It depends on your GAP insurance policy rules. GAP insurance pays the difference between what is owed and what the Physical Damage Insurance Company pays. Some policies pay the deductible and some do not.

So if your car was totaled in the rear-end collision and you are putting it through your own collision coverage, instead of a third party claim through the property damage liability coverage of the at-fault driver, and thus have a deductible to pay then your GAP insurer may or may not pay your deductible amount. It will depend upon the terms of your GAP insurance policy.

GAP insurance pays the difference between the actual cash value of the vehicle and the current outstanding balance on your loan or lease. Sometimes it will also pay your regular insurance deductible when you place your primary claim for your totaled vehicle.

If however your car is not found to be a total loss from this rear end accident but will be repaired by either your insurer or the property damage policy of the at-fault driver then your GAP insurance policy would not even be involved. For gap insurance to be involved, and possibly pay your deductible, your car would need to be totaled out and actual cash value (ACV) paid out so that the gap between your ACV and loan amount needed to be paid by your gap insurance provider.