Bening brings her children (from left) Kathlyn, Isabel and Benjamin to see “Spring Awakening” in 2007. Later that year, Kathlyn (right with Beatty), started going by the name of “Stephen.” (FilmMagic)

Minutes after leaving Le Pain Quotidien in Los Angeles, “The Kids Are All Right” writer and director Lisa Cholodenko called producer, Jeff Levy-Hinte.

“I just found Nic at the coffee shop,” she told him. “It’s Annette Bening.”

At first, Levy-Hinte was skeptical about Bening playing the movie’s lead lesbian character Nic.

“We were familiar with her work, but we didn’t see her in the role,” he recalls. “But she came in and it felt so natural that now it’s like, ‘How could it have been anyone else?’”

Bening is now nominated for lead actress in a comedy or musical at tonight’s Globes and is the buzzed-about contender for the Best Actress Oscar.

The movie itself — about two teens struggling with their identities and two moms (Bening and also-nominated Julianne Moore) fighting to overcome the doldrums of marriage after the kids’ sperm donor (Mark Ruffalo) appears on the scene — is up for Best Picture.

“I see Nic as pretty straightforward,” Bening has said. “I loved playing her because of that. She wants to do the best she can, [she] doesn’t always get it right, but [she] wants to take care of her family.”

In the “Kids are Alright,” she’s the steely center of her family; an obstetrician who likes her wine, loves her kids and feels her wife slipping away.

“Annette made ‘Nic’ more humorous than the script had written her, and tougher, too,” says Levy-Hinte. “She turned her into the dominant character in the film. As soon as we saw her performance, we were like, ‘Wow.’”

The film, which was shot in 23 days on a $5 million budget, deals with difficult themes of a modern family — gay parenting, infidelity, finding one’s path in life — and perhaps Bening felt comfortable with such a nuanced role because she’s reportedly facing similar tough themes at home.

Her eldest child of four with husband Warren Beatty is reportedly transgender and wants to follow in the footsteps of Chaz Bono, the child of Cher and Sonny Bono, by having gender reassignment surgery. Born Kathlyn Beatty, the 18-year-old now lives as a man and goes by the name Stephen Ira Beatty. Stephen is enrolled at Sarah Lawrence College upstate, and has posted photos of himself wearing a tuxedo on Facebook.

Bening is supportive of the decision, while Beatty is reportedly struggling with it. Neither have spoken publicly about the matter.

Stephen left the prestigious Buckley School in Sherman Oaks, Calif., to attend a more progressive institution, the Arete Prepatory School, from which he graduated this summer. Pictures of the graduation ceremony showed a beaming Bening and a glum Beatty.

“Usually parents require a lot of support around their child’s gender transition,” says Dr. Katherine Rachlin, a clinical psychologist and gender specialist in the city. “It’s definitely something that the family needs to deal with together, and it’s hard. The more he moves towards his gender, the better he will feel, and the other people in the family may feel more lost as that happens.”

Bening, 52, wanted to be a mother ever since she was a child.

“It’s always been in me,” Bening has said. “I’m not somebody that came to that later and thought, ‘Well, maybe I will and maybe I won’t.’ It was always just there.”

Born in Topeka, Kan., the youngest of four children, Bening found acting as a high schooler after her father, an insurance salesman, relocated the family to San Diego. She studied acting in college and after a brief first marriage to actor J. Steven White, moved to New York where she immediately was nominated for a Tony for her role in “Coastal Disturbances” on Broadway in 1987.

With her serious-acting prowess, she easily made the jump to film, starring as Dan Aykroyd’s wife in the goofy comedy “The Great Outdoors” the following year. Her sit-up-and-take-notice-role was in 1990’s “The Grifters,” opposite John Cusack and Anjelica Huston, for which she was nominated for a Best Supporting Actress Oscar. The statue went to Goldberg for “Ghost.”

In 1992, Bening starred as a mobster’s moll in “Bugsy,” opposite Beatty, the most infamous Lothario in Tinsletown. But Bening changed all that when she got pregnant with Kathlyn and finally made an honest man of him through marriage in 1992. He was 55 and she was 33. The two have been a rock-steady couple since then, and had three more children: Benjamin, 16, Isabel, 13, and Ella, 10.

After being nominated by the Academy in 2000 for her role as the tightly wound real estate agent wife of Kevin Spacey in “American Beauty,” Bening took time off to stay home with her kids, a luxury she says she cherishes.

“I’m lucky I can stop and start,” she has said. “As I was getting into movies, I didn’t realize how incredible that would be. I do a project for a couple of months and then I go away and I’m not working for long periods of time.”

Staying around, no doubt, to make sure her “kids are all right.”