Table 2 List of genes with the corresponding PDAVs that were validated as true positive in the corresponding BC patient
Gene | Variant type | Transcript: Base change (Protein change) | Exon (Intron) | MAF 1000 g [gnomAD] | rsID (dbsnp147) | BC Patients | Controls |
|---|---|---|---|---|---|---|---|
ABCC11 | splice-site substitution | NM_032583.3:c.395 + 2 T > C (p.?) | 4 | − [0.000004061] | – | BB44 | 0 |
ABCC11 | nonsense substitution | NM_032583.3:c.297G > A (p.Trp99*) | 4 | − [0.0007676] | rs145048685 | BB12 | 1x |
BARD1 | nonsense substitution | NM_000465.3:c.1690C > T (p.Gln564*) | 8 | − [0.00002032] | rs587780021 | BB13 | 0 |
BBS10 | frameshift insertions | NM_024685.3:c.271dup (p.Cys91Leufs*5) | 2 | − [0.0005626] | rs549625604 | BB15 ** | 1x |
BBS10 | frameshift insertions | NM_024685.3:c.1543_1546dup (p.Thr516Argfs*7) | 2 | − [−] | – | BB48 | 0 |
CCNH | frameshift deletion | NM_001239.3:c.643_646del (p.Thr215Profs*21) | 5 | − [0.000008149] | – | BB15** | 0 |
CD96 | frameshift insertions | NM_198196.2:c.766dup (p.Ile256Asnfs*13) | 5 | − [0.00001625] | rs766366613 | BB10 | 0 |
CD96 | nonsense substitution | NM_198196.2:c.1321C > T (p.Arg441*) | 11 | − [0.0001056] | rs201691670 | BB54** | 0 |
CHEK2 | frameshift deletion | NM_001005735.1:c.1229del (p.Thr410Metfs*15) | 12 | 0.001 [0.002077] | rs555607708 | BB17 | 0 |
CYP1A1 | frameshift deletion | NM_000499.3:c.1371del (p.Cys457*) | 7 | 0.0006 [0.0009096] | rs561096394 | BB1 | 0 |
DCLRE1A | nonsense substitution | NM_001271816.1:c.412C > T (p.Arg138*) | 2 | 0.002 [0.00279] | rs41292634 | BB41 | 0 |
DCLRE1C | nonsense substitution | NM_001033855.2:c.241C > T (p.Arg81*) | 3 | − [0.00001221] | rs121908156 | BB33*** | 0 |
DHCR7 | splice-site substitution | NM_001360.2::c.964-1G > C (p.?) | 9(8) | 0.0026 [0.003762] | rs138659167 | BB21 | 0 |
DNAH11 | frameshift deletion | NM_001277115.1:c.2081_2082del (p.Val694Glyfs*2) | 12 | − [−] | – | BB29** | 0 |
ESCO2 | frameshift deletion | NM_001017420.2:c.876_879del (p.Asp292Glufs*48) | 4 | − [0.00000409] | rs80359856 | BB35** | 0 |
EXO1 | splice-site substitution | NM_006027.4:c.2212-1G > C (p.?) | 13(12) | 0.0012 [0.001644] | rs4150000 | BB35** | 0 |
FANCA | splice-site substitution | NM_000135.2:c.2152-2A > G (p.?) | 24(23) | − [−] | – | BB45 | 0 |
FLT4 | nonsense substitution | NM_182925.4:c.3048C > A (p.Cys1016*) | 22 | − [−] | – | BB38 | 0 |
HPS6 | stop-loss substitution | NM_024747.5:c.2326 T > C (p.*776Argext*38) | 1 | − [0.0001577] | rs200206362 | BB33*** | 0 |
MUS81 | nonsense substitution | NM_025128.4:c.392G > A (p.Trp131*) | 4 | − [0] | – | BB7 | 0 |
MYH8 | nonsense substitution | NM_002472.2:c.1209C > A (p.Cys403*) | 13 | 0.0004 [0.001105] | rs144321381 | BB31 | 0 |
NME8 | splice-site substitution | NM_016616.4:c.454 + 1G > A (p.?) | 8 | − [0.00006108] | rs538425312 | BB3** | 0 |
NME8 | nonsense substitution | NM_016616.4:c.1600C > T (p.Arg534*) | 17 | 0.0008 [0.0003171] | rs142525551 | BB33*** | 0 |
PALB2 | frameshift insertions | NM_024675.3:c.1674dup (p.Gln559Serfs*19) | 4 | − [−] | – | BB36 | 0 |
PDE11A | frameshift deletion | NM_016953.3:c.1660del (p.Cys554Valfs*14) | 9 | 0.0008 [0.001214] | rs573163079 | BB5 | 1x |
RAD51C | frameshift deletion | NM_058216.2:c.181_182del (p.Leu61Alafs*11) | 2 | − [0.00001624] | rs754525165 | BB54** | 0 |
RECQL4 | frameshift deletion | NM_004260.3:c.1573del (p.Cys525Alafs*33) | 9 | − [0.0002387] | rs386833845 | BB52 | 0 |
RECQL4 | frameshift deletion | NM_004260.3:c.3439del (p.Leu1147Cysfs*3) | 20 | − [−] | – | BB34 | 0 |
RINT1 | nonsense substitution | NM_021930.4:c.64G > T (p.Glu22*) | 2 | − [−] | – | BB3** | 0 |
TDP1 | frameshift deletion | NM_018319.3:c.502del (p.Leu168Serfs*45) | 3 | − [0.00002039] | rs762302264 | BB32 | 0 |
TTC8 | nonsense substitution | NM_001288781.1:c.736C > T (p.Gln246*) | 9 | − [−] | – | BB29** | 0 |