Table 2. Classification of de novo variants using in silico prediction programs.
| Ext-Code | Variant | HGNC | MutCDNA | gnomAD (MAF) | SIFT | LRT | Mutation Taster | Mutation Assessor | FATHMM | PROVEAN | Meta SVM | Meta LR | Fathmm MKL_coding | CADD Score |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4_501 | 1 | EEF1D | c.874C>T | - | N | A | - | - | - | - | - | N | 28,5 | |
| 2 | CELSR1 | c.4357G>A | 3/282,594 (0.00001) | T | U | N | N | T | N | T | T | D | 15,3 | |
| 21_501 | 3 | HPS3 | c.1189C>T | 10/282,776 (0.00004) | D | D | A | M | T | D | D | T | D | 35 |
| 27_501 | 4 | PIGC | c.716C>T | T | D | D | M | T | N | T | T | D | 11,6 | |
| 35_501 | 5 | NFX1 | c.1723G>A | D | N | N | L | T | N | T | T | D | 20,8 | |
| 36_501 | 6 | ZFHX3 | c.1601C>G | D | N | D | L | T | N | T | T | D | 22,3 | |
| 41_501 | 7 | MTA3 | c.393C>A | 1/237,600 (0.000004) | D | D | D | H | D | D | D | D | D | 26 |
| 46_501 | 8 | FANCB | c.782G>A | T | N | N | N | T | N | T | T | N | 7,2 | |
| 9 | PLEC | c.6704G>A | 17/272,690 (0.00006) | D | U | D | N | T | N | T | T | D | 26,5 | |
| 63_501 | 10 | PPIP5K2 | c.686G>A | 2/247,732 (0.000008) | D | D | D | M | T | D | T | T | D | 34 |
| 88_501 | 11 | CLP1 | c.814C>A | 1/251,486 (0.000003) | T | D | D | L | T | N | T | T | D | 17,4 |
| 12 | GPR133 | c.1033G>A | 6/282,534 (0.00002) | T | N | N | N | T | N | T | T | N | 0,016 | |
| 13 | SLC5A2 | c.644T>C | D | D | D | H | D | D | D | D | D | 27,6 | ||
| 90_501 | 14 | KIAA0556 | c.3730C>T | D | N | N | L | T | N | T | T | N | 1,9 | |
| 141_501 | 15 | STAB1 | c.6145C>T | 9/278,948 (0.00003) | T | N | N | M | T | D | T | T | N | 24,1 |
| 154_501 | 16 | GGT6 | c.1045A>G | D | N | N | N | T | D | T | T | N | 5,9 | |
| 167_501 | 17 | CHD7 | c.4187C>G | D | D | D | H | T | D | D | D | D | 33 | |
| 172_501 | 18 | NPR2 | c.952C>G | T | N | D | L | D | D | T | T | D | 22,2 | |
| 174_501 | 19 | UBA3 | c.1088C>T | D | D | D | L | T | D | T | T | D | 27,8 | |
| 181_501 | 20 | TANC2 | c.2357C>T | T | D | D | L | T | D | T | T | D | 22,7 | |
| 288_501 | 21 | TRPS1 | c.1630C>T | - | D | A | - | - | - | - | - | D | 36 | |
| 22 | APOL2 | c.319G>C | T | N | N | N | T | N | T | T | N | 0,004 | ||
| 750_501* | 23 | ZFHX3 | c.6377C>T | 5/250,880 (0.00002) | D | D | D | L | T | D | D | D | D | 19,2 |
*A: automatic disease causing; D: disease causing; H: high functional; L: non-functional; M: medium functional; N: neutral; T: tolerant. Annotations marked in bold red represent: “variants that are classified to be disease causing by at least eight out of ten in silico prediction programs (except for truncating variants) used by dbNSFP v3.0 (https://sites.google.com/site/jpopgen/dbNSFP)”.