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Table 3 Analyses of rare variants with missense substitutions stratified by Align-GVGD gradea

From: Rare, evolutionarily unlikely missense substitutions in CHEK2contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study

Class Patients, n Controls, n Crude OR (95% CI) Adjusted OR (95% CI)
Noncarriers 1,242 1,089   
T+SJV 17 3 4.97 (1.45 to 17.0) 6.18 (1.76 to 21.8)
Any rMS 44 17 2.27 (1.29 to 4.00) 2.20 (1.20 to 4.01)
rMS stratified by Align-GVGD gradeb  
   C0 12 9 1.17 (0.49 to 2.79) 1.39 (0.55 to 3.56)
   C15 14 5 2.46 (0.88 to 6.84) 1.82 (0.62 to 5.34)
   C25 7 2 3.07 (0.64 to 14.8) 2.47 (0.45 to 13.49)
   C35 1 0    -  
   C45 0 0    -  
   C55 1 0    -  
   C65 9 1 7.89 (1.00 to 62.4) 8.75 (1.06 to 72.2)
rMS stratified by SIFT gradec  
   S > 0.05 21 8 2.30 (1.02 to 5.22) 1.99 (0.83 to 4.77)
   0.05 ≥ S > 0.00 12 5 2.10 (0.74 to 5.99) 1.91 (0.63 to 5.86)
   S = 0.00 11 4 2.41 (0.77 to 7.59) 3.03 (0.91 to 10.0)
rMS stratified by PolyPhen-2 grade  
   Benign 16 7 2.00 (0.82 to 4.89) 1.69 (0.64 to 4.41)
   Possibly Dd 10 6 1.46 (0.53 to 4.03) 1.65 (0.55 to 4.89)
   Probably De 18 4 3.95 (1.33 to 11.7) 3.87 (1.25 to 12.0)
  1. a Odds ratios are adjusted for race or ethnicity (Caucasian, East Asian, African American or Latina), study center, and age as categorical variables; OR, odds ratio; 95% CI, 95% confidence interval; T+SJV, protein-truncating variants plus splice junction variant; rMS, rare missense substitution; S, SIFT score; bUsing the CHEK2 sequence alignment through S. purpuratus (sea urchin); cUsing the CHEK2 sequence alignment through D. melanogaster (fruit fly); dPolyPhen-2 grade "Possibly Damaging"; ePolyPhen-2 grade "Probably Damaging."