Hello,
In the damaging mutation matrix, 0 means no mutation. If there are one or more damaging mutations in the same gene for the same cell line, the allele frequencies are summed, and if the sum is greater than 0.95, a value of 2 is assigned and if not, a value of 1 is assigned. In short 2 indicates a higher likelihood for complete loss of function.
You might find this post relevant as well. Hope this helps!
Simone
