Table II.
Computational predictions of deleterious missense mutations.
| A, APC | ||||
|---|---|---|---|---|
| Variant | Functional class | PolyPhen-2 | SIFT | SNPs&GO |
| c.2350T>A (p.Ser784Thr) | Missense mutation | BENIGN (0.017) | Tolerated (0.41) | Neutral (RI: 5) |
| c.2638A>C (p.Ile880Leu) | Missense mutation | BENIGN (0.376) | Tolerated (0.92) | Disease (RI: 6) |
| c.3511C>G (p.Arg1171Gly) | Missense mutation | BENIGN (0.000) | Tolerated (0.11) | Disease (RI: 1) |
| c.3775A>C (p.Ile1259Leu) | Missense mutation | BENIGN (0.008) | Tolerated (0.58) | Disease (RI: 7) |
| c.4557T>A (p.Asp1519Glu) | Missense mutation | N/A | Tolerated (0.16) | Disease (RI: 6) |
| c.4655A>T (p.Glu1552Val) | Missense mutation | BENIGN (0.104) | Tolerated (0.24) | Neutral (RI: 1) |
| c.6646C>A (p.Pro2216Thr) | Missense mutation | BENIGN (0.000) | Tolerated (0.12) | Neutral (RI: 0) |
| B, MUTYH | ||||
| Variant | Functional class | PolyPhen-2 | SIFT | SNPs&GO |
| c.553G>C (p.Glu185Gln) | Missense mutation | BENIGN (0.020) | Tolerated (0.08) | Neutral (RI: 8) |
| c.1232A>T (p.Gln411Leu) | Missense mutation | BENIGN (0.000) | Tolerated (0.10) | Neutral (RI: 9) |
| c.1268G>A (p.Arg423His) | Missense mutation | BENIGN (0.001) | Tolerated (0.12) | Neutral (RI: 4) |
| c.1483C>G (p.Gln495Glu) | Missense mutation | BENIGN (0.146) | Tolerated (1.00) | Neutral (RI: 9) |
PolyPhen-2, >0.50 is predicted to be damaging; SIFT, <0.05 is predicted to be deleterious; RI, prediction reliability scored between 0 (unreliable) and 10 (reliable). Disease, disease-associated polymorphism; neutral, neutral polymorphism; PolyPhen, polymorphism phenotype; SIFT, Sorting Intolerant From Tolerant; SNPs&GO, Single Nucleotide Polymorphisms & Gene Ontology; RI, reliability index; APC, adenomatous polyposis coli; MUTYH, mutY DNA glycosylase.