Sometimes, when you try to modify a database in phpMyAdmin, you can get this error message when you try to execute the SQL query:
#1064 - You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use...
This is a known issue in cPanel which occurs when you access your cPanel via the Access cPanel Normally button in your Customer Area.
In other words, this issue appears when you access your cPanel using the cPanel proxy, i.e:
In order to avoid it, please access your cPanel via:
or using the Access cPanel Securely button in your Customer Area.
If the above doesn't help, you should check the syntax of the query you are trying to execute and make sure it is correct.