Mutations in the Notch signaling cell surface ligand Jagged1 (JAG1) predominantly cause Alagille syndrome (ALGS), an autosomal dominant disorder that causes congenital defects in multiple organs. ALGS is highly variably expressed, with patients displaying a wide array of phenotypes of differing severities. JAG1 has also been implicated in the pathogenesis of other diseases, including isolated cardiac defects (ICD) such as tetralogy of Fallot or peripheral pulmonic stenosis, as well as extrahepatic biliary atresia (BA). Previous functional analysis of JAG1 missense mutations revealed two types of effect on protein function. Mutations found in patients with ALGS caused the JAG1 mutant protein to be improperly post-translationally modified and retained intracellularly. Conversely, missense mutations identified in patients with ICD only partially affected JAG1 function, with a fraction of the mutant protein processed correctly and expressed at the cell surface. It was postulated that the partial expression of the JAG1 protein prevented the manifestation of a liver phenotype, presumably because the developing heart is more sensitive to fluctuations in Notch signaling then the developing liver. In this work, I perform functional analysis on an additional 13 mutations found in patients with ALGS and 4 mutations identified in patients with isolated cardiac disease. I also expand the functional studies to 11 missense mutations identified in patients with BA. I report a previously unobserved third affect that missense mutations can have on JAG1 protein function. I refute the hypothesis that a genotype-phenotype correlation exists with respect to JAG1 missense mutations, as all 3 mutation effects are seen in cohorts of patients with ALGS as well as ICD. Finally, I determine that missense mutations in patients with BA have a different effect on protein function than that observed in both ALGS and ICD, suggestive of a new genotype-phenotype correlation. To better understand ALGS disease pathogenesis, I expand our studies to ALGS-associated mutations found in the Notch receptor NOTCH2. I also begin preliminary work on genome wide investigation of copy number variation in our ALGS patient cohort.