Bardet-Biedl syndrome (BBS) is a genetic disease that affects cilia function and/or maintenance. Other cellular functions, however, have not been well investigated. In this study we provide evidence that implicates BBS proteins as modulators of cytoplasmic-nuclear transport in addition to their cilia roles. To date, 20 genes have been identified as causes of BBS in patients. While BBS genes are from diverse gene-families, many of the BBS proteins form two major complexes: the BBSome (BBS1, 2, 4, 5, 7-9, and BBIP10) and the BBS chaperonin complex (BBS6, 10, and 12). The BBSome, which localizes to the basal body, is the main functional complex and is involved in trafficking of cargo to the cilium. Correct assembly of the large BBSome is mediated by the BBS chaperonin complex. Our lab has established the zebrafish as an in vivo model for BBS, and we have previously identified cilia-dependent as well as cilia-independent phenotypes. This has led us to investigate functions of BBS proteins outside of their defined roles in the cilia. Because of the similarities between the cilia transition zone (CTZ) and nuclear pores we hypothesized that BBS proteins regulate nuclear-cytoplasmic transport in addition to ciliary transport. Using zebrafish in conjunction with human tissue culture we identified an interaction between BBS6 and the SWI/SNF chromatin remodeler SMARCC1 (BAF155). We determined that BBS6 is actively transported between the nucleus and the cytoplasm and that perturbations of BBS6, as well as other BBS chaperonin complex members, affects the sub-cellular localization of SMARCC1. We conclude that BBS6 has a functional role beyond being a scaffold for BBSome assembly. Our work demonstrates that BBS6 functions (likely with other BBS proteins) to modulate nuclear-cytoplasmic transport of nuclear proteins and disruption of this may manifest as disease. This highlights the importance of looking at disease causing genes and alleles from a broader perspective.