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Table 2 List of genes with the corresponding PDAVs that were validated as true positive in the corresponding BC patient

From: Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families

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
  1. In addition to the details of each variant (variant type, transcript ID, base change, protein change, exon/intron), its frequency in controls, dbsnp147, global MAF in 1000 genome [2015 August release] and gnomAD [Ensembl GRCh37 release 95] are also given. ** = BC patient with PDAV in two genes, *** = BC patient with PDAV in three genes and “−” = not available