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Table 1 Revised multifactorial likelihood analysis of BRCA1 unclassified variants

From: Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

BRCA1 variant Previous multifactorial likelihood classification: odds for causalitya Evolutionary conservation to Tetraodon and in BRCT domain Sequence alignment prior probabilityb Myriad frequency (in trans with deleterious mutation) LR from co-occurrence with a deleterious mutation Segregation analysis: Bayes factor Tumour histology (number analysed) Grade ER CK 5/6 CK14 LR pathology Multifactorial likelihood odds: co-occurrence, segregation, and pathology Posterior probability of a variant being deleterious
BRCA1 5215 G>A (R1699Q) 141:1 Invariant, to Tetraodon, inside BRCT 0.73 33 (0) 3.010 1.043 Not BRCA1-like (1) 1 Pos Neg Neg 0.14 0.440 0.543
BRCA1 5242 C>T (A1708V) 41:1 Invariant, to Tetraodon, inside BRCT 0.73 6 (0) 1.220 0.227 BRCA1-like (1) 3 Neg NA NA 2.95 0.817 0.668
BRCA1 5242 C>A (A1708E) 262:1 Invariant, to Tetraodon, inside BRCT 0.73 76 (0) 12.700 4.470 BRCA1-like (1) 3 Neg Pos Pos (focal) 27.38 1554.024 0.999
BRCA1 5331 G>A (G1738R) 5871:1 Invariant, to Tetraodon, inside BRCT 0.73 8 (0) 1.300 20.250 BRCA1-like (1) 3 Neg Neg Pos (strong) 0.37 9.724 0.963
        Not BRCA1-like (1) 0 Pos Neg Neg    
  1. aChenevix-Trench and colleagues [5] and Lovelock and colleagues [3]; bEaston and colleagues [19]. CK, cytokeratin; ER, estrogen receptor; LR, likelihood ratio; NA, not applicable; Neg, negative; Pos, positive.