Understanding monogenic diabetes has been challenging due to the lack of human model but also because mouse models do not recapitulate the disease. Here, we use human pluripotent stem cells (ESCs) and CRISPR-CAS9 (Clustered Regularly Interspaced Short Palindromic Repeat)/Cas9) nucleases to understand the most common form of monogenic diabetes, Maturity Onset Diabetes of the Young 3 (MODY3) caused by heterozygous mutations in the transcription factor HNF1A. In this thesis research, we found that the lack of HNF1A does not impair the generation of beta-like cells; Wild-type (WT) and mutant cell lines presented similar differentiation efficiency between genotypes. HNF1A is necessary to repressed alpha cell fate; loss of HNF1A leads skew beta-like cell differentiation towards alpha cell type. We also explore beta cell function related to insulin secretion and cellular bioenergetics; we found that HNF1A needs it for proper insulin secretion and cellular respiration leading to lower glycolysis metabolism and mitochondrial respiration. We explore the HNF1A relationship between phenotype and genotype by generating a genome profiling analysis of HNF1A. We MODY3 models confirmed that many of the genes that are dis-regulated in the Hnf1α mouse model such us HNF4A, PCSK1, GC, DDP4, KIF12 6GPC2 and others. Besides, we also found a large number of genes to be uniquely dis-regulated in the human model, which could explain the species-specific phenotype. These genes include the transcription factors RFX6, GLIS3 and PAX4, the metallothionein gene family a novel long non-coding (lnc)RNA LINC01139. This lncRNA is only present in primates, and also it is expressed in human endocrine cells. We interrogate the role of this lncRNA, and we found that it recapitulates a subset of phenotypes seen in HNF1A, related with defects in glycolysis, mitochondrial respiration, and downregulation of group of genes downstream of HNF1A. Our work offers a model to define the unique biology of HNF1A in humans that may be distinct from rodent models leading to a better understanding of human beta cell physiology with clinical implications for MODY3 patients but also with broader applications to diabetes.