BLS II is a rare condition. At least 100 cases have been reported in the medical literature. While BLS II has been found in several populations throughout the world, it appears to be especially prevalent in the Mediterranean region and North Africa.

BLS II is caused by mutations in the CIITA, RFX5, RFXANK, or RFXAP gene. Each of these genes provides instructions for making a protein that plays a role in controlling the activity (transcription) of genes called MHC class II genes. Transcription is the first step in the production of proteins, and the CIITA, RFX5, RFXANK, and RFXAP proteins are critical for the production of MHC class II proteins from these genes.

The RFX5, RFXANK, and RFXAP proteins come together to form the regulatory factor X (RFX) complex, which attaches (binds) to specific regions of DNA involved in the regulation of MHC class II gene activity. The CIITA protein interacts with the RFX complex and brings together other proteins that turn on gene transcription, leading to the production of MHC class II proteins.

MHC class II proteins play an important role in the body's immune response to foreign invaders, such as bacteria, viruses, and fungi. To help the body recognize and fight infections, MHC class II proteins on lymphocytes bind to fragments of proteins (peptides) from foreign invaders so that other specialized immune system cells can interact with them. When these immune system cells recognize the peptides as harmful, they trigger the lymphocytes to launch immune responses to get rid of the foreign invaders.

Mutations in the CIITA, RFX5, RFXANK, or RFXAP gene prevent transcription of MHC class II genes, which leads to an absence of MHC class II proteins on the surface of certain lymphocytes. Lack of these proteins on lymphocytes impairs the body's immune response to bacteria, viruses, and fungi, leading to persistent infections in individuals with BLS II syndrome.