Table 1.
ATM mutations detected in colorectal tumors from patients with known pathogenic germline ATM mutations
| Patient | Germline ATM Mutation | VAF in Tumor | Somatic ATM Mutation | VAF in Tumor | Tumor Content | Tumor Supports ATM In Tumorigenesis? |
|---|---|---|---|---|---|---|
| 1 | p.E2052K, c.6154G > A^ | 50% | p.R2227C, c.6679C > T | 26% | 45% | Yes |
| 2 | p.F2799Kfs*4,c.8395_8404del | 24%* | c.4611 + 4A > G | 23% | 50% | Yes |
| 3** | p.R2993*, c.8977C > T | 49% | p.Y741C, c.2222A > G | 21% | 40% | Yes |
| 4 | p.Q522Ifs*43, c.1564_1565del | 78% | Loss of Heterozygosity | NA | 60% | Yes |
| 5 | p.S1905Ifs*25, c.5712dup | 79% | Loss of Heterozygosity | NA | 70% | Yes |
| 6*** | p.V2424G, c.7271 T > G | 82% | Loss of Heterozygosity | NA | 80% | Yes |
^Germline classification is conflicting depending on laboratory (ranging to variant of uncertain significance to Pathogenic)
*VAF was identical in germline and tumor samples at 24%. Reference allele bias accounts for the lower than expected VAF
**Patient 3 also carried a germline pathogenic NBN Slavic Founder mutation, p.K219Nfs*16, c.657_661del
***Patient 6 also carried a germline pathogenic CHEK2 p.T367Mfs*15, c.1100delC mutation
VAF = variant allele fraction
NM_000051.3 is the ATM reference transcript used for mutation annotations