Table 4.
The number of ns cSNVs deemed “novel” with predicted functional consequence scores greater than that assigned a known CMT syndrome-inducing variant as function of the reference panel used for five individual genomes of diverse ancestry.
| Indiv | Source | ALLDB | Polyphen score >0.825 (N = 506) |
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|---|---|---|---|---|---|---|---|---|---|---|
| All 1000k | 1000k EUR | 1000k ASN | 1000k AFR | All CGI | CGI EUR | CGI ASN | CGI AFR | |||
| 1000+ | ∼500 | ∼500 | ∼500 | 52 | 8 | 8 | 8 | |||
| European | STSI | 101/1593 | 179/1593 | 194/1593 | 317/1593 | 680/1593 | 174/1593 | 439/1593 | 588/1593 | 669/1593 |
| African American | CGI | 185/1938 | 262/1938 | 795/1938 | 1068/1938 | 991/1938 | 995/1938 | 568/1938 | ||
| Mexican | CGI | 169/1595 | 272/1595 | 362/1595 | 676/1595 | 491/1595 | 566/1595 | 681/1595 | ||
| East Indian | CGI | 257/1685 | 329/1685 | 405/1685 | 669/1685 | 533/1685 | 538/1685 | 680/1685 | ||
| Puerta Rican | CGI | 220/1664 | 287/1664 | 417/1664 | 683/1664 | 491/1664 | 576/1664 | 654/1664 | ||
| Indiv | Source | ALLDB |
Sift score >0.931 (N = 506) |
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| All 1000k | 1000k EUR | 1000k ASN | 1000k AFR | All CGI | CGI EUR | CGI ASN | CGI AFR | |||
| n = 1000+ | ∼500 | ∼500 | ∼500 | 52 | 8 | 8 | 8 | |||
| European | STSI | 127/2593 | 232/2593 | 252/2593 | 394/2593 | 947/2593 | 221/2593 | 627/2593 | 843/2593 | 930/2593 |
| African American | CGI | 241/3199 | 319/3199 | 1174/3199 | 1662/3199 | 1557/3199 | 1569/3199 | 828/3199 | ||
| Mexican | CGI | 221/2565 | 311/2565 | 449/2565 | 963/2565 | 689/2565 | 831/2565 | 948/2565 | ||
| East Indian | CGI | 353/2856 | 433/2856 | 537/2856 | 1070/2856 | 803/2856 | 835/2856 | 1016/2856 | ||
| Puerta Rican | CGI | 289/2657 | 351/2657 | 502/2657 | 963/2657 | 676/2657 | 809/2657 | 900/2657 | ||
| Indiv | Source | ALLDB |
Sift score >0.878 (N = 506) |
|||||||
| All 1000k | 1000k EUR | 1000k ASN | 1000k AFR | All CGI | CGI EUR | CGI ASN | CGI AFR | |||
| n = 1000+ | ∼500 | ∼500 | ∼500 | 52 | 8 | 8 | 8 | |||
| European | STSI | 90/1269 | 157/1269 | 169/1269 | 268/1269 | 563/1269 | 146/1269 | 362/1269 | 478/1269 | 551/1269 |
| African American | CGI | 148/1524 | 197/1524 | 628/1524 | 871/1524 | 800/1524 | 802/1524 | 466/1524 | ||
| Mexican | CGI | 145/1229 | 204/1229 | 279/1229 | 556/1229 | 396/1229 | 455/1229 | 565/1229 | ||
| East Indian | CGI | 213/1321 | 255/1321 | 315/1321 | 562/1321 | 428/1321 | 429/1321 | 556/1321 | ||
| Puerta Rican | CGI | 173/1281 | 208/1281 | 309/1281 | 546/1281 | 391/1281 | 461/1281 | 531/1281 | ||
The numerator in each cell entry provides the number of ns cSNVs with functional consequence scores greater than the average of (N = 506) known CMT mutations that would be deemed novel on the basis of the different reference panels associated with each column of the table for the individuals’ whole genome variant lists denoted in the “Indiv” column. The denominator provides the total number of ns cSNVs on each individual’s (“Indiv”) genome with scores higher than the CMT mutation.