Understanding how different regions of the central nervous system (CNS) are affected by genetic insults is critical to advancing the study of CNS pathologies. The cerebellum is one such region which is disproportionately hypoplastic in the majority of cases of CASK gene mutation in humans. CASK is an enigmatic multi-domain scaffolding protein which plays a vital role in organizing protein complexes at the pre-synapse through interactions with both active zone proteins and trans-synaptic adhesion molecules such as liprins-α and neurexins. Mutations in the X-linked CASK gene in humans are largely post-natally lethal in the hemizygous condition and result in microcephaly with pontine and cerebellar hypoplasia (PCH) and also optic nerve hypoplasia (ONH) in heterozygous mutations. Herein, I used various molecular and genetic strategies to uncover the role of the CASK protein in brain function and pathogenesis of cerebellar hypoplasia associated with CASK mutations/deletions. First, using the face- and construct-validated heterozygous CASK knockout (Cask+/-) murine model, I conducted bulk RNA-sequencing and proteomics experiments from whole brain lysates to uncover changes in the Cask+/- brain. RNA-sequencing revealed the majority of changes to be broadly categorized into metabolic, nuclear, synaptic, and extracellular-matrix associated transcripts. Proteomics revealed the majority of changes cluster as synaptic proteins, metabolic proteins, and ribosomal subunits. Thus, absence of CASK in half of brain cells seems to affect synaptic protein content, cell metabolism, and protein homeostasis. Extending these observations, I conducted GFP-trap immunoprecipitation followed by tandem mass spectroscopy to reveal protein complexes in which CASK participates. Commensurate with proteomic changes, CASK was found to complex with synaptic proteins, metabolic proteins, cytoskeletal elements, ribosomal subunits, and protein folding machinery. Next, in order to investigate the pathogenesis of CASK-linked cerebellar hypoplasia, I utilized a human case of early truncation wherein the 27th arginine of CASK is converted to a stop codon. Immunohistochemical analysis of this brain revealed an upregulation of glial fibrillary acidic protein, a common marker for degenerative cell death. To mechanistically test the hypothesis that cerebellar hypoplasia results from cell death rather than developmental failure, I created a murine model wherein CASK is deleted from the majority of cerebellar cells post-development using Cre recombinase driven by the Calb2 promoter. Deleting CASK from all cerebellar granule neurons post-migration indeed leads to degeneration of the cerebellum via massive depletion of granule cells while sparing Purkinje cells. Overall, the cerebellum shrinks by approximately half in cross-sectional area and degeneration is accompanied by a collapsing of the molecular layer and of Purkinje cell dendrites. In addition, cerebellar degeneration presents with a profound locomotor ataxia. In conclusion, CASK seems to be affecting brain energy homeostasis and synaptic connections via interactions with metabolic proteins, synaptic proteins, and protein homeostatic elements. Further, alterations in brain volume associated with CASK-linked disorders is the result of degenerative cell death rather than developmental failure as previously posited. / Doctor of Philosophy / One of the main challenges facing modern neuroscience is the question of how constitutive mutations in genes present in every cell can cause different effects on different parts of the brain. CASK is one such gene which is expressed in every cell of the brain and, when mutated, typically results in an overall smaller brain volume. However, the cerebellum is one region of the brain involved in motor coordination which is disproportionately smaller than the rest of the brain. Through this gene, I investigate here two questions principally: (1) what is the role of the CASK protein in cells? And (2) how is the cerebellum differentially affected? Firstly, I conduct a molecular investigation into what changes in the brain of a mouse model of CASK deletion which recapitulates the majority of human cases found in girls. This genetic model results in half of cells in the body lacking CASK and leads to smaller brain volume with disproportionate reduction in cerebellum size, as in the human subjects. Using a variety of molecular and biochemical methods, I uncover that several classes of proteins are changed in this brain, primarily those associated metabolism and cell-to-cell communication. Further, my experiments indicate that CASK interacts with many of these proteins. Next, I use human cases as well as a novel mouse model to uncover the trajectory of CASK-linked reduction in cerebellar size. The human case indicates molecular signatures of cell death, a surprising finding given that CASK-linked disorders are thought to result from developmental failure. Investigating this mechanistically in a mouse model, I uncover that when CASK is deleted after development, cerebellar cells still die and the cerebellum actually shrinks. Thus, my work herein elucidates potential roles for the CASK molecule in cells and shows, for the first time, that CASK-linked cerebellar size diminishment is degenerative in nature rather than developmental. This degeneration of the cerebellum occurs very early on in infancy and so was missed until now. The most important implication is that a degenerative process could be halted with therapies other than relying exclusively on genetic therapies.