Table 1.
SNAP and PolyPhen-2 neutrality prediction
| SNAP |
PolyPhen-2 | ||||
|---|---|---|---|---|---|
| Human NPHP4 mutation | C. elegans NPHP-4 mutation | C. elegans mutation prediction | Predicted accuracy, % | C. elegans mutation prediction | PSIC** |
| D3Y | D5Y | Non-neutral | 78 | Probably damaging | 2.025 |
| F91L | F83L | Non-neutral | 70 | Benign | 1.350 |
| R342C | R321C | Non-neutral | 82 | Possibly damaging | 1.800 |
| A654G | A603G | Neutral | 53 | Benign | 0.675 |
| G754R | S691R* | Non-neutral | 82 | Benign | 1.125 |
| F991S | F903S | Non-neutral | 70 | Possibly damaging | 1.800 |
| A1098T | A985T | Neutral | 85 | Benign | 0.000 |
| T1225M | T1101M | Non-neutral | 70 | Benign | 1.350 |
Prediction of pathogenicity of the mutations in NPHP-4 is based on Screening for Non-Acceptable Polymorphisms (SNAP, http://cubic.bioc.columbia.edu/services/SNAP/) and PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/). The predicted accuracy reflects SNAP's assignment confidence.
*Amino acid which was not conserved in C. elegans NPHP-4 but located in a highly conserved domain.
**Position-Specific Independent Counts (PSIC) and is an assessment of the likelihood of given amino acid occurring at a particular position to the likelihood of this amino acid occurring at any position (background frequency) (see http://genetics.bwh.harvard.edu/pph2/).