Table 1.
Pattern of molecular mutations in the autophagy network
| # | Gene | Type of mutation | RefSeq Gene | AA change | cDNA change | Genomic location (start) | Protein Location/Interaction |
|---|---|---|---|---|---|---|---|
| 1 (MDS stage) | BCL2 | nonsynonymous substitution | NM_000633 | p.S105P | c.T313C | 60985587 | |
| 1 (MDS stage) | BCL2 | nonsynonymous substitution | NM_000633 | p.P57L | c.C170T | 60985730 | |
| 1 (MDS stage) | ULK4 | stopgain | NM_017886 | p.L1220X | c.T3659A | 41439589 | Repeat (Heat 5) |
| 1 (MDS stage) | PPP2R2A | nonsynonymous substitution | NM_002717 | p.A423D | c.C1268A | 26227853 | Repeat (WD 7) |
| 1 (MDS stage) | RICTOR | nonsynonymous substitution | NM_152756 | p.W295C | c.G885T | 38975643 | |
| 1 (MDS stage) | MTOR | nonsynonymous substitution | NM_004958 | p.K1471N | c.G4413T | 11217265 | Repeat (TPR 4) |
| 1 (AML stage) | PPP2R3A | nonsynonymous substitution | NM_002718 | p.Q88K | c.C262A | 135720602 | |
| 1 (AML stage) | PIK3C2G | nonsynonymous substitution | NM_004570 | p.A899D | c.C2696A | 18649021 | |
| 1 (AML stage) | PRKACB | splice site | NM_182948 | e9-1 | 84679835 | ||
| 1 (AML stage) | NOD2 | nonsynonymous substitution | NM_022162 | p.K118R | c.A353G | 50733678 | Domain (CARD 1) |
| 2 | WDFY3 | nonsynonymous substitution | NM_014991 | p.G3362V | c.G10085T | 85600134 | Region of interaction with SQSTM1 and ATG5 and LIR motif |
| 2 | ULK4 | nonsynonymous substitution | NM_017886 | p.P1003L | c.C3008T | 41705161 | |
| 3 | PIK3CB | nonsynonymous substitution | NM_006219 | p.V349E | c.T1046A | 138452207 | |
| 4 | ATG2A | nonsynonymous substitution | NM_015104 | p.A1533P | c.G4597C | 64666182 | |
| 5 | WDFY4 | splice site | NM_020945 | e48+2 | 50149895 | ||
| 6 | KIF1B | nonsynonymous substitution | NM_015074 | p.E1460K | c.G4378A | 10425470 | |
| 6 | SEC22B | nonsynonymous substitution | NM_004892 | p.T192P | c.A574C | 145115815 | Domain (v-SNARE coiled-coil homology) |
| 7 | CDKN2AIPNL | nonsynonymous substitution | NM_080656 | p.D100A | c.A299C | 133745634 | |
| 8 | PIK3C2B | non-frameshift deletion | NM_002646 | p.232_232del | c.694_696del | 204438235 | Region: of interaction with GRB2 |
| 9 | PRKAG2 | nonsynonymous substitution | NM_016203 | p.V533G | c.A1598C | 151257690 | Domain (CBS 4) |
| 10 | RPTOR | nonsynonymous substitution | NM_001163034 | p.A61D | c.C182A | 78599510 | |
| 10 | SQSTM1 | nonsynonymous substitution | NM_003900 | p.D347Y | c.G1039T | 179260656 | Proximal region to the LIR motif (amino-acid 336-341) |
| 10 | GYS1 | nonsynonymous substitution | NM_001161587 | p.G400V | c.G1199T | 49477908 | |
| 11 | SMURF1 | nonsynonymous substitution | NM_020429 | p.R564L | c.G1691T | 98636086 | Domain (HECT) |
| 12 | VTI1A | stopgain | NM_145206 | p.E53X | c.G157T | 114224309 | Region (Coiled coiled) |
| 12 | TAB2 | nonsynonymous substitution | NM_015093 | p.A152S | c.G454T | 149699505 | |
| 13 | TNFSF10 | nonsynonymous substitution | NM_003810 | p.A32D | c.C95A | 172241080 | |
