Recurrent somatic SNVs and indels found in 50 AML patients
| Gene . | Mutation type . | Position . | Allele . | Amino acid change . | Patient ID . | AML type . | SIFT . | Polyphen . |
|---|---|---|---|---|---|---|---|---|
| DNMT3A | Frameshift | chr2:25457180 | */−G | p.A903fs | 13 | CK-AML | NA | NA |
| DNMT3A | Missense | chr2:25457243 | G>A | p.R882C | 31 | CN-AML with NPM1 | deleterious(0); | probably_damaging(0.996); |
| DNMT3A | Missense | chr2:25457242 | C>T | p.R882H | 33 | CN-AML with NPM1/FLT3-ITD | deleterious(0); | benign(0.048); |
| GATA2 | Missense | chr3:128202797 | C>T | p.R308Q | 01 | CN-AML with CEBPA | deleterious(0.03); | probably_damaging(1); |
| GATA2 | Missense | chr3:128199888 | A>G | p.S473P | 30 | CN-AML | deleterious(0); | probably_damaging(1); |
| GATA2 | Missense | chr3:128202761 | C>T | p.G320D | 32 | CN-AML with CEBPA | deleterious(0); | probably_damaging(1); |
| IDH1 | Missense | chr2:209113112 | C>T | p.R132H | 02 | CN-AML with NPM1 | deleterious(0.02); | probably_damaging(0.999); |
| IDH1 | Missense | chr2:209113113 | G>A | p.R132C | 39 | CN-AML | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599321 | A>T | p.D816V | 47 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599321 | A>T | p.D816V | 06 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599340 | T>G | p.N822K | 07 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Frameshift | chr4:55589769 | */−TA | p.Y418fs | 37 | CBF-AML, inv(16) | NA | NA |
| KRAS | Missense | chr12:25398284 | C>T | p.G12D | 14 | CK-AML | deleterious(0); | probably_damaging(0.877); |
| KRAS | Frameshift | chr12:25398287 | */+CTC | p.A11fs | 30 | CN-AML | NA | NA |
| KRAS | Missense | chr12:25398284 | C>A | p.G12V | 35 | CN-AML with NPM1 | deleterious(0); | probably_damaging(0.943); |
| NRAS | Missense | chr1:115258747 | C>T | p.G12D | 16 | CN-AML | deleterious(0); | possibly_damaging(0.844); |
| NRAS | Missense | chr1:115256536 | C>T | p.A59T | 34 | CN-AML with NPM1 | deleterious(0,01); | benign(0.123); |
| NRAS | Missense | chr1:115256528 | T>A | p.Q61H | 48 | CBF-AML, t(8;21) | deleterious(0,01); | benign(0.017); |
| NRAS | Missense | chr1:115256528 | T>A | p.Q61H | 52 | CBF-AML, inv(16) | deleterious(0,01); | benign(0.017); |
| NRAS | Missense | chr1:115256530 | G>T | p.Q61K | 49 | CBF-AML, inv(16) | deleterious(0,01); | benign(0.006); |
| NRAS | Missense | chr1:115256529 | T>C | p.Q61R | 18 | CN-AML | deleterious(0,01); | benign(0.004); |
| NSD1 | Missense | chr5:176636989 | C>T | p.P530L | 06 | CBF-AML, t(8;21) | deleterious(0); | possibly_damaging(0.697); |
| NSD1 | Missense | chr5:176709485 | A>G | p.Y1971C | 35 | CN-AML with NPM1 | deleterious(0); | probably_damaging(1); |
| RAD21 | Nonsense | chr8:117864815 | G>A | p.Q432X | 08 | CK-AML | nonsense | nonsense |
