This error was there in user’s cpanel section and no database, no db users etc were showing in the cpanel for the users.

On checking the /varlib/mysql/server.domain.com.err (mysql error log) I can see the mysql user table was corrupted and needed repair

141204 12:13:56 [ERROR] /usr/sbin/mysqld: Table ‘./mysql/user’ is marked as crashed and should be repaired

You can repair mysql database via command line

# mysqlcheck -r mysql

================
mysql.user
warning : Number of rows changed from 282 to 283
status : OK
================

You can see table mysql.user is crashed and after repairing the issue will get fixed.