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Table 1 Association of rare coding variants with breast cancer, for the 113 DNA repair genes sequenced in the GENESIS population [20]

From: Diagnostic chest X-rays and breast cancer risk among women with a hereditary predisposition to breast cancer unexplained by a BRCA1 or BRCA2 mutation

Gene Any variant
Control carriers Case carriers ORa (95% CI) P value Groupb
BABAM1/MERIT40 4 2 0.5 (0.1, 2.8) 0.43 Low
BACH1 22 21 0.8 (0.4, 1.5) 0.55 Low
BRCC3/BRCC36 3 1 0.3 (0.0, 3.2) 0.34 Low
BRE 11 7 0.6 (0.2, 1.6) 0.35 Low
CDH1 14 11 0.8 (0.4, 1.7) 0.54 Low
CDKN1A 13 11 0.8 (0.4, 1.9) 0.66 Low
COBRA1 6 4 0.7 (0.2, 2.4) 0.55 Low
DLG1 25 15 0.6 (0.3, 1.2) 0.12 Low
ESR1 10 6 0.6 (0.2, 1.5) 0.26 Low
EXO1 45 37 0.8 (0.5, 1.3) 0.41 Low
FAM175A/ABRAXAS 7 5 0.7 (0.2, 2.3) 0.56 Low
FANCA 19 15 0.8 (0.4, 1.6) 0.53 Low
FANCD2 20 15 0.7 (0.4, 1.4) 0.33 Low
FANCF 6 5 0.8 (0.3, 2.8) 0.77 Low
FANCG 6 4 0.7 (0.2, 2.4) 0.55 Low
FANCI 22 13 0.6 (0.3, 1.2) 0.13 Low
IRS2 13 9 0.7 (0.3, 1.5) 0.33 Low
KIAA1967 22 17 0.8 (0.4, 1.5) 0.41 Low
LIG4 15 13 0.7 (0.3, 1.6) 0.46 Low
MLH3 21 10 0.5 (0.2, 1.0) 0.06 Low
MUS81 10 7 0.6 (0.2, 1.6) 0.30 Low
MYC 2 2 0.8 (0.1, 5.5) 0.78 Low
NAT1 3 1 0.4 (0.0, 3.4) 0.37 Low
PMS2 22 16 0.7 (0.3, 1.3) 0.24 Low
POLH 13 5 0.4 (0.1, 1.1) 0.07 Low
POLQ 43 36 0.8 (0.5, 1.2) 0.43 Low
PRKAA2 8 3 0.4 (0.1, 1.5) 0.16 Low
RAD51D/RAD51L3 9 4 0.4 (0.1, 1.4) 0.17 Low
RAD54L 21 12 0.6 (0.3, 1.2) 0.14 Low
RTEL1 20 8 0.4 (0.2, 0.9) 0.03 Low
TIMELESS 28 23 0.8 (0.5, 1.4) 0.44 Low
TP53BP1 27 21 0.8 (0.5, 1.5) 0.51 Low
TP63 6 3 0.5 (0.1, 2.0) 0.33 Low
TTI2 9 7 0.8 (0.3, 2.2) 0.67 Low
WDR48 15 10 0.7 (0.3, 1.5) 0.36 Low
XRCC1 31 21 0.7 (0.4, 1.2) 0.14 Low
APEX1 10 10 1.0 (0.4, 2.4) 0.98 No effect
AR 32 31 1.0 (0.6, 1.6) 0.94 No effect
ATR 30 29 1.0 (0.6, 1.6) 0.92 No effect
BAP1 4 4 1.0 (0.3, 4.0) 1.00 No effect
BLM 35 31 0.9 (0.5, 1.4) 0.59 No effect
CDC27 12 12 1.0 (0.5, 2.3) 0.98 No effect
CDKN2A 3 3 1.0 (0.2, 4.9) 0.99 No effect
EIF4G1 26 29 1.1 (0.7, 1.9) 0.67 No effect
EP300 21 18 0.9 (0.5, 1.6) 0.66 No effect
ERCC6 47 53 1.1 (0.8, 1.7) 0.55 No effect
FANCB 9 9 0.9 (0.4, 2.4) 0.87 No effect
FANCC 11 10 0.9 (0.4, 2.2) 0.87 No effect
FANCE 11 10 0.9 (0.4, 2.2) 0.86 No effect
FANCL 9 10 1.1 (0.4, 2.8) 0.84 No effect
FLNA 25 24 1.0 (0.6, 1.7) 0.94 No effect
MAGI3 26 28 1.1 (0.6, 1.8) 0.82 No effect
MAST2 46 50 1.1 (0.7, 1.7) 0.66 No effect
