Table 1 Fixed variants with predicted loss-of-function effect in known cancer associated genes according to the COSMIC database (CGC), known disease genes (OMIM) or genes highly expressed in the brain according to the Human Protein Atlas (HPA).
From: Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium
Sample | Gene | HGVS | List | OMIM-G | OMIM-P | Phenotype | Inh. | pLI |
|---|---|---|---|---|---|---|---|---|
i82A-S1-022 | IL1RAPL1 | c.1372+1G>T, p.? | OMIM, HPA | *300206 | #300143 | Mental retardation, XLR 21/34 | XLR | 1.00 |
p82A-R1-001 | ADAT3 | c.485G>A, p.(Trp162*) | OMIM | *615302 | #615286 | Mental retardation, AR 36 | AR | 0.00 |
i82A-R1-001 | RP1 | c.3949C>T, p.(Gln1317*) | OMIM | *603937 | #180100 | Retinitis pigmentosa 1 | AR, AD | 0.00 |
i82A-S1-022 | MMP20 | c.1381dupA, p.(Thr461Asnfs*5) | OMIM | *604629 | #612529 | Amelogenesis imperfecta, type IIA2 | AR | 0.00 |
i82A-R1-001 | GPR162 | c.747_748delinsTT, p.(Arg250*) | HPA | na | na | na | na | 0.02 |
i88H-R1-002 | BRAF | c.981-2A>G, p.? | CGC, OMIM | *164757 | #115150, #613707, #613706 | Cardiofaciocutaneous syndrome; LEOPARD syndrome 3; Noonan syndrome 7 | AD, AD, AD | 1.00 |
i88H-R1-002 | TWIST2 | c.3G>T, p.? | OMIM | *607556 | #200110, #209885, #227260 | Ablepharon-macrostomia syndrome; Barber-Say syndrome; Focal facial dermal dysplasia 3, Setleis type | AD, AD, AR | 0.44 |
i88H-R1-002 | PAM16 | c.285_288del, p.(Ser96Argfs*44) | OMIM | *614336 | #613320 | Spondylometaphyseal dysplasia, Megarbane-Dagher-Melike type | AR | 0.14 |
i88H-R1-001 | CDT1 | c.352-1G>A, p.? | OMIM | *605525 | #613804 | Meier-Gorlin syndrome 4 | AR | 0.00 |
i88H-R1-002 | LAMB1 | c.869_870del, p.(Val290Glyfs*13) | OMIM | *150240 | #615191 | Lissencephaly 5 | AR | 0.00 |
i88H-R1-002 | MTM1 | c.1497del, p.(Trp499Cysfs*3) | OMIM | *300415 | #310400 | Myotubular myopathy, XLR | XLR | 1.00 |
i88H-R1-001 | DOCK2 | c.3060_3072+6del, p.? | OMIM | *603122 | #616433 | Immunodeficiency 40 | AR | 1.00 |
i88H-R1-002 | CYP46A1 | c.894_897del, p.(Phe299Serfs*16) | HPA | *604087 | na | na | na | 0.75 |
i88H-R1-002 | MCF2 | c.541G>T, p.(Glu181*) | HPA | *311030 | na | na | na | 0.94 |
iAY6-R1-003 | GRIK2 | c.723+1G>A, p.? | OMIM, HPA | *138244 | #611092 | Mental retardation, AR, 6 | AR | 0.99 |
iAY6-R1-003 | SYNE2 | c.4051C>T, p.(Gln1351*) | OMIM | *608442 | #612999 | Emery-Dreifuss muscular dystrophy 5 | AD | 0.00 |
iAY6-R1-003 | C2CD3 | c.1726_1730+2delinsC, p.? | OMIM | *615944 | #615948 | Orofaciodigital syndrome XIV | AR | 0.00 |
iAY6-R1-003 | ANKRD11 | c.5759_5763delinsG, p.(Thr1920Argfs*42) | OMIM | *611192 | #148050 | KBG syndrome | AD | 1.00 |
iPX7-R1-001 | CARD11 | c.214C>T, p.(Arg72*) | CGC, OMIM | *607210 | #616452, #615206, #617638 | B-cell expansion with NFKB and T-cell anergy; Immunodeficiency 11 A; Immunodeficiency 11B | AD, AR, AD | 1.00 |
iPX7-R1-001 | ALG2 | c.32C>A, p.(Ser11*) | OMIM | *607905 | #616228 | Myasthenic syndrome, congenital, 14, with tubular aggregates | AR | 0.02 |
iPX7-S1-004 | DNAH5 | c.2049del, p.(Gln684Lysfs*7) | OMIM | *603335 | #608644 | Ciliary dyskinesia, primary, 3, with or without situs inversus | AR | 0.00 |
iPX7-S1-004 | ITCH | c.540dup, p.(Cys181Leufs*7) | OMIM | *606409 | #613385 | Autoimmune disease, multisystem, with facial dysmorphism | AR | 1.00 |
iPX7-S1-004 | VCAN | c.2492_2495del, p.(Leu831Glnfs*5) | OMIM | *118661 | #143200 | Wagner syndrome 1 | AD | 1.00 |
iPX7-S1-004 | ARPP21 | c.1923T>G, p.(Tyr641*) | HPA | *605488 | na | na | na | 0.00 |
iPX7-S1-004 | WBSCR17 | c.1081-1_1081delinsAA, p.? | HPA | *615137 | na | na | na | 0.10 |
