Github Gist via SSH protocol doesn't work

I'm using two-factor auth and that's why HTTPS isn't convenient way to work with GitHub repos and gists.

I have correct config and github_pr_key files in my ~/.ssh directory.

I'm able to clone all my personal and public repos.

But I can't clone via SSH any of my private or public gists, I have this error:

~/Desktop >> git clone [email protected]:d1b8041051e62aa34f337b3dabc77d9a.git                                                                                                                                
Cloning into 'd1b8041051e62aa34f337b3dabc77d9a'...
The authenticity of host 'gist.github.com (192.30.253.118)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl22E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'gist.github.com,192.30.253.118' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

How it can be fixed?

Solution

Check first the reasons mentioned in "Error: Permission denied (publickey)".
Double-check the output of ssh -Tv [email protected], to confirm your public key is registered on your GitHub account.

But don't forget that you can still use https with 2FA.
Create a PAT (Personnal Access Token), and use it as password.
That should be enough to allow you to clone anything, including your private Gists.

Finally, try to clone through ssh with [email protected], not [email protected] (as seen in 2013, even though [email protected] should work):

git clone [email protected]:d1b8041051e62aa34f337b3dabc77d9a.git <=== does work 
NOT
git clone [email protected]:d1b8041051e62aa34f337b3dabc77d9a.git

Just for testing, try also:

git clone ssh://[email protected]/d1b8041051e62aa34f337b3dabc77d9a.git

(this time with [email protected])

As noted by Jacktose in the comments:

If ssh -Tv [email protected] works, try ssh -Tv [email protected] and compare.

In my case, the latter was using the wrong public key because .ssh/config specified IdentityFile under Host github.com.
I changed that to Host github.com *.github.com and problems solved.