It happened around 7:20 a.m. on East 223rd Street in the Edenwald section.
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The victim, Khamani Garrett, who attends Manhattan Business Academy in Chelsea, was walking to the subway by himself at the time.
Police say the gunman, who they believe is emotionally disturbed, walked up to him and opened fire.
Garrett was taken to Jacobi Hospital to undergo surgery and is expected to survive.
"He said he was walking, and then the guy just shot him," mom Abigail James said.
13-year-old shot in neck while walking to school in NYC
Authorities say the 36-year-old suspect, identified as Hubert Wiggs, lives on the street, a location known to the police for guns activity, and that as the child walked by his house, the suspect was outside waving a gun and acting erratically.
He then walked up to the boy and shot him, police said, with the bullet entering and exiting his neck without severing an artery.
"He said the man couldn't even look at him in his eye, he didn't look at him in his eye," sister Sanaa Garrett said. "He didn't know that he got shot. He thought it was a firework...I was suppose to leave with him but I didn't have everything together. So I left like two minutes after him, so when I got the block, there was nothing there. So I didn't see anything."
The disoriented boy stumbled away, bleeding and looking for help. A passerby saw him and called 911.
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"The first person he asked for help didn't want to help him," James said. "So then he asked somebody else for help, and they helped him. That actually hurt my soul. I could've been burying my son."
Officers arrived and encountered Wiggs, still acting erratically, and took him into custody.
"They gave verbal commands for that individual to drop that firearm," NYPD Assistant Chief Kenneth Lehr said. "The individual's initial reaction was to try and hide it in his waistband. They gave further verbal commands, at which time the individual dropped that object on the ground. When the officers moved in, took that individual into custody without incident and recovered a firearm."
His .38 caliber revolver with one spent round was recovered at the scene, officials said.
Wiggs is charged with attempted murder, assault, criminal possession of a weapon, reckless endangerment and menacing.
James said Khamani will celebrate his 14th birthday on Monday.
"Straight home after school, I have no problems with him," she said. "He's just a video game fanatic or on his phone, that's all he does."
Police say Wiggs was arrested for criminal possession of a loaded firearm in 2019 while he was still on parole for a 2010 gun arrest in Harlem.
On February 24, 2019, authorities say he broke into a vehicle in East Harlem and was in possession of a loaded .38 firearm, as well as drugs, at the time of his arrest.
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That case has yet to go to trial, with his next court date scheduled for January.
On April 22, 2010, he was arrested for criminal possession of a controlled substance and was found to be in possession of a .32 caliber Smith and Wesson.
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He has had another arrest during his time on parole, in 2018, for grand larceny.
He was conditionally released in 2015 on parole, which set to expire next April.
Police officials said he should never have been out on the street.
"You're talking about a 13 year old boy here going to school," Lehr said. "And he winds up having to have this traumatic experience with somebody who's out on parole for firearm, out on bail for a different firearm, and today, he shoots this boy in the neck."
Wiggs has spent a lot of time at Bronx criminal court. But he wasn't there Tuesday night because he is instead having a psych consult.
When he is eventually arraigned on second degree attempted murder, he will be eligible for bail. Again.
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