The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. Chloride channel 6 and 7 belong to a subbranch of this family. Chloride channel 6 has four different alternatively spliced transcript variants. This gene is in close vicinity to two other kidney-specific chloride channel genes, CLCNKA and CLCNKB.

The predicted 869-amino acid protein was called CLC6 by them. The amino acid sequence of CLCN6 is 45% identical to that of CLCN7 but only 23 to 29% identical to the sequences of other known CLCNs.