Primary Immunodeficiencies (PID) are hereditary diseases of the immune system that generally present with an increased susceptibility to infections, an increased risk of malignancy and/or with symptoms of immune dysregulation. With the rise of next generation sequencing (NGS) over the last years, the number of genetic variants leading to PIDs has grown dramatically. This means there are many new PIDs for which the disease mechanisms are not well understood yet and accordingly best treatment practices have also not been established. Furthermore due to NGS the phenotypic variability of known genotypes is also becoming increasingly apparent. PIDs are usually caused by germline mutations and thus commonly have multisystemic effects, which can make diagnosis and treatment difficult. In order to provide adequate treatment the mechanisms of a PID often needs to be fist understood. This can be quite complex and requires research to not only focus on cells of the immune system. To this effect research not only needs to make use of primary patient material but also of novel gene editing techniques applied to animal models and cell lines. Similarly in order to better diagnose patients it is important to report on patients with atypical phenotypes with a known genotype. The three studies presented here are all on known PIDs and use different approaches to address these various diagnostic and therapeutic challenges mentioned above. The first study on TTC7A deficiency uses the flaky skin (fsn) mouse model, to evaluate the role of epithelial barriers in this disease. It shows that the skin phenotype in the fsn mouse is driven by fibroblasts and develops independent of the adaptive immune system. Furthermore it establishes that Ttc7 influences cell interactions, which has allowed us to identify novel therapeutic targets to be evaluated in humans. The second study on patients with gain of function (GOF) mutations in signal transducer and activator of transcription (STAT) 3 is based on an example of an atypical presentation of a known PID, which led us to evaluate the effect STAT3 GOF mutations have on erythropoiesis. We could show that STAT3 GOF mutation reduce polarisation of cells towards the erythroid lineage, making patients less resistant to autoimmune attack of the erythroid lineage. Thus STAT3 GOF mutations also have multisystemic effects leading to a complexity of phenotypes that can be seen in patients. The final study on Major histocompatibility complex (MHC) II deficiency is a case series of Egyptian patients, diagnosed by whole exome sequencing (WES). This study exemplifies how variable phenotypes can be in genetically similar patients. Interestingly some of these patients present with a surprisingly severe phenotype more reminiscent of Severe Combined Immunodeficiency (SCID) than of MHCII deficiency. Thus exemplifying how important access to genetic sequencing is in the correct diagnosis of patients and their adequate treatment.