop codon and affects protein function Non-sense Coding Risk level Possible functional effect Risk type Coding type

13. Performance A benchmarking test result of 10 variations analysis 1 47 Result pages 118 s 3968 s Time 170 Calculation 120 Fas-ESS 120 Rescue-ESE 100 SIFT 80 Ensembl 4 940 350 NCBI Steps FANS Manual