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Table 4 Summary of putative pathogenic mutations and their bioinformatics predictions

From: Targeted next generation sequencing for molecular diagnosis of Usher syndrome

Patient Gene Exon Nucleotide Change Amino Acid Change Classification SIFT (score) PolyPhen-2 (score) NetGene2 Human Splicing Finder NNSPLICE RESCUE-ESE
RP-1948 MYO7A 7 c.707T>A p.Leu236Gln UV3 deleterious (0) probably_damaging (1) Neutral Neutral Neutral A new ESE site is created
RP-807 RP-1924 MYO7A 27 c.3503G>A p.Arg1168Gln UV3 deleterious (0) probably_damaging (1) Score for the main donor site decreases from 95 to 75 Score for the main donor site decreases from 90 to 80 The main donor site is not recognized Neutral
RP-807 MYO7A 40 c.5516T>C p.Leu1839Pro UV3 deleterious (0) probably_damaging (1) Score for the main acceptor site decreases from 80 to 77 Neutral Neutral Neutral
RP-1614 MYO7A 40 c.5537C>A p.Prp1846His UV3 deleterious (0.01) possibly_damaging (0.85) Score for the main acceptor site decreases from 80 to 77 and one acceptor site is not recognized Neutral Neutral Neutral
RP-808 CDH23 10 c.871G>A p.Gly291Arg UV3 deleterious (0) probably_damaging (1) Neutral Neutral Neutral A new ESE site is created
RP-1426 CDH23 39 c.5068-2A>T c.5068-2A>T UV4 --- --- The main acceptor site is not recognized Score for the main acceptor site decreases from 95 to 66 The main acceptor site is not recognized ---
RP-1781 CDH23 68 c.9569C>T p.Ala3190Val UV3 deleterious (0) probably_damaging (1) Neutral Neutral Neutral Neutral
RP-1927 USH2A 2 c.269A>G p.Tyr90Cys UV3 tolerated (0.17) possibly_damaging (0.796) Score for acceptor site decreases from 82 to 80 Neutral Score for acceptor site decreases from 75 to 69 A ESE site is not recognized
RP-1835 USH2A 22 c.4758+3A>G c.4758+3A>G UV3 --- --- The main donor site is not recognized Neutral The main donor site decreases from 98 to 73 ---
RP-1960 USH2A 25 c.5167G>C p.Gly1723Arg UV3 deleterious (0) probably_damaging (0.994) The main donor site is not recognized Score for the main donor site decreases from 86 to 75 The main donor site is not recognized Neutral
RP-1455 USH2A 28 c.5666A>G p.Asp1889Gly UV3 deleterious (0) probably_damaging (0.982) The main donor and acceptor sites decrease from 82 to 80 and from 53 to 48 respectively and a new acceptor site is created Neutral Neutral Two ESEs are not recognized
RP-1496 GPR98 19 c.3443G>A p.Gly1148Asp UV3 deleterious (0) probably_damaging (0.999) Neutral Neutral Neutral Neutral
RP-1929 GPR98 58 c.11974G>A p.Asp3992Asn UV3 deleterious (0.01) probably_damaging (0.999) Neutral Neutral Neutral A ESE is not recognized
RP-1950 GPR98 70 c.14278C>T p.Pro4760Ser UV3 deleterious (0) probably_damaging (0.998) Neutral Neutral Neutral Neutral
RP-1923 DFNB31 9 c.2234G>A p.Arg745His UV3 deleterious(0.01) probably_damaging (0.984) Neutral Neutral The main donor site increases from 66 to 86 Neutral
  1. SIFT: SIFT Score ranges from 0 to 1. The amino acid substitution is predicted to be damaging if the score is < 0.05, and tolerated if the score is > 0.05.
  2. PolyPhen stablish three classifications: "Probably damaging" (it is believed most likely to affect protein function or structure), "Possibly damaging" (it is believed to affect protein function or structure), "Benign" (most likely lacking any phenotypic effect).
  3. ESE: Exonic Splicing Enhancer.