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 |