Table 3 genes, novel variants hg38 and their phenotypes and in silico predictions
No. | Gene | Nucleotide variant | AA change | Predictions | ACMG classification | |||
|---|---|---|---|---|---|---|---|---|
MutationTaster | SIFT | Polyphen-2 | CADD score GRCh38-v1.6 | |||||
1 | APTX | c.793 A > T | p.Ser265Cys | DC | D | NA | 27.7 | VUS |
2 | APTX | c.582del | p.Lys194AsnfsTer20 | NA | NA | NA | NA | Pathogenic |
3 | APTX | c.734G > A | p.Arg245His | DC | T | NA | 22.5 | VUS |
4 | APTX | c.376delA | p.Arg126GlyfsTer26 | NA | NA | NA | NA | Pathogenic |
5 | ATM | c.3320T > G | p.Leu1107Ter | DC | NA | NA | 34 | Pathogenic |
6 | ATM | c.8050 C > T | p.Gln2684Ter | DC | NA | NA | 38 | Pathogenic |
7 | ATM | c.3895del | p.Ala1299ProfsTer50 | NA | NA | NA | NA | Pathogenic |
8 | ATM | c.6453-2 A > G | - | DC | NA | NA | 34 | Pathogenic |
9 | BRAT1 | c.398 A > G | p.His133Arg | DC | D | PD | 24.8 | VUS |
10 | CEP120 | c.2230 C > T | p.Arg744Cys | DC | T | B | 25.3 | VUS |
11 | CLN3 | c.1073_1074insAGAGAAATGAATGAGCCTACAGATGATAGGATGTGGTGTT | p.Cys359GlufsTer3 | NA | NA | NA | NA | Pathogenic |
12 | COQ8A | c.1162G > A | p.Gly388Ser | DC | D | PD | 35 | VUS |
13 | CWF19L1 | c.574T > C | p.Tyr192His | DC | D | PD | 27.9 | VUS |
14 | DARS2 | c.1781G > A | p.Gly594Glu | DC | T | PD | 24.8 | VUS |
15 | ELP2 | c.1580G > A | p.Arg527Gln | DC | T | B | 10.43 | VUS |
16 | ERLIN2 | c.299-3 C > T | - | NA | NA | NA | 16.97 | VUS |
17 | FAT2 | c.12913G > T | p.Ala4305Ser | DC | D | PD | 24.7 | VUS |
18 | FI.G4 | c.1766 A > G | p.Asp589Gly | DC | T | B | 23.5 | VUS |
19 | FTL | c.325 C > T | p.Gln109Ter | DC | NA | NA | 37 | Likely pathogenic |
20 | GRID2 | c.1033 C > T | p.Arg345Ter | DC | NA | NA | 35 | Pathogenic |
21 | KIF1C | c.1996G > T | p.Glu666Ter | DC | NA | NA | 50 | Pathogenic |
22 | MFSD8 | c.62 + 1G > A | - | DC | NA | NA | 33 | Likely pathogenic |
23 | MFSD8 | c.439 + 2T > C | - | DC | NA | NA | 33 | Likely pathogenic |
24 | MME | c.2242 C > T | p.Arg748Trp | DC | D | PD | 28.1 | VUS |
25 | NPC2 | c.272 A > T | p.Asp91Val | DC | D | PD | 27.8 | VUS |
26 | PLA2G6 | c.2108T > A | p.Val703Glu | DC | D | PD | 29.4 | VUS |
27 | PLA2G6 | c.962T > C | p.Leu321Pro | DC | D | PD | 26.9 | Likely pathogenic |
28 | PLA2G6 | c.1972 A > G | p.Asn658Asp | DC | D | PD | 28.3 | Likely pathogenic |
29 | PLA2G6 | c.865_869dup | p.Leu291AlafsTer16 | NA | NA | NA | NA | Pathogenic |
30 | PLA2G6 | c.1622 A > C | p.Tyr541Ser | DC | D | PD | 28.3 | Likely pathogenic |
31 | PLA2G6 | c.1427 + 1G > C | - | DC | NA | NA | 33 | Pathogenic |
32 | PLA2G6 | c.2015 A > T | p.Asn672Ile | DC | D | PD | 29.8 | VUS |
33 | POLG | c.3482 + 6 C > T | - | NA | NA | NA | 1.24 | VUS |
34 | RNASET2 | c.345G > A | p.Trp115Ter | DC | NA | NA | 36 | Pathogenic |
35 | RUBCN | c.1721 C > G | p.Ser574Ter | DC | NA | NA | 38 | Pathogenic |
36 | SACS | c.10,625 A > G | p.Asp3542Gly | DC | D | PD | 27.3 | VUS |
37 | SACS | c.12831_12841dupTCCTCTTTTCT | p.Ser4281PhefsTer31 | NA | NA | NA | NA | Likely pathogenic |
38 | SAMD9 | c.4558G > T | p.Glu1520Ter | DC | NA | NA | 34 | Likely pathogenic |
39 | SIL1 | c.910 C > T | p.Gln304Ter | DC | NA | NA | 41 | Pathogenic |
40 | THG1L | c.388G > A | p.Ala130Thr | DC | T | B | 22.3 | VUS |
41 | TMEM237 | c.550dup | p.Ser184LysfsTer8 | NA | NA | NA | NA | Pathogenic |
42 | TPP1 | c.1425 + 1G > T | - | DC | NA | NA | 34 | Likely pathogenic |
43 | TTPA | c.798del | p.Glu267LysfsTer27 | NA | NA | NA | NA | Likely pathogenic |
44 | VPS13D | c.8305G > C | p.Glu2769Gln | DC | NA | PD | 27.9 | VUS |
45 | WDR81 | c.1585 C > G | p.Arg529Gly | DC | D | PD | 23.2 | VUS |