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Table 3 Number of carriers with loss-of-function and missense variants detected in case and control cohorts

From: Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs

Gene Selection criteria Number of carriers with loss-of-function variants Number of carriers with missense variants
Case Control p Valuea OR 95% CI Case Control p Valuea OR 95% CI
TET2 GWAS proposed 5 2 0.456 2.27 0.37–23.87 20 18 1 1.01 0.50–2.03
NRIP1 GWAS proposed 3 0 0.251 Und 0.37–∞ 21 17 0.632 1.12 0.56–2.28
RAD51B GWAS proposed 2 0 0.501 Und 0.17–∞ 6 4 0.756 1.36 0.32–6.57
SNX32 Neighbouring genes 2 0 0.501 Und 0.17–∞ 3 6 0.323 0.45 0.07–2.12
ZNF226 Neighbouring genes 2 2 1 0.91 0.07–12.5 24 18 0.640 1.21 0.63–2.39
ADAM29 GWAS proposed 1 0 1 Und 0.02–∞ 13 11 1 1.07 0.44–2.65
CASP8 GWAS proposed 1 0 1 Und 0.02–∞ 8 2 0.113 3.64 0.72–35.26
CDKN2A GWAS proposed 1 0 1 Und 0.02–∞ 3 3 1 0.91 0.12–6.77
DCLRE1B Neighbouring genes 1 1 1 0.91 0.01–71.08 7 6 1 1.06 0.30–3.82
FTO GWAS proposed 1 0 1 Und 0.02–∞ 10 11 0.668 0.82 0.31–2.14
LGR6 GWAS proposed 1 0 1 Und 0.02–∞ 16 8 0.217 1.82 0.73–4.94
MUS81 Neighbouring genes 1 1 1 0.91 0.01–71.08 8 9 0.808 0.80 0.27–2.36
NFRKB Neighbouring genes 1 1 1 0.91 0.01–71.08 17 12 0.577 1.29 0.58–2.97
PDE4D GWAS proposed 1 0 1 Und 0.02–∞ 6 3 0.512 1.81 0.39–11.24
SETMAR Neighbouring genes 1 2 0.607 0.45 0.01–8.70 7 3 0.349 2.12 0.48–12.73
SLC4A7 GWAS proposed 1 0 1 Und 0.02–∞ 14 10 0.682 1.27 0.52–3.21
USHBP1 Neighbouring genes 1 1 1 0.91 0.01–71.08 14 11 0.841 1.15 0.48–2.82
CDKN2B GWAS proposed 0 1 0.475 0 0–35.30 1 1 1 0.91 0.01–71.08
TCF7L2 GWAS proposed 0 1 0.475 0 0–35.30 5 8 0.406 0.56 0.14–1.96
TPK1 Neighbouring genes 0 1 0.475 0 0–35.30 2 2 1 0.91 0.07–12.50
ZNF283 Neighbouring genes 17 6 0.057 2.59 0.97–8.06
HNF4G GWAS proposed 4 1 0.377 3.63 0.36–178.82
TERT GWAS proposed 5 6 0.765 0.75 0.18–2.97
UNC13A Neighbouring genes 17 8 0.158 1.94 0.79–5.21
LSP1 GWAS proposed 11 15 0.327 0.66 0.27–1.55
XRCC1 Neighbouring genes 6 12 0.153 0.45 0.14–1.30
ZMIZ1 GWAS proposed 15 11 0.694 1.24 0.53–3.00
EMID1 Neighbouring genes 11 8 0.654 1.25 0.46–3.59
FGFR2 GWAS proposed 4 4 1 0.91 0.17–4.87
CCDC88C GWAS proposed 38 45 0.219 0.76 0.47–1.20
ITPR1 Neighbouring genes 17 20 0.507 0.77 0.37–1.55
MKL1 GWAS proposed 26 19 0.547 1.24 0.66–2.40
CHST9 GWAS proposed 7 9 0.617 0.70 0.22–2.13
PEX14 GWAS proposed 9 6 0.613 1.36 0.43–4.66
PAX9 GWAS proposed 3 7 0.207 0.39 0.06–1.70
PTHLH GWAS proposed 3 1 0.626 2.72 0.22–142.85
CDCA7 GWAS proposed 5 3 0.729 1.51 0.29–9.76
MAP3K1 GWAS proposed 20 11 0.206 1.66 0.75–3.85
RANBP9 GWAS proposed 10 5 0.309 1.82 0.56–6.80
DNAJC1 GWAS proposed 8 9 0.808 0.80 0.27–2.36
TOX3 GWAS proposed 7 7 1 0.90 0.27–3.03
EPB41L5 Neighbouring genes 8 8 1 0.90 0.29–2.78
ESR1 GWAS proposed 3 6 0.323 0.45 0.07–2.12
MDM4 GWAS proposed 7 3 0.349 2.12 0.48–12.73
CDYL2 GWAS proposed 11 5 0.217 2 0.64–7.37
TNP1 Neighbouring genes 0 2 0.226 0 0–4.82
BABAM1 Neighbouring genes 4 3 1 1.21 0.20–8.27
TGFBR2 GWAS proposed 4 3 1 1.21 0.20–8.27
ELL GWAS proposed 9 5 0.430 1.63 0.49–6.23
NF2 Neighbouring genes 12 5 0.150 2.19 0.71–7.95
KCNN4 Neighbouring genes 8 4 0.393 1.82 0.49–8.27
DLX2 Neighbouring genes 7 4 0.553 1.59 0.40–7.42
KAT5 Neighbouring genes 3 2 1 1.36 0.16–16.29
COX11 GWAS proposed 2 1 1 1.81 0.09–106.93
EBF1 GWAS proposed 2 3 0.673 0.60 0.05–5.27
RAD23B Neighbouring genes 0 1 0.475 0 0–35.30
GWAS proposed genes 17 4 0.008 3.89 1.26–15.95 287 251 0.679b 1.05 0.86–1.28
Neighbouring genes 9 9 1 0.90 0.32–2.58 168 138 0.392b 1.12 0.87–1.44
Total 26 13 0.077 1.83 0.90–3.90 406 353 0.512b 1.07 0.89–1.28
  1. Abbreviations: GWAS Genome-wide association study, Und undefined
  2. aFisher’s exact test, two-sided
  3. bPearson’s chi-square test with the Yates correction