Setting back to incomplete due to your last comment.

Indeed, $HOME/.profile and /etc/profile are what you're looking for.

These files are sourced from /etc/gdm/Xsession (.gnomerc has been
deprecated a while ago) and read by your login shell. (From sh man page
"A login shell first reads commands from the files /etc/profile and
.profile if they exist.") All environment variables set in these files
will be available whether you're logging in through gdm or a virtual
console.

- Please, can you describe the steps to follow to reproduce your issue ?
- Can you provide the output of the command "lsb_release -rd"
- Can you provide the output of the command "apt-cache policy gdm"
- Can you provide the value of the shell returned by "getent passwd $USER" when 
logged in with the user with this issue.

Thanks in advance.

** Changed in: ubuntu
       Status: Invalid => Incomplete

-- 
Feature Request: Provide a single configuration file for user settings
https://bugs.launchpad.net/bugs/134378
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