MCM4 25 29 1.1 (0.7, 1.9) 0.70 No effect
MCPH1 27 28 1.0 (0.6, 1.8) 0.92 No effect
MDC1 24 22 0.9 (0.5, 1.7) 0.81 No effect
MSH2 18 17 0.9 (0.5, 1.8) 0.76 No effect
MSH6 16 16 0.9 (0.5, 1.9) 0.86 No effect
NBN 26 27 1.0 (0.6, 1.8) 0.87 No effect
PHLPP2 32 34 1.0 (0.6, 1.7) 0.97 No effect
POLK 22 22 1.0 (0.5, 1.8) 0.99 No effect
RAD51B/REC2/RAD51L1 6 5 0.9 (0.3, 2.8) 0.80 No effect
RECQL4 49 55 1.1 (0.8, 1.7) 0.59 No effect
RINT1 8 8 1.0 (0.4, 2.8) 0.95 No effect
SETX 25 24 1.0 (0.6, 1.7) 0.91 No effect
TELO2 17 18 1.1 (0.5, 2.1) 0.89 No effect
XRCC2 7 6 0.9 (0.3, 2.7) 0.84 No effect
APLF 7 11 1.5 (0.6, 3.9) 0.40 High
ATM 40 77 1.9 (1.3, 2.9) 0.001 High
BARD1 7 9 1.3 (0.5, 3.6) 0.59 High
BRIP1/FANCJ 16 25 1.5 (0.8, 2.8) 0.25 High
CHEK1 4 6 1.2 (0.3, 4.5) 0.75 High
CHEK2 22 62 3.0 (1.9, 5.0) 0.00001 High
CHGB 9 11 1.2 (0.5, 3.0) 0.65 High
DCLRE1C 9 14 1.6 (0.7, 3.7) 0.28 High
DGKZ 33 38 1.2 (0.7, 1.9) 0.52 High
ERCC2 17 27 1.6 (0.9, 3.0) 0.13 High
EYA3 6 7 1.2 (0.4, 3.5) 0.77 High
FANCM 23 38 1.7 (1.0, 2.8) 0.06 High
FEN1 6 7 1.2 (0.4, 3.6) 0.74 High
FOXO1 6 7 1.8 (0.5, 6.0) 0.38 High
FOXO3 0 8 - - High
FOXO4 0 4 - - High
MAST1 8 17 2.2 (0.9, 5.1) 0.07 High
MCM7 10 18 1.8 (0.8, 4.0) 0.13 High
MLH1 15 19 1.3 (0.6, 2.5) 0.52 High
MRE11A 12 14 1.2 (0.6, 2.6) 0.64 High
MSH3 25 30 1.2 (0.7, 2.1) 0.49 High
NTHL1 18 22 1.2 (0.6, 2.2) 0.65 High
NUMA1 36 51 1.4 (0.9, 2.2) 0.12 High
PALB2 9 30 3.5 (1.7, 7.5) 0.001 High
PIK3R1 1 4 4.3 (0.5, 38.3) 0.20 High
PMS1 6 10 1.5 (0.6, 4.3) 0.41 High
PPM1D 4 6 1.5 (0.4, 5.4) 0.53 High
PTEN 0 4 - - High
RAD50 30 37 1.2 (0.7, 2.0) 0.44 High
RAD51C 7 10 1.5 (0.6, 4.0) 0.41 High
RAD9B 4 6 1.5 (0.4, 5.2) 0.55 High
RECQL5 20 29 1.5 (0.9, 2.7) 0.14 High
REV3L 31 39 1.3 (0.8, 2.1) 0.30 High
RNF168 13 16 1.2 (0.6, 2.6) 0.59 High
RPA1 9 14 1.5 (0.7, 3.6) 0.32 High
SLX4/FANCP 36 44 1.2 (0.8, 1.9) 0.38 High
STK11 1 2 2.1 (0.2, 22.9) 0.55 High
TGFB1 5 9 1.6 (0.5, 4.9) 0.38 High
TOP3A 22 31 1.4 (0.8, 2.5) 0.23 High
TP53 3 6 2.0 (0.5, 8.0) 0.34 High
TSC2 45 56 1.3 (0.9, 1.9) 0.23 High
TTI1 26 30 1.2 (0.7, 2.0) 0.57 High
UIMC1/RAP80 12 15 1.2 (0.6, 2.7) 0.58 High
USP8 9 16 1.7 (0.7, 3.8) 0.23 High
WRN 47 59 1.3 (0.9, 1.9) 0.23 High
XRCC3 4 7 1.8 (0.5, 6.2) 0.36 High
  1. Abbreviations: OR (95%CI) odds ratio (95% confidence interval)
  2. aReference group: non-carrier of a variant in the tested gene
  3. bGroup “Low”: OR <0.9; Group “No Effect”: 0.9≤ OR ≤1.1; Group “High”: OR >1.1