Table 4.
Population frequencies and bioinformatic predictions of the rare variants identified in this study
| ExAC | gnomAD | Polyphen-2 | SIFT | I-Mutant | CADD | BDGP | |
|---|---|---|---|---|---|---|---|
| POLR3A | |||||||
| p.M1I | 0/0/121360 | 0/1/246230 | Probably damaging | Damaging | Decreased stability | 33 | − |
| p.R254* | 0/3/121300 | 0/9/277188 | − | − | − | 37 | − |
| c.3337-5T > A | 0/1/108818 | 0/1/242920 | − | − | − | 8.67 | 0.79–>0.32 |
| c.3337-1G > A | 0/0/108818 | 0/0/242920 | − | − | − | 3.95 | 0.79–>0 |
| PYCR1 | |||||||
| p.K71Nfs*10 | 0/0/113986 | 0/1/30918 | − | − | − | 33 | − |
| p.I74Tfs*10 | 0/0/113986 | 0/0/245176 | − | − | − | 32 | − |
| p.R119C | 0/10/114118 | 0/34/273316 | Probably damaging | Damaging | Decreased stability | 28.8 | − |
| p.R119H | 0/3/114566 | 0/3/242550 | Probably damaging | Damaging | Decreased stability | 28.9 | − |
| p.A179T | 0/3/113196 | 0/5/272934 | Probably damaging | Damaging | Decreased stability | 33 | − |
| c.540 + 1G > A | 0/3/112300 | 0/5/242262 | − | − | − | 25.8 | 0.98–>0 |
| c.633 + 1G > C | 0/2/21260 | 0/6/199450 | − | − | − | 31 | 0.49–>0 |
| p.A257T | 0/5/109454 | 0/9/274864 | Probably damaging | Damaging | Decreased stability | 30 | − |
| p.V258L | 0/0/109454 | 0/0/274864 | Probably damaging | Damaging | Decreased stability | 29.5 | − |
| c.797 + 2_5delTGGG | 0/0/107108 | 0/0/243200 | − | − | − | 24.2 | 0.30–>0 |
| p.R313L | 0/0/120196 | 0/0/245668 | Benign | Tolerated | Decreased stability | 2.5 | − |
| COL1A1 | |||||||
| p.G22R | 0/0/118552 | 0/0/245568 | Probably damaging | Tolerated | Decreased stability | 23.9 | − |
| SMC2 | |||||||
| p.K921N | 0/0/120326 | 0/0/274588 | Benign | Tolerated | Decreased stability | 16.95 | − |
ExAC Exome Aggregation Consortium, gnomAD genome aggregation database, Polyphen2 polymorphism phenotyping v2, SIFT sorting intoler-ant from tolerant, I-Mutant neural network-based predictor of protein stability, CADD combined annotation-dependent depletion, BDGP splice site prediction by neural network