Officials say 31-year-old James Weldon was arrested Friday morning on the 1300 block of S. Dover Street.
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Weldon was wanted for firearms violations and endangering the welfare of a child after his son was shot on Sunday in the city's Gray Ferry neighborhood.
The incident started just after 5 p.m. when police responded to the Philadelphia fire station on Grays Ferry Avenue for reports of a child shot.
The child's mother, 23-year-old Laylaah Muhammad, originally told police her son had been struck by a stray bullet while out on a walk.
However, investigators later determined the child was shot inside a home on the 1500 block of Taney Street.
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On Thursday, officers announced the arrest of Muhammad. She has been charged with criminal conspiracy, endangering the welfare of a child, unsworn falsifying, tampering with evidence, obstruction of justice, and false reports.
Officials say the child is still recovering after suffering a gunshot wound to the cheek.
The circumstances surrounding the shooting, including how the child was shot, is still under investigation.