Table 3.
Details of 32 Variants Identified in Four ALL Cases
| No. | Chr: Position | Gene symbol | Ref/ Mut | Protein Impact | Predicted protein change | PolyPhen-2 prediction | SIFT prediction** |
|---|---|---|---|---|---|---|---|
| 1. | 1: 47685455 | TAL1 | T>C | Synonymous | K-311-K | - | - |
| 2. | 2:100218080 | AFF3 | G>A | Synonymous | A-421-A; A-396-A | - | - |
| 3. | 2:121726447 | GLI2 | G>A | Synonymous | S-267-S | - | - |
| 4. | 2:121747406 | G>A | Missense | D-1306-N | Benign | Tolerated | |
| 5. | 2:121747429 | A>G | Synonymous | P-1313-P | - | - | |
| 6. | 2:231149108 | SP140 | G>A | Missense | E-489-K; E-516-K; E-456-K; E-402-K | Benign | Tolerated |
| 7. | 3:128204951 | GATA2 | C>T | Missense | A-164-T | Benign | Tolerated |
| 8. | 3:187447032 | BCL6 | G>A | Synonymous | N-387-N | - | - |
| 9. | 5:135513086 | SMAD5 | InsC | Frameshift | H-439-PS | Unknown | Unknown |
| 10. | 5:176636882 | NSD1 | C>T | Synonymous | C-225-C; C-494-C | - | - |
| 11. | 5:176637149 | G>A | Synonymous | E-314-E; E-583-E | - | - | |
| 12. | 5:176721198 | T>C | Synonymous | L-2008-L; L-2277-L | - | - | |
| 13. | 7:151927021 | KMT2C | C>A | Missense | C-988-F | Unknown | Damaging |
| 14. | 7:151932908 | T>C | Synonymous | L-921-L | - | - | |
| 15. | 7:151945007 | C>T | Missense | G-838-S | Unknown | Damaging | |
| 16. | 7:151945204 | G>A | Missense | S-772-L | Unknown | Damaging | |
| 17. | 7:151970856 | T>A | Missense | T-316-S | Possibly damaging | Tolerated | |
| 18. | 7:151970931 | G>A | Missense | L-291-F | Probably damaging | Unknown | |
| 19. | 8:90967711 | NBN | A>G | Synonymous | D-399-D | - | - |
| 20. | 8:95143172 | CDH17 | T>G | Missense | E-739-A | Benign | Tolerated |
| 21. | 8:95143186 | C>G | Missense | E-734-D | Benign | Tolerated | |
| 22. | 9:139391636 | NOTCH1 | G>A | Synonymous | D-2185-D | - | - |
| 23. | 10:104160434 | NFKB2 | A>G | Synonymous | A-607-A | - | - |
| 24. | 13:28537317 | CDX2* | G>A | Missense | P-293-S | Benign | Tolerated |
| 25. | 13:28624294 | FLT3* | G>A | Missense | T-227-M | Probably damaging | Tolerated |
| 26. | 15:74328116 | PML | A>G | Missense | S-772-G; S-724-G | Unknown | Tolerated |
| 27. | 19:15271771 | NOTCH3 | G>A | Missense | A-2223-V | Benign | Tolerated |
| 28. | 19:15285052 | T>C | Synonymous | P-1521-P | - | - | |
| 29. | 19:15295134 | G>A | Synonymous | C-846-C | - | - | |
| 30. | 19:15302844 | T>C | Synonymous | A-202-A | - | - | |
| 31. | 22:50555619 | MOV10L1 | C>T | Synonymous | L-431-L; L-411-L | - | - |
| 32. | 22:50582626 | A>G | Missense | Q-820-R; Q-800-R | Benign | Tolerated |
Chr, chromosome; Ref, reference; Mut, mutant;
*
Validated with PCR and cycle sequencing (data not shown);
**
SIFT prediction score ≤0.05