Table 2 Pathological prediction and frequency in controls of selected SLX4 missense variants
From: Analysis of SLX4/FANCP in non-BRCA1/2-mutated breast cancer families
Exon | Nucleotide change | Amino acid change | dbSNP† | Pathological prediction | Controls tested (n) | Number of control carriers (%) | |||
|---|---|---|---|---|---|---|---|---|---|
SIFT (score < 0.05, deleterious) | PolyPhen-2 (false positive rate) | Condel (weighted average of scores) | Condel prediction | ||||||
2 | c.248G > C | p.Gly83Ala | NA | 0.14 | 0.15 | 0.15 | Neutral | 283 | 0 |
2 | c.421G > T | p.Gly141Trp | NA | 0.00 | 0.86 | 0.86 | Deleterious | 284 | 2 (0.7) |
3 | c.590T > C | p.Val197Ala | NA | 0.48 | 0.01 | 0.00 | Neutral | 284 | 1 (0.4) |
3 | c.710G > A | p.Arg237Gln | NA | 0.49 | 0.00 | 0.38 | Neutral | 284 | 4 (1.4) |
8 | c.1846G > A | p.Val616Met | NA | 0.17 | 0.62 | 0.80 | Deleterious | 281 | 0 |
12 | c.2469G > C | p.Trp823Cys | NA | 0.01 | 1.00 | 0.97 | Deleterious | 282 | 0 |
12 | c.3872C > T | p.Thr1291Met | NA | 0.05 | 0.98 | 0.99 | Deleterious | 283 | 0 |
12 | c.4261A > T | p.Ille1421Phe | NA | 0.08 | 0.77 | 0.77 | Deleterious | 285 | 0 |
12 | c.4409C > T | p.Pro1470Leu | rs72778139 | 0.02 | 0.99 | 0.96 | Deleterious | 283 | 0 |
14 | c.5072A > G | p.Asn1691Ser | NA | 0.56 | 0.00 | 0.01 | Neutral | 285 | 0 |