Table 3.
POLD1 variants found in the analysis of the brain tumor of individual III.2. In silico predictions based on Alamut software.
| Variant Calling | Coverage | Rs ID | MAF | |||
|---|---|---|---|---|---|---|
| Gene (transcript) | cDNA change | Predicted protein change | Allelic frequency | Read depth | (ExAC/ESP) | |
| POLD1 (NM_001256849.1) | c.952G>A | p.Glu318Lys | 0.264 | 772 | rs775232133 | 0.000010/NR |
| c.1096G>A | p.Ala366Thr | 0.235 | 267 | – | NR/NR | |
| c.2788G>A | p.Ala930Thr | 0.482 | 410 | rs144111108 | 0.00010/0.00008 | |
| c.3157C>T | p.Arg1053Cys | 0.62 | 91 | rs779208942 | 0.00004/NR | |
| In Silico Predictions | Protein Domain | |||||
| Protein Function | ||||||
| Gene (transcript) | Splicing | SIFT (score) | Mutation Taster (p-value) | Polyphen2/HumDiv (score) | Polyphen2/HumVar (score) | |
| POLD1 (NM_001256849.1) | No changes | Deleterious (0) |
Disease causing (1) | Probably damaging (1.000) | Probably damaging (0.998) | Exonuclease(catalytic residue) |
| Unconclusive | Deleterious (0.05) |
Disease causing (0.956) | Benign (0.087) | Benign (0.271) | Exonuclease | |
| No changes | Tolerated (0.13) |
Disease causing (1) | Probably damaging (1.000) | Probably damaging (0.998) | – | |
| No changes | Deleterious (0) |
Disease causing (1) | Probably damaging (0.999) | Probably damaging (0.973) | – | |
Abbreviations: NR, not reported.