It appears the summary output is not saving genes that only have indel mutations.
Gene Tumor_Sample Tumor_Type Chromosome Start_Position End_Position Variant_Classification Reference_Allele Tumor_Allele Protein_Change DNA_Change
A1CF ICGC_0063 Pancreatic Adenocarcinoma 10 52573738 52573738 Missense_Mutation C T p.R401Q c.?
ABCB4 TCGA-IB-7897 Pancreatic Adenocarcinoma 7 87074281 87074282 Frame_Shift_Indel - T p.S339fs c.?
It appears the summary output is not saving genes that only have indel mutations.