Autoimmune hepatitis (AIH) is a chronic progressive autoimmune liver disease characterized by hypergammaglobulinemia, interface hepatitis, female preponderance and presence of autoantibodies in most patients. The presence of HLA-DR3/DR4 and functional impairments in regulatory T cells are associated with AIH. However, AIH is a multifactorial complex disease. In this report, we present a case of a seronegative AIH girl with chronic hepatitis, hyper-IgE, perforating nodular dermatitis and sheer eosinophilia. To re-evaluate the diagnosis, whole exon sequencing was performed. We determined that the patient has the ancestral haplotype A1-B8-DR3 associated with autoimmunity. More importantly, we found an undocumented point mutation (Ala627Thr) of the FMS-like-tyrosine 3 kinase (FLT3) receptor. This FLT3 receptor gain-of-function mutation is associated with the activation of the mammalian target of rapamycin (mTOR) instigating dendritic cell activation. Furthermore, a loss-of-function mutation in the melanocortin-3 receptor (MC3R) gene paramount in inhibiting IL4 was detected. The constellation of these immune deregulatory factors may have propagated auto-aggression of the liver causing chronic hepatitis with AIH features. Albeit, the seronegativity with eosinophilia and hyper-IgE let us hypothesize that the pathognomonic mechanisms, in this case, diverts from classical AIH pathophysiology. As mTOR is constitutively activated, mTOR inhibitors may be used to treat AIH and dermatitis