Table 2.
Possible causative variant identified in this study.
| Prediction Score | Allele Frequency in Controls | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Amino | |||||||||||||
| Nucleotide | Acid | PolyPhen | Mut_ | Mut_ | ACMG | ||||||||
| Changes | Change | SIFT * | 2_HVAR * | LRT * | Taster * | Assessor * | REVEL * | Cadd | Exac | Gnomad | 3.5kJPN | Guidelines | |
| c.235C>T | p.(Arg79Trp) | D(0.4) | B(0.166) | N(0.132) | N(0.09) | M(0.552) | 0.21 | 23.6 | 0.00000824 | 0.00000812 | N/A | Uncertain Significance | PM2,PM3 |
| c.442C>T | p.(Arg148*) | - | - | N(0.225) | A(0.81) | - | - | 35 | 0.0000247 | 0.0000163 | N/A | Likely Pathogenic | PVS1, PM2 |
| c.469C>T | p.(Arg157Cys) | D(0.912) | D(0.916) | D(0.629) | D(0.548) | M(0.752) | 0.285 | 34 | 0.0000165 | 0.0000203 | N/A | Uncertain Significance | PM2,PM3 |
| c.1705A>G | p.(Lys569Glu) | D(0.427) | D(0.875) | D(0.629) | D(0.441) | M(0.567) | 0.598 | 31 | N/A | N/A | N/A | Uncertain Significance | PM2,PM3 |
| c.647T>C | p.(Phe 216Ser) | D(0.721) | D(0.764) | D(0.629) | D(0.412) | M(0.741) | 0.326 | 24.3 | N/A | N/A | N/A | Uncertain Significance | PM2 |
* The Prediction Score of each algorithm included in the ANNOVAR software was converted from the original scoring system. A score closer to 1.0 indicated the variant was predicted to be more damaging. A, disease causing automatic (Mutation Taster); B, benign (PolyPhen2_HVAR); D, deleterious (SIFT, LRT), probably damaging (PolyPhen2), or disease causing (Mutation Taster); M, medium (Mutation Assessor); N, Neutral (LRT). PVS: evidence of Pathogenicity—Very Strong, PM: evidence of Pathogenicity—Moderate.