Code datasets, often collected from diverse and uncontrolled sources such as GitHub, potentially suffer from quality issues, thereby affecting the performance and training efficiency of Large Language Models (LLMs) optimized for code generation. Previous studies demonstrated the benefit of using embedding spaces for data pruning, but they mainly focused on duplicate removal or increasing variety, and in other modalities, such as images. Our work focuses on using embeddings to identify and remove low-quality'' code data. First, we explore features oflow-quality'' code in embedding space, through the use of synthetic corruptions. Armed with this knowledge, we devise novel pruning metrics that operate in embedding space to identify and remove low-quality entries in the Stack dataset. We demonstrate the benefits of this synthetic corruption informed pruning (SCIP) approach on the well-established HumanEval and MBPP benchmarks, outperforming existing embedding-based methods. Importantly, we achieve up to a 3% performance improvement over no pruning, thereby showing the promise of insights from synthetic corruptions for data pruning.