Synovial sarcoma (SS) is characterized by the t(X;18)(p11.2;q11.2) chromosomal translocation detected in >95% of cases. Through this translocation, one of the SYT genes, SYT4 on chromosome 18, is fused to one of the SSX genes on chromosome X. SYT4-SSX1 is the most common fusion subtype, present in approximately two thirds of the cases, followed by SYT4-SSX2 and, very rarely, SYT4-SSX4. Variant fusion transcripts occur less often, and most of the reported cases are the result of small insertions. Described here is a novel fusion variant containing a small deletion resulting in an alternative reading frame of the SSX part of the fusion gene. This fusion transcript may provide further insight into the oncogenic function of the SSX partner of the fusion gene.