'Wonder' author on her inspiration for the book and meeting an 'Auggie Pullman come to life' "I remember thinking, 'Oh my goodness, this is Auggie Pullman come to life.'"

 -- Starting at a new school with new classmates can be a daunting task for most children. But for Nathaniel Newman, the first day of middle school was extra intimidating, because he’s not like most kids.

Nathaniel was born with Treacher Collins syndrome, an extremely rare craniofacial disorder caused by mutations in the POLR1C gene. It affects an estimated 1 in 50,000 people in the United States.

In the first year of his life, Nathaniel had more than 10 surgeries because of the malformations in his face. But despite the hardships he’s faced so far in his short life, Nathaniel said he "kind of" likes being different.

“I know everyone looks different, except I look a lot more different than everyone else,” Nathaniel, 13, told ABC News’ Elizabeth Vargas.

“I kind of like it,” Nathaniel added. “It just seems fun ‘cause I stand out.”

So in the fall of 2015, when Nathaniel was about to attend his first day of sixth grade at B.D. Billinghurst Middle School in Reno, Nevada, his parents Magda and Russel Newman had a plan to ease his transition.

“Russel and Nathaniel sit down and write a letter,” Magda Newman told “20/20.”

“My name is Nathaniel Newman, and I am 12 years old. I am different. I don’t want you to be surprised when we meet,” part of the letter read. “I have three dogs. I like 'Pokémon' a lot, as well as 'Star Wars.' I really just want you to treat me like everyone else.”

The letter included a photo of Nathaniel, as well as a mention of the bestselling children’s book “Wonder.”

“Like, ‘Hey, you might have read “Wonder” now. Well, I’m a kid just like Auggie Pullman,’” Russel Newman recalled of the letter.

“Wonder” tells the story of the fictional character 10-year-old Auggie Pullman, who was born with a facial difference -- much like Treacher Collins.

While “Wonder” isn’t based on real people, its author R.J. Palacio says she was inspired to write it by a chance encounter she had with a young girl while she was at an ice cream shop with her two sons.

“I realized that there was a little girl sitting directly next to me,” Palacio told “20/20.” “She had a very severe cranial facial difference, and I kind of panicked ‘cause my little boy started to cry hysterically.”

In her haste to protect the girl from her son’s reaction, Palacio said, she turned the stroller around and started quickly pushing it away.

“It was terrible, and I was so mad at myself for the way that I handled it,” Palacio said. “For the rest of the day, I just kept thinking about all the things I wished I’d said and done.”

Palacio started writing with the hope that her story could inspire parents and children alike.

“I just thought, ‘OK, I’m going to write a book, and it’s going to be about what it must be like to face a world every day that doesn’t know how to face you back,’” Palacio said.

When the book came out in 2012, nurse Pat Chibbaro, who worked with the Newman family, read it and immediately told the Newmans about it.

“I literally read it in three hours, cried the whole time,” Russel Newman said. “I remember calling back Pat and going, ‘Pat, did she spy on us? Like, this is freaky.’”

Russel and Magda Newman and their sons Nathaniel and Jacob got to meet Palacio face to face. “And when she saw Nathaniel, you could just see this look in her face,” Russel Newman recalled.

“I remember thinking, ‘Oh my goodness, this is Auggie Pullman come to life,’” Palacio said.