The preteen boy, whom authorities won't name because of his age, was charged as a juvenile with capital murder. A judge Wednesday ordered him held in juvenile detention.
The 10-month old, Deandre Washington, was injured on March 12 and died two days later at a hospital, said Child Protective Services spokeswoman Estella Olguin.
Authorities still are trying to determine how many children were in the house in a working class section of southeast Houston when the mothers of the two sets of siblings left them alone. They also don't yet know whether the 12-year-old, who was the oldest in the group, was specifically left in charge.
The boy was not in school that day because he had been suspended for fighting.
"It's not clear whether the mothers told the 12-year-old, 'You are in charge,' and left with the intention of coming back. He would have been the oldest so more than likely you would think he would be in charge," Olguin said.
The 12-year-old has nine siblings, and all but two live with their mother, Tawanna Scott. Deandre's mother has three other kids.
The two mothers came home after the 12-year-old boy called them to say Deandre was not breathing, calling 911 after they got home, Olguin said. She said the other children witnessed the 12-year-old throw the baby to the floor.
Deandre suffered two skull fractures and bleeding in multiple organs.
CPS has not taken custody of any of the two mothers' children. It is legal to leave children alone as long as one child is 12 or older.
If convicted, the boy could receive a maximum 40-year prison sentence, probation or commitment to the Texas Youth Commission system, said Bill Moore, the chief of the juvenile division for the Harris County District Attorney's Office.
The minimum age to be certified as an adult in Texas is 14.
"We will get all the information we can on the facts of the case and at that point we will get together and decide if we should present it to a grand jury or go to juvenile court and we're not there yet," Moore said.
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