| 13 | LAMP2 | nonsynonymous substitution | NM_002294 | p.A314S | c.G940T | 119575738 | Region (Second lumenal domain) |
| 13 | PTPN2 | nonsynonymous substitution | NM_080423 | p.Q264L | c.A791T | 12814269 | Domain (Tyrosine-protein phosphatase) |
| 14 | PRKACB | nonsynonymous substitution | NM_001242862 | p.W184C | c.G552T | 84663456 | |
| 15 | NOD2 | stopgain | NM_022162 | p.E1008X | c.G3022T | 50763784 | |
| 15 | NOD2 | nonsynonymous substitution | NM_022162 | p.E1008G | c.A3023G | 50763785 | |
| 16 | TNFSF13B | nonsynonymous substitution | NM_001145645 | p.N164D | c.A490G | NA | |
| 17 | PTPN2 | stopgain | NM_001207013 | p.R26X | c.C76T | NA | |
| 18 | COG8 | nonsynonymous substitution | NM_032382 | p.P369S | c.C1105T | NA | |
| 19 | DNM1L | nonsynonymous substitution | NM_005690 | p.G362S | c.G1084A | 32883952 | |
| 20 | HIF1A | nonsynonymous substitution | NM_181054 | p.P429S | c.C1285T | NA | |
| 21 | MLST8 | nonsynonymous substitution | NM_001199173 | p.R221S | c.C661A | 2258298 | Repeat (WD 6) |
| 22 | PIK3C2A | nonsynonymous substitution | NM_002645 | p.P723S | c.C2167T | 17153527 | Domain (C2 PI3K-type) |
| 23 | PRKAA1 | nonsynonymous substitution | NM_206907 | p.A573V | c.C1718T | NA | |
| 24 | PRKACB | nonsynonymous substitution | NM_182948 | W244R | c.T730A | 84663454 | |
| 25 | PRKAG1 | nonsynonymous substitution | NM_001206709 | p.N15S | c.A44G | 49406859 | |
| 26 | PRKAG1 | nonsynonymous substitution | NM_002733 | p.R152G | c.A454G | NA | Domain (CBS 2) |
| 27 | SEC22B | nonsynonymous substitution | NM_004892 | p.T192P | c.A574C | 145115815 | Domain (v-SNARE coiled-coil homology) |
| 28 | STAT3 | nonsynonymous substitution | NM_003150 | p.G618R | c.G1852C | 40475058 | |
| 29 | VPS11 | frameshift insertion | NM_021729 | p.S74fs | 118939937 | ||
| 30 | VPS11 | nonsynonymous substitution | NM_021729 | p.S74P | c.T220C | 118939939 | |
| 31 | VPS33B | nonsynonymous substitution | NM_018668 | p.E128Q | c.G382C | 91553052 | |
| 32 (TCGA3009) | DNM2 | frameshift insertion | NM_001005360.1 | p.T471fs*11 | c.1411_1412insGCCATCGT | 10770237 | Domain (Pleckstrin homology) |
| 32 (TCGA3009) | WAC | frameshift insertion | NM_016628.3 | p.E87fs | ->AGGGC | 28864676 | |
| 33 (TCGA2871) | ATG14 | nonsynonymous substitution | NM_014924.3 | p.T213M | G>A | 54922339 | |
| 34 (TCGA2870) | ATG4C | nonsynonymous substitution | NM_032852.2 | p.D354Y | G>T | 63073082 | |
| 35 (TCGA2821) | ATG16L1 | nonsynonymous substitution | NM_030803.3 | p.L558Q | c.T1673A | 233866685 | |
| 36 (TCGA2919) | SUPT20H | nonsynonymous substitution | NM_001014286.2 | p.L635V | G>C | 36489471 | |
| 37 (TCGA2864) | PPP2R2B | nonsynonymous substitution | NM_181676.1 | p.R374C | G>A | 145949924 | Repeat (WD6) |
| 38 (TCGA2978) | PRKAA2 | stopgain | NM_006252.3 | p.R227* | C>T | 56934311 | Domain (Protein kinase) |
| 39 (TCGA2859) | USP10 | frameshift deletion | NM_005153.2 | p.P386fs | C>- | 83336744 | |
| 40 (TCGA3001) | WAC | splice site | NM_016628.3 | e12+1 | G>A | 28945298 |