Autophagy has previously been linked to mechanisms that can both promote and suppress tumour growth in cancer. However, it is not broadly known how autophagy genes are mutated in different tumour types, and what the functional implications of these mutations are. In a new study published in Oncotarget, Costa et al. use genomic data from cancer genomics databases (including cBIO Cancer Genomics Portal) to systematically assess the mutations and expression of key autophagy genes in various cancers. They report that autophagy genes are affected in a wide variety of tumour types, with the most common alteration being copy number amplifications. In addition, certain autophagy genes are affected by point mutations. The ubiquitin-like protein MAP1LC3A is closely related to LC3B, which is important for autophagosome formation. A point mutation that leads to an amino acid substitution (R70H) in the arginine-rich stretch of MAP1LC3A was detected in multiple independent tumour samples. The authors demonstrated experimentally that this mutation slows the proteolytic processing of this MAP1LC3A by its regulatory protease ATG4B, both in vitro and in cells, suggesting a functional effect of this mutation in cancer.