Table 1.
Overview of SHOX2 variants identified in AF (atrial fibrillation) and SND (sinus node dysfunction) patients and control databases: 1,000 gnomes project (TGP) and the genome Aggregation Database (gnomAD); only the European Non-Finnish populations were considered. Novel variants were selected for further functional studies based on the predicted pathological potential via CADD (combined annotation dependent depletion).
| Patient cohort | Genomic position (GRCh37) | Transcript consequence | Protein consequence | Patient cohort allele frequency | TGP allele frequency | gnomAD v2.1 (non-TOPMed) allele frequency | CADD score |
|---|---|---|---|---|---|---|---|
| Atrial fibrillation n = 378 Hoffmann et al., 2016 |
3:157823572 C > T | c.242G > A | p.G81E | 0.0013227 (1/378) |
– | 0.00005404 (2/18504) |
22.7 |
| 3:157816035 G > T | c.849C > A | p.H283Q | 0.0013227 (1/378) |
– | – | 25.2 | |
| Atrial fibrillation n = 162 Li et al., 2018 |
3:157820514 G > A | c.580C > T | p.R194X | 0.0030864 (1/162) |
– | – | 38.0 |
| Atrial fibrillation n = 450 current study |
3:157823584 C > T | c.230G > A | p.G77D | 0.0011111 (1/450) |
– | – | 22.2 |
| 3:157822878 C > T | c.387G > A | p.L129= | 0.0033333 (3/450) |
– | 0.0003306 (22/33275) |
10.68 | |
| 3:157822877 G > A | c.388C > T | p.L130F | 0.0011111 (1/450) |
– | 0.00001795 (1/27852) |
9.02 | |
| 3:157816005 G > A | c.879C > T | p.A293= | 0.0011111 (1/450) |
– | 0.0004573 (55/60141) |
20.6 | |
| Sinus node dysfunction n = 98 current study |
3:157823716 G > C | c.98C > G | p.P33R | 0.0051020 (1/98) |
– | 0.000009848 (1/50770) |
25.8 |