At a court hearing for Singer, prosecutor Amanda Skillern also told a judge that an autopsy found multiple bed sores on the boy, who had been emaciated, and that there were "visible signs of injury upon the body."
Jonathan, who had cerebral palsy and was partially or completely blind, was found in the early hours of Sunday after the boy's grandfather called police and said Singer -- his son -- had stashed the boy's body in a cardboard box inside the family's sport utility vehicle.
Skillern told a judge that Singer had admitted to his brother that the boy drowned in a bathtub on April 12, five days before authorities discovered the body. The family lives in an apartment in Pasadena, a suburb southeast of Houston. The grandfather lives in a north Houston suburb.
Skillern said Singer's brother first called police in Pasadena on Saturday evening, telling officers he was worried about his nephew's welfare.
"The defendant admitted to his brother he put his son into the bathtub, went to the store and when he returned his son was dead," Skillern said, reading a probable cause statement on the case to state District Judge Jim Wallace.
Skillern said Singer had attempted to perform CPR but was unable to revive his son.
Singer, who did not say anything during the brief court hearing, cried after Skillern read the probable cause statement.
After the hearing, Singer's attorney, Jim Lindeman, said his client, who is unemployed, is "distraught" and "devastated" by his son's death.
Lindeman said he believes the autopsy report, which has not yet been finished, will "substantiate my client's claim of not guilty."
"This isn't an appropriate time to respond to this," Lindeman said, referring to the claims by prosecutors that the boy drowned. "We'll continue to investigate. We don't have any comment on the facts (in the case). We'll try those in a courtroom."
Singer's next court hearing was set for May 26.
The boy's family had twice been investigated by Texas social workers, though no abuse was found in the first case and the second claim couldn't be fully investigated.
In January 2010, Child Protective Services officials looked into a claim that the boy, then 9, might have been neglected and suffered some kind of abuse by both parents. No abuse was found.
Four months later, the agency began investigating a claim that the boy's mother may not have been fully able to take care of her son because she was ill. But the investigation was cut short because the family moved and couldn't be located.
Police in Pasadena said the boy's mother could also be charged, though investigators were waiting for the autopsy results. The boy's two sisters, who are 15 and 17, are staying with relatives, according to officials with the Texas Department of Family and Protective Services.
Lindeman said he doesn't know where the boy's mother is and he has instructed Singer not to speak with his wife.