The custom permission could be assigned via a Permission Set or a Permission Group set. Sometimes, we need to check the logged in user has custom permission assigned.
FeatureManagement system method
salesforce winter 18's release introduced a new system class FeatureManagement. It has a methods checkPermission to check current logged user has specific permissions or not. It will return true or false based on custom permission assignment. It don't required SOQL.
Boolean isUserHasCP = FeatureManagement.checkPermission('Custom Permission API Name');Source:
https://developer.salesforce.com/docs/atlas.en-us.apexref.meta/apexref/apex_class_System_FeatureManagement.htm#apex_System_FeatureManagement_checkPermission