Disease-associated genes with potential roles in Hh and Wnt signaling. Disease-associated genes that were confirmed by siRNA retesting (either by two nonredundant siRNA pools or by three or more individual siRNAs; see fig. S2) were grouped on the basis of disease type. NC, no change; +, gain in response (normalized response >1.2; see table S4). Multiple names for a single gene are separated by a slash.
| Pathological condition | Gene | Function | Associated disease | RNAi specificity test | Wnt pathway response |
| Malformation | G1i2 | Transcription | Holoprosencephaly | 2x pools | NC |
| Stk22B/Tssk2 | Kinase | DiGeorge syndrome candidate gene (velocardiofacial syndrome) | 2x pools | NC | |
| Dgkq | Kinase | Wolf-Hirschhom syndrome candidate gene (midline fusion defect) | 3 | + | |
| Gpc1 | Receptor | Albright hereditary osteodystrophy (AHO)–like syndrome candidate gene (obesity, brachydactyly, and ectopic ossifications) | 3 | + | |
| Degenerative disease | Rlbp1 | Signaling | Retinitis pigmentosa (retinal degeneration) | 4 | NC |
| Aaas | Nuclear pore | Triple A syndrome (adrenal insufficiency, alacrima, achalasia) | 2x pools | NC | |
| Ift57/Hippi | Signaling | Bardet-Biedl type 3 syndrome candidate gene (renal failure) | 3 | + | |
| Cancer | Smo | Signaling | Gorlin’s syndrome (basal cell carcinoma, medulloblastoma, rhabdomyosarcoma) | 4 | NC |
| Prkar1a | Kinase | Camey complex, type 1 (myxomas of the heart and skin, endocrine tumors, lentiginosis) | 4 | + | |
| Stk11/Lkb1 | Kinase | Peutz-Jeghers syndrome (pancreatic cancer, melanoma, testicular cancer, endocrine tumors; lentiginosis) | 3 | + |