In the comics, she left to be a nun when Matt was small.
The phone call you mentioned seems to be the only reference to Matt's mother in the TV series (so far - it's speculated here that this plot thread might be picked up in a later season). But in the original comics, we know quite a bit about her.
From Marvel Wikia (sourced to the original comics):
Maggie is the mother of Matt Murdock, the vigilante known as Daredevil. She and Jack had Matt when they were a young couple. However, Maggie soon suffered from postpartum depression, feeling constantly anxious regarding Matt's safety, thoughts which soon developed into self-loath, as she considered herself to be a bad mother.
Her depression became a paranoia. She began thinking that Jack was plotting against her, and that Matt was there to tear them apart. One night, under the influence of her mental illness, Maggie tried to assault the baby. As soon as she came to her senses, she ran away in shame. She was taken in by a church, and took the name of Margaret. With the help of doctors and counseling, she recovered from her depression.
See also her entry at ComicVine.