MySQL Preference Pane is specifying a port number when it runs mysqld
You may change the port in the file com.oracle.oss.mysql.mysqld.plist file in /Library/LaunchDaemons by editing it with 

sudo nano /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist


Change the port at

  &lt;string&gt;--port=3307&lt;/string&gt;


near the end of the file to whatever you need it to be and reboot your Mac or restart the service.