Table 3.
Characteristics of Germline SEC23B Variants in TCGA Thyroid, Breast, and Endometrial Cancer Datasets
| Cancer Datasets | Variants | NHLBI ESPaMAF | SIFT | PolyPhen-2 | MutationTaster |
Conservation |
|
|---|---|---|---|---|---|---|---|
| Phylob | PhastConsc | ||||||
| THCA (n = 494) | c.1661G>A (p.Arg554Gln) | 0 | damaging (0.02) | probably damaging (0.998) | disease causing | 5.365 | 1 |
| c.1598T>G (p.Val533Gly) | 0 | damaging (0) | possibly damaging (0.621) | disease causing | 4.497 | 1 | |
| c.167A>G (p.Tyr56Cys) | 0 | damaging (0) | possibly damaging (0.752) | disease causing | 4.798 | 1 | |
| c.301A>G (p.Ile101Val) | 0 | damaging (0.04) | possibly damaging (0.643) | disease causing | 4.760 | 1 | |
| c.689+1G>C | 0 | – | – | disease causing | 5.047 | 1 | |
| c.2101C>T (p.Arg701Cys) | 0 | damaging (0) | probably damaging (1.000) | disease causing | 2.648 | 0.988 | |
| c.1636C>T (p.Arg546Trp) | T = 1, C = 13,005 (0.000077) | damaging (0) | probably damaging (1.000) | disease causing | 1.987 | 1 | |
| c.2031G>A (p.Met677Ile) | A = 2, G = 13,004 (0.000154) | damaging (0.02) | benign (0.014) | disease causing | 5.584 | 1 | |
| c.40C>T (p.Arg14Trp) | T = 3, C = 13,003 (0.000231) | damaging (0.01) | probably damaging (0.999) | disease causing | 2.132 | 1 | |
| c.1484G>A (p.Arg495His) | A = 95, G = 12,911 (0.007358) | tolerated (0.12) | probably damaging (0.961) | disease causing | 5.579 | 1 | |
| c.490G>T (p.Val164Leu) | T = 97, G = 12,909 (0.0075) | damaging (0.01) | possibly damaging (0.870) | disease causing | 5.615 | 1 | |
| BRCA (n = 222) | c.884C>A (p.Pro295His) | 0 | damaging (0) | probably damaging (0.983) | disease causing | 5.778 | 1 |
| c.985G>T (p.Ala329Ser) | T = 4, G = 13,002 (0.000307) | damaging (0.04) | possibly damaging (0.601) | disease causing | 5.591 | 1 | |
| c.74C>A (p.Pro25His) | A = 5, C = 13,001 (0.000385) | damaging (0) | probably damaging (1.000) | disease causing | 5.701 | 1 | |
| c.490G>T (p.Val164Leu) | T = 97, G = 12,909 (0.0075) | damaging (0.01) | possibly damaging (0.870) | disease causing | 5.615 | 1 | |
| UCEC (n = 156) | c.389T>C (p.Ile130Thr) | 0 | damaging (0.05) | benign (0.006) | disease causing | 4.638 | 1 |
| c.649C>T (p.Arg217∗) | T = 1, C = 13,005 (0.000077) | – | – | disease causing | −0.056 | 0.031 | |
| c.490G>T (p.Val164Leu) | T = 97, G = 12,909 (0.0075) | damaging (0.01) | possibly damaging (0.870) | disease causing | 5.615 | 1 | |
a
NHLBI Exome Sequencing Project (ESP) Exome Variant Server v.0.0.28 (accessed May 9, 2015).
b
PhyloP scores range between −14 and +6; conserved sites have positive scores.
c
PhastCons scores range between 0 and 1; values closer to 1 have a higher probability of nucleotide conservation.