Table 2.
List of recurrent somatic SNVs affecting uAUG and aTIS codons selected for experimental analysis.
| Gene Symbol RefSeq ID | Genomic Position |
Codon Variant |
Functional Effect |
Type of Cancer (% of Patients) | uORF Size in bp | # of uAUG in TLS |
uStop to CDS Distance (bp) | Kozak Context | TV with uORF |
|---|---|---|---|---|---|---|---|---|---|
| ASNS NM_001352496.2 |
chr7: 97928300 |
AUG.2 > GUG | uAUG > aTIS | BRCA (0.4) | 303 | 4 | 74 | ++ | 1/7 |
| BAGE2 NM_182482.2 |
chr21: 10413537 |
CUG.1 > CCG | loss of aTIS | COAD (2.1); LUAD (1.4); LAML (1.3); SKCM (0.9); PRAD (0.6); BRCA (1.0) | 78 | 3 | 126 | + | 5/5 |
| BAGE2 NM_182482.2 |
chr21: 10413594 |
UUG.1 > GUG | syn aTIS | SKCM (1.9); BRCA (1.3); PRAD (0.8); COAD (0.6) |
105 | 3 | 41 | − | 5/5 |
| CFH NM_000186.3 |
chr1: 196651949 |
UUG.3 > UUU/ GUG.5 > UUG |
loss of aTIS/ syn aTIS |
BRCA (2.2) | 39/138 | 1 | 132/31 | + | 2/2 |
| CHCHD2 NM_001320327.1 | chr7: 56106490 |
AUC.1 > AUU | loss of aTIS | SKCM (8.1) | 63 | 1 | 16 | − | 2/2 |
| DIS3L NM_133375.4 |
chr15: 66294990 |
AUG.1 > AUU | uAUG > aTIS | SKCM (0.9) | 27 | 2 | 83 | ++ | 10/13 |
| ESRRG NM_001438.4 |
chr1: 216723407 |
GUG.1 > GGG | loss of aTIS | BRCA (3.0) | 39 | 1 | 70 | + | 4/20 |
| FANK1 NM_145235.5 |
chr10: 125896600 | AGG.2 > ACG | syn aTIS | COAD (1.6) | 105 | 0 | 44 | + | 2/3 |
| FRG2C NM_001124759.3 |
chr3: 75664297 |
ACG.2 > AUG | aTIS > uAUG | LAML (6.0); SKCM (2.1); LUAD (0.7); PRAD (0.4) |
21 | 3 | 63 | + | 1/1 |
| HLA-DRB1 NM_002124.3 | chr6: 32589821 |
AUG.1 > AUA/ GUG.1 > AUG |
uAUG > aTIS/ aTIS > uAUG |
LAML (1.3); LUAD (1.1); PRAD (0.6); BRCA (0.6); SKCM (0.4) |
36/30 | 1 | 45/49 | + | 2/4 |
| HLA-DRB1 NM_002124.3 | chr6: 32589752 |
CUG.1 > CUC | loss of GTG | COAD (1.6); SKCM (1.3); LUAD (0.5); BRCA (0.2) |
66 | 1 | −13 | + | 2/4 |
| HLA-DRB1 NM_002124.3 | chr6: 32589795 |
CUG.6 > GUG | syn aTIS | LAML (2.7); LUAD (0.3); BRCA (0.3) |
813 | 1 | −801 | − | 2/4 |
| NDST3 NM_004784.3 |
chr4: 118053872 |
AUG.4 > AUU | uAUG > aTIS | SKCM (1.1) | 21 | 4 | 20 | + | 1/1 |
| PJA2 NM_014819.4 |
chr5: 109383504 |
UUG.2 > UUU | loss of aTIS | LAML (2.0); LUAD (1.4); BRCA (1.3); PRAD (0.4) |
15 | 0 | 58 | + | 1/1 |
| PRKCQ NM_001282644.2 | chr10: 6515109 |
UUG.2 > UUU | loss of aTIS | LAML (3.4); BRCA (2.8); LUAD (1.8); PRAD (0.6); SKCM (0.4) |
156 | 1 | −74 | + | 4/7 |
| PRMT8 NM_019854.5 |
chr12: 3491521 |
UUG.5 > GUG | syn aTIS | BRCA (1.7) | 1290 | 1 | −1185 | ++ | 1/2 |
| RBBP4 NM_001135256.1 |
chr1: 32651992 |
AUG.3 > UUG | uAUG > aTIS | LAML (2.0) | 12 | 3 | −1 | − | 1/3 |
| ROPN1 NM_017578.4 |
chr3: 123980570 |
GUG.6 > GGG | loss of aTIS | BRCA (2.2); LAML (1.3) | 54 | 4 | 36 | − | 1/3 |
| SETD4 NM_001007261.2 |
chr21: 36058888 |
AUG.1 > UUG | uAUG > aTIS | LAML (1.3) | 174 | 3 | −8 | + | 4/4 |
| SYNPR NM_144642.5 |
chr3: 63443357 |
GUG.2 > GGG | loss of aTIS | BRCA (8.2); COAD (4.4); LAML (3.4) |
30 | 1 | 57 | − | 1/2 |
| TEDDM1 NM_172000.4 |
chr1: 182400520 |
AUG.2 > UUG | uAUG > aTIS | LAML (2.7) | 39 | 2 | −4 | + | 1/1 |
| TMIGD3 NM_001081976.2 | chr1: 111563996 |
UUG.1 > GUG | syn aTIS | LAML (4.0); LUAD (0.7); PRAD (0.4); BRCA (0.3) |
138 | 0 | −94 | + | 2/3 |
| TNFSF8 NM_001244.3 |
chr9: 114930326 |
AUG.6 > GUG | uAUG > aTIS | LAML (1.4) | 147 | 6 | −147 | + | 2/2 |
# = number; negative values in “uStop to CDS distance in bp” indicate overlap of the uORF into the CDS; The Kozak sequences surrounding the uORF initiation sites are classified as strong (++) if both core bases (underlined) match, adequate (+) if one of the core bases matches or weak (−) if none of the core bases match with the optimal Kozak consensus sequence (GCCRCCaugG).