The MALT1 gene is located on chromosome 18q21.32. The MALT1 Break Apart FISH probe is designed to label both ends of the MALT1 gene, respectively. A 600 Kb orange probe is designed at the 3′ end of the MALT1 gene, and a 800 Kb green probe is designed at the 5′ end of the MALT1 gene.

The MALT1 gene was identified through t(11;18)(q21;q21), found in 30% of MALT lymphomas. This translocation is exclusive to MALT lymphomas and absent in nodal/splenic marginal zone lymphomas, diffuse large B-cell lymphomas, or other NHLs. The second most common translocation in MALT lymphoma is t(14;18)(q32;q21) IGH/MALT1, predominantly occurring in non-gastric MALT lymphomas and present in 5-25% of cases in ocular adnexa, lung, salivary
gland, and skin.