Summary of mismatch repair (MMR) variants identified in the general Chinese population
| A. MMR variants identified | ||||||
| Data source | Cases | Variants identified | Total | |||
| MLH1 | MSH2 | MSH6 | PMS2 | |||
| ChinaMAP study7 | 10 588 | 3065 | 6586 | 2140 | 2222 | 14 013 |
| Singapore 10k study18 | 2657 | 1006 | 3012 | 715 | 855 | 5588 |
| 597 Han individuals19 | 597 | 18 | 57 | 31 | 59 | 165 |
| 90 Han individuals20 | 90 | 154 | 547 | 89 | 169 | 959 |
| Normal control21 | 610 | 145 | 701 | 169 | 176 | 1191 |
| Macau individuals | 4302 | 143 | 239 | 0 | 0 | 382 |
| Total | 18 844 | 4531 | 11 142 | 3144 | 3481 | 22 298 |
| B. Types of coding variants | |||||
| Type | MLH1 (%) | MSH2 (%) | MSH6 (%) | PMS2 (%) | Total (%) |
| Missense | 117 (10.0) | 131 (11.2) | 214 (18.4) | 124 (10.6) | 586 (50.3) |
| Synonymous SNV | 44 (3.8) | 48 (4.1) | 85 (7.3) | 54 (4.6) | 231 (19.8) |
| Splice site | 3 (0.3) | 6 (0.5) | 18 (1.5) | 11 (0.9) | 38 (3.3) |
| Stopgain | 0 (0.0) | 1 (0.1) | 3 (0.3) | 4 (0.3) | 8 (0.7) |
| Frameshift insertion | 0 (0.0) | 1 (0.1) | 3 (0.3) | 2 (0.2) | 6 (0.5) |
| Frameshift deletion | 0 (0.0) | 3 (0.3) | 0 (0.0) | 1 (0.1) | 4 (0.3) |
| Splice acceptor | 0 (0.0) | 0 (0.0) | 0 (0.0) | 4 (0.3) | 4 (0.3) |
| Nonframeshift insertion | 0 (0.0) | 0 (0.0) | 2 (0.2) | 0 (0.0) | 2 (0.2) |
| Nonsense | 0 (0.0) | 2 (0.2) | 0 (0.0) | 0 (0.0) | 2 (0.2) |
| Splice donor | 0 (0.0) | 1 (0.1) | 0 (0.0) | 1 (0.1) | 2 (0.2) |
| Nonframeshift deletion | 0 (0.0) | 0 (0.0) | 1 (0.1) | 0 (0.0) | 1 (0.1) |
| Stoploss | 0 (0.0) | 0 (0.0) | 1 (0.1) | 0 (0.0) | 1 (0.1) |
| Unclassifiable | 46 (3.9) | 55 (4.7) | 166 (14.2) | 14 (1.2) | 281 (24.1) |
| Total | 210 (18.0) | 248 (21.3) | 493 (42.3) | 215 (18.4) | 1166 (100.0) |
| C. Novel variants | ||||||
| Item | MLH1 (%) | MSH2 (%) | MSH6 (%) | PMS2 (%) | Total (%) | |
| Coding variants | Total | 210 | 248 | 493 | 215 | 1166 |
| Novel | 102 (8.7) | 90 (7.7) | 261 (22.4) | 74 (6.3) | 527 (45.2) | |
| Non-coding variants | Total | 3416 | 8629 | 2052 | 2424 | 16 521 |
| Novel | 2471 (14.5) | 5867 (35.5) | 1433 (8.7) | 1690 (10.2) | 11 528 (69.8) | |
| Total | 2573 (15.1) | 5957 (33.7) | 1694 (9.6) | 1764 (10.0) | 12 055 (68.2) | |
| D. Ts/Tv ratios | ||||
| Mutation type | Change | Coding (%) | Non-coding (%) | Total (%) |
| Transition | C>T | 182 (16.9) | 3068 (20.7) | 3250 (20.4) |
| G>A | 202 (18.8) | 2545 (17.2) | 2747 (17.3) | |
| A>G | 172 (16.0) | 2171 (14.7) | 2343 (14.7) | |
| T>C | 131 (12.2) | 1526 (10.3) | 1657 (10.4) | |
| Transversion | A>C | 38 (3.5) | 523 (3.5) | 561 (3.5) |
| A>T | 31 (2.9) | 492 (3.3) | 523 (3.3) | |
| C>A | 49 (4.6) | 615 (4.2) | 664 (4.2) | |
| C>G | 92 (8.6) | 1165 (7.9) | 1257 (7.9) | |
| G>C | 57 (5.3) | 818 (5.5) | 875 (5.5) | |
| G>T | 61 (5.7) | 855 (5.8) | 916 (5.8) | |
| T>A | 26 (2.4) | 478 (3.2) | 504 (3.2) | |
| T>G | 35 (3.3) | 561 (3.8) | 596 (3.8) | |
| Ts/Tv* | 3.53 | 3.38 | 3.39 | |
| E. Location of non-coding variants | |||||
| Non-coding variants | MLH1 (%) | MSH2 (%) | MSH6 (%) | PMS2 (%) | Total (%) |
| Intron | 3351 (20.3) | 7328 (44.4) | 1904 (11.5) | 2424 (14.7) | 14 941 (90.4) |
| UTR3 | 63 (0.4) | 867 (5.2) | 0 (0.0) | 52 (0.3) | 982 (5.9) |
| UTR5 | 2 (0.0) | 0 (0.0) | 148 (0.9) | 14 (0.1) | 316 (1.9) |
| Downstream | 0 (0.0) | 282 (1.7) | 0 (0.0) | 0 (0.0) | 282 (1.7) |
| Total | 3416 (20.7) | 8629 (52.2) | 2052 (12.4) | 2424 (14.7) | 16 521 (100.0) |
*Ts/Tv ratio was calculated by 2×Ts/Tv.