Table 2.

Cross validation of the transcription assay with genetic data.

Variantsa	Genetic or Integrative Classification	Functional Classification	References
H1402Y	Neutral	Neutral	Judkins et al. 2005; Phelan et al. 2005
R1443G	Neutral	Neutral	Overall odds against causalityb >50:1; Carvalho et al. 2007
S1512I	Neutral	Neutral	Tavtigian et al. 2006; Phelan et al. 2005
V1534M	Neutral	Neutral	Chenevix-Trench et al. 2006; Easton et al. 2007; Carvalho et al. 2007
D1546N	Neutral	Neutral	Tavtigian et al. 2006; Carvalho et al. 2007
T1561I	Neutral	Neutral	Judkins et al. 2005; Hayes et al. 2000
L1564P	Neutral	Neutral	Judkins et al. 2005; Tavtigian et al. 2006; Carvalho et al. 2007
S1613G	Neutral	Neutral	Tavtigian et al. 2006; Phelan et al. 2005
P1614S	Neutral	Neutral	Judkins et al. 2005; Carvalho et al. 2007
M1628T	Neutral	Neutral	Judkins et al. 2005; Tavtigian et al. 2006; Phelan et al. 2005
M1652I	Neutral	Neutral	Tavtigian et al. 2006; this study
A1669S	Neutral	Neutral	Judkins et al. 2005; Vallon-Christersson et al. 2001
T1685I	Deleterious	Deleterious	Easton et al. 2007; Carvalho et al. 2007
V1688del	Deleterious	Deleterious	Easton et al. 2007; Vallon-Christersson et al. 2001; Malacrida et al. 2008
M1689R	Deleterious	Deleterious	Easton et al. 2007; Mirkovic et al. 2004
R1699W	Deleterious	Deleterious	Easton et al. 2007; Vallon-Christersson et al. 2001
R1699Q	Deleterious	Deleterious	Chenevix-Trench et al. 2006; Vallon-Christersson et al. 2001
G1706E	Deleterious	Deleterious	Easton et al. 2007; Carvalho et al. 2007
A1708E	Deleterious	Deleterious	Easton et al. 2007; Carvalho et al. 2007
S1715R	Deleterious	Deleterious	Easton et al. 2007; Vallon-Christersson et al. 2001
T1720A	Neutral	Neutral	Easton et al. 2007; Phelan et al. 2005
V1736A	Neutral	Deleterious	Easton et al. 2007; Carvalho et al. 2007
G1738R	Deleterious	Deleterious	Chenevix-Trench et al. 2006; Easton et al. 2007; Carvalho et al. 2007
5382insC	Deleterious	Deleterious	Miki et al. 1994; Monteiro et al. 1996;
L1764P	Deleterious	Deleterious	Easton et al. 2007; Carvalho et al. 2007
I1766S	Deleterious	Deleterious	Easton et al. 2007; Carvalho et al. 2007
M1775K	Deleterious	Deleterious	Tischkowitz et al. 2008
M1775R	Deleterious	Deleterious	Miki et al. 1996; Phelan et al. 2005
G1788V	Deleterious	Deleterious	Easton et al. 2007; Phelan et al. 2005
V1804D	Neutral	Neutral	Easton et al. 2007; Carvalho et al. 2007
Y1853X	Deleterious	Deleterious	Friedman et al. 1994; Phelan et al. 2005

^aVariants in bold are nonsense, frameshift or deletions.

^bD. Goldgar, personal communication.