Understanding the pathogenesis of genetic diseases through different gene activities and their relations to relevant diseases is important for new drug discovery and drug repositioning. In this paper, we present a joint deep learning model in a multi-task learning paradigm for gene mutation-disease knowledge extraction, DeepGeneMD, which adapts the state-of-the-art hierarchical multi-task learning framework for joint inference on named entity recognition (NER) and relation extraction (RE) in the context of the AGAC (Active Gene Annotation Corpus) track at 2019 BioNLP Open Shared Tasks (BioNLP-OST). It simultaneously extracts gene mutation related activities, diseases, and their relations from the published scientific literature. In DeepGeneMD, we explore the task decomposition to create auxiliary subtasks so that more interactions between different learning subtasks can be leveraged in model training. Our model achieves the average F1 score of 0.45 on recognizing gene activities and disease entities, ranking 2nd in the AGAC NER task; and the average F1 score of 0.35 on extracting relations, ranking 1st in the AGAC RE task.