Police spokeswoman Jodi Silva said the man cornered the officer in his wheelchair and was making threats while trying to stab the officer with the pen. At the time, the officer did not know what the metal object was that the man was waving, Silva said.
She said the man came "within inches to a foot" of the officer and did not follow instructions to calm down and remain still.
"Fearing for his partner's safety and his own safety, he discharged his weapon," Silva told The Associated Press.
Police did not immediately release the name of the man who was killed. They had been called to the home after a caretaker there called and reported that the man in wheelchair was causing a disturbance.
The owner of the group home, John Garcia, told the Houston Chronicle that the man had a history of mental illness and had been living at the house about 18 months. Garcia said the man had told him that he lost a leg above the knee and all of one arm when he was hit by a train.
"He sometimes would go off a bit, but you just ignore it," Garcia told the newspaper.
Silva identified the officer as Matthew Jacob Marin, a five-year veteran of the department. He was immediately placed on three-day administrative leave, which is standard in all shootings involving officers.
Houston police records indicate that Marin also fatally shot a suspect in 2009. Investigators at the time said Marin came upon a man stabbing his neighbor to death at an apartment complex and opened fired when the suspect refused to drop the knife.
On Saturday, Marin and his partner arrived at the group home around 2:30 a.m. Silva said there were several people at the house at the time. The caretaker who called police waited on the porch while the officers went inside, she said.
"It was close quarters in the area of the house," Silva said. "The officer was forced into an area where he had no way to get out."
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