| RAD21 | Frameshift | chr8:117870615 | */+GA | p.S153fs | 35 | CN-AML with NPM1 | NA | NA |
| RAD21 | Frameshift | chr8:117866622 | */+TTAG | p.S342fs | 48 | CBF-AML, t(8;21) | NA | NA |
| TET2 | Splice site, frameshift | chr4:106164082 | */−G | p.W1219-spl.site/fs | 03 | CN-AML | NA | NA |
| TET2 | Nonsense | chr4:106197149 | C>T | p.Q1849X | 13 | CK-AML | nonsense | nonsense |
| TET2 | Nonsense | chr4:106196306 | C>T | p.Q1568X, | 25 | CN-AML with NPM1/FLT3-ITD | nonsense | nonsense |
| TET2 | Nonsense | chr4:106196309 | C>T | p.Q1569X | 32 | CN-AML with CEBPA | nonsense | nonsense |
| TET2 | Frameshift | chr4:106164851 | */−G | p.L1261fs | 46 | CBF-AML, t(8;21) | NA | NA |
| WT1 | Frameshift | chr11:32417942 | */−C | p.R370fs | 12 | CK-AML | NA | NA |
| WT1 | Frameshift | chr11:32417911 | +C/+C | p.S381fs | 14 | CK-AML | NA | NA |
| WT1 | Frameshift | chr11:32417907 | */+CCGA | p.A380fs | 18 | CN-AML | NA | NA |
| WT1 | Frameshift | chr11:32414251 | */+AGAAAACC | p.R431fs | 20 | CN-AML with CEBPA | NA | NA |
| WT1 | Frameshift | chr11:32417914 | */+T | p.R379fs | 33 | CN-AML with NPM1/FLT3-ITD | NA | NA |
| WT1 | Frameshift | chr11:32417941 | */+AA | p.V371fs | 42 | CN-AML with FLT3-ITD | NA | NA |
| Gene . | Mutation type . | Position . | Allele . | Amino acid change . | Patient ID . | AML type . | SIFT . | Polyphen . |
|---|---|---|---|---|---|---|---|---|
| DNMT3A | Frameshift | chr2:25457180 | */−G | p.A903fs | 13 | CK-AML | NA | NA |
| DNMT3A | Missense | chr2:25457243 | G>A | p.R882C | 31 | CN-AML with NPM1 | deleterious(0); | probably_damaging(0.996); |
| DNMT3A | Missense | chr2:25457242 | C>T | p.R882H | 33 | CN-AML with NPM1/FLT3-ITD | deleterious(0); | benign(0.048); |
| GATA2 | Missense | chr3:128202797 | C>T | p.R308Q | 01 | CN-AML with CEBPA | deleterious(0.03); | probably_damaging(1); |
| GATA2 | Missense | chr3:128199888 | A>G | p.S473P | 30 | CN-AML | deleterious(0); | probably_damaging(1); |
| GATA2 | Missense | chr3:128202761 | C>T | p.G320D | 32 | CN-AML with CEBPA | deleterious(0); | probably_damaging(1); |
| IDH1 | Missense | chr2:209113112 | C>T | p.R132H | 02 | CN-AML with NPM1 | deleterious(0.02); | probably_damaging(0.999); |
| IDH1 | Missense | chr2:209113113 | G>A | p.R132C | 39 | CN-AML | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599321 | A>T | p.D816V | 47 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599321 | A>T | p.D816V | 06 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Missense | chr4:55599340 | T>G | p.N822K | 07 | CBF-AML, t(8;21) | deleterious(0); | probably_damaging(1); |
| KIT | Frameshift | chr4:55589769 | */−TA | p.Y418fs | 37 | CBF-AML, inv(16) | NA | NA |
| KRAS | Missense | chr12:25398284 | C>T | p.G12D | 14 | CK-AML | deleterious(0); | probably_damaging(0.877); |
| KRAS | Frameshift | chr12:25398287 | */+CTC | p.A11fs | 30 | CN-AML | NA | NA |
