Table 1.
SETD2 and SETD1A variant details
| Sample ID | Variant | Age/sex | Previously published | ACMG-AMP criteria |
|---|---|---|---|---|
| SETD2-R1740Q-P1 | c.5219G > A p.(Arg1740Gln) de novo missense |
12/F | PM1, PM2, PM6, PP3 | |
| SETD2-R1740Q-P2 | c.5219G > A p.(Arg1740Gln) de novo missense |
5/M | “ | |
| SETD2-R1740W-P1 | c.5218C > T p.(Arg1740Trp) de novo missense |
0.5/M | Patient 7 (25) | PM1, PM2, PM6, PP3 |
| SETD2-R1740W-P2 | c.5218C > T p.(Arg1740Trp) de novo missense |
10/M | Patient 11 (25) | “ |
| SETD2-R1740W-P3 | c.5218C > T p.(Arg1740Trp) de novo missense |
10/F | Patient 9 (25) | “ |
| SETD2-R1740W-P4 | c.5218C > T p.(Arg1740Trp) de novo missense |
12/F | Patient 4 (25) | “ |
| SETD2-LLS-P1 | c.4438_4441del p.(Val1480fs) de novo frameshift |
12/M | PVS1, PM2, PM6, PP3 | |
| SETD2-LLS-P2 | c.1647_1667delinsTG p.(Ser550AspfsTer23) de novo frameshift |
4.5/M | Case 1 (30) | PVS1, PM2, PM6, PP3 |
| SETD2-LLS-P3 | c.513del p.(Pro172fs) de novo frameshift |
2/M | PVS1, PM2, PM6, PP3 | |
| SETD2-LLS-P4 | c.4457_4460delAGAA p.(Lys1486ArgfsTer28) de novo frameshift |
20/F | PVS1, PM2, PM6, PP3 | |
| SETD1A-P1 | c.4582-2_4582-1del de novo splice acceptor |
3/M | “ | |
| SETD1A-P2 | c.4582-2_4582-1del de novo splice acceptor |
17/F | “ | |
| SETD1A-P3 | c.4582-2_4582-1del de novo splice acceptor |
13/F | “ | |
| SETD1A-P4 | c.4711C > T p.(Arg1571Ter) Nonsense |
3/F | PVS1, PM2, PP3 | |
| SETD1A-P5 | c.2289dup p.Val764Serfs*61 de novo frameshift |
7/F | PVS1, PM2, PM6, PP3 | |
| SETD1A-P6 | Whole gene deletion CNV (852 kb loss of 41 genes) |
12/F | PVS1, PM2, PP3 |