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Table 2 Exonic mutations in silico prediction

From: NPHS2 mutations account for only 15 % of nephrotic syndrome cases

Enhancer motifs analysis through ESE finder matrices for SRp40, SC35, SF2/ASF and SRp55 proteins
Sequence Variant Sequence positiona Linked SRb protein Reference motif Linked SRb protein Mutant motif Variation
(value 0–100)c (value 0–100)c
c.779 T > A 776 - - SF2/ASF AAGAGGA (80.37) New ESS site
c.851C > T 845 - - SF2/ASF CTGAAGT (75.38) New ESS site
c.928G > A 923 SF2/ASF CAGCTGA (78.10) - - Site broken
Potencial splice sites prediction through HSF matrices
Sequence Variant Sequence position Splice site type Motif New splice site Wild typed Mutantd Variaton
c.779 T > A 769 Acceptor GGAATCAAAGTGGA ggaatcaaagagGA 38.61 67.56 New site +74.98
  1. aPosition in cDNA from ATG codon; bSR = serine/arginine rich proteins; c = Consensus values go from 0 to 100 and the threshold is defined differently for each algorithm. Threshold for SF2/ASF from ESE finder matrices is 72.98. Every signal with a score above the defined threshold is considered to be a potential ESE/ESS. dFor HSF matrices consensus values go from 0 to 100 and threshold is 65. Every signal with a score above the threshold is considered to be a splice site (donor or acceptor). When a mutation occurs if the WT score is under the threshold and the score variation is above +10 % for HSF it is considered that the mutation creates a new splice site