TABLE 1.
Detailed description of the observed rare variants in CYLD.
| Case No. | Exon | c.DNA | Amino acid change | Depth | Alt reads | dbSNP | ExAC East Asia | gnomAD East Asia | SIFT | Poly phen2 | LRT | Mutation taster | ACMG classification |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0412 | 4 | c.98A > G | p.K33R | 157 | 88 | rs565310513 | 0.000116 | 0.000173 | T | B | D | D | VUS |
| 3886 | 4 | c.467G > A | p.R156K | 155 | 77 | — | — | — | T | D | D | D | VUS |
| 7781 | 5 | c.570T > G | p.D190E | 90 | 43 | — | — | — | T | B | N | D | VUS |
| 7923 | 5 | c.608A > T | p.E203V | 154 | 71 | — | — | — | D | D | D | D | VUS |
| 0659 | 8 | c.982G > C | p.D328H | 37 | 24 | — | — | — | D | P | D | D | VUS |
| 0872 | 9 | c.1130T > A | p.I377N | 63 | 26 | — | — | — | D | B | D | D | VUS |
| 0952 | 10 | c.1189C > A | p.R397S | 98 | 48 | rs149427272 | 0.000348 | 0.000231 | T | B | N | D | VUS |
| 0240 | 10 | c.1327C > A | p.Q443K | 203 | 100 | rs764952788 | 0.000348 | 0.000289 | T | P | D | D | VUS |
| 3098 | 10 | c.1360G > A | p.V454I | 94 | 42 | rs200451975 | 0.000116 | 0.000058 | T | T | N | D | VUS |
SIFT:D: deleterious (0–0.05), T: tolerated (>0.05).
PolyPhen2: D: Probably damaging (≥0.909), P: possibly damaging (0.447 ≤ pp2_hvar ≤ 0.909), B: benign (pp2_hvar ≤ 0.446).
LRT: likelihood ratio test; D: Deleterious; N: Neutral (identification of deleterious mutations within three human genomes).
Mutation Taster: D: disease causing; N: polymorphism; P: polymorphism automatic.
VUS: variant of uncertain significance.