Synaptojanin1, the major constitutively active PtdInsP3 5-phosphatase activity in rat brain, is one of two closely related proteins both extensively spliced in their C-terminal proline rich domain. We describe here the discovery of a novel splice variant of synaptojanin1 which misses the major N-terminal part of the SAC1 domain. This deltaSAC-synaptojanin1 is expressed in rat brain tissue as shown by Northern and Western analysis. However, the deletion of the SAC1 domain does not alter PtdInsP3 5-phosphatase activity demonstrating that the SAC1 domain is not necessary for catalytic function.