| KRAS | Missense | chr12:25398284 | C>A | p.G12V | 35 | CN-AML with NPM1 | deleterious(0); | probably_damaging(0.943); |
| NRAS | Missense | chr1:115258747 | C>T | p.G12D | 16 | CN-AML | deleterious(0); | possibly_damaging(0.844); |
| NRAS | Missense | chr1:115256536 | C>T | p.A59T | 34 | CN-AML with NPM1 | deleterious(0,01); | benign(0.123); |
| NRAS | Missense | chr1:115256528 | T>A | p.Q61H | 48 | CBF-AML, t(8;21) | deleterious(0,01); | benign(0.017); |
| NRAS | Missense | chr1:115256528 | T>A | p.Q61H | 52 | CBF-AML, inv(16) | deleterious(0,01); | benign(0.017); |
| NRAS | Missense | chr1:115256530 | G>T | p.Q61K | 49 | CBF-AML, inv(16) | deleterious(0,01); | benign(0.006); |
| NRAS | Missense | chr1:115256529 | T>C | p.Q61R | 18 | CN-AML | deleterious(0,01); | benign(0.004); |
| NSD1 | Missense | chr5:176636989 | C>T | p.P530L | 06 | CBF-AML, t(8;21) | deleterious(0); | possibly_damaging(0.697); |
| NSD1 | Missense | chr5:176709485 | A>G | p.Y1971C | 35 | CN-AML with NPM1 | deleterious(0); | probably_damaging(1); |
| RAD21 | Nonsense | chr8:117864815 | G>A | p.Q432X | 08 | CK-AML | nonsense | nonsense |
| RAD21 | Frameshift | chr8:117870615 | */+GA | p.S153fs | 35 | CN-AML with NPM1 | NA | NA |
| RAD21 | Frameshift | chr8:117866622 | */+TTAG | p.S342fs | 48 | CBF-AML, t(8;21) | NA | NA |
| TET2 | Splice site, frameshift | chr4:106164082 | */−G | p.W1219-spl.site/fs | 03 | CN-AML | NA | NA |
| TET2 | Nonsense | chr4:106197149 | C>T | p.Q1849X | 13 | CK-AML | nonsense | nonsense |
| TET2 | Nonsense | chr4:106196306 | C>T | p.Q1568X, | 25 | CN-AML with NPM1/FLT3-ITD | nonsense | nonsense |
| TET2 | Nonsense | chr4:106196309 | C>T | p.Q1569X | 32 | CN-AML with CEBPA | nonsense | nonsense |
| TET2 | Frameshift | chr4:106164851 | */−G | p.L1261fs | 46 | CBF-AML, t(8;21) | NA | NA |
| WT1 | Frameshift | chr11:32417942 | */−C | p.R370fs | 12 | CK-AML | NA | NA |
| WT1 | Frameshift | chr11:32417911 | +C/+C | p.S381fs | 14 | CK-AML | NA | NA |
| WT1 | Frameshift | chr11:32417907 | */+CCGA | p.A380fs | 18 | CN-AML | NA | NA |
| WT1 | Frameshift | chr11:32414251 | */+AGAAAACC | p.R431fs | 20 | CN-AML with CEBPA | NA | NA |
| WT1 | Frameshift | chr11:32417914 | */+T | p.R379fs | 33 | CN-AML with NPM1/FLT3-ITD | NA | NA |
| WT1 | Frameshift | chr11:32417941 | */+AA | p.V371fs | 42 | CN-AML with FLT3-ITD | NA | NA |
The chromosomal coordinates refer to the human reference genome hg19 (GRCh37). The predicted effect on protein function was analyzed using the indicated algorithms.
SNV indicates single nucleotide variation; AML, acute myeloid leukemia; chr, chromosome; CN-AML, cytogenetically normal AML; CBF-AML, core-binding factor AML; CK-AML, complex karyotype AML; fs, frameshift; NA, not applicable; Spl. site, mutation in splicing site; and fs, frameshift.