Student or Learner
Can we ever use "how come" with the question form?
E.g: How come do you never phone me?
It's idiomatic, yes, though honestly I have no idea if it's grammatically correct or explainable. It's certainly been around for many years as an alternative to "Why..." or "How is it that..." or "What's the reason for..." etc.
How come the sky is blue?
How come nobody learns to play the harpsichord any more?
How come my laces always come undone when I'm halfway up the stairs?
How come you're so tanned?