It happened around 3:30 a.m. on FM-1960 near Steepletop Drive in northwest Harris County.
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The deputy was at an eastbound traffic signal on FM-1960 when he was rear-ended by the other car, according to HCSO Sgt. Daniel Cooper.
"He was stopped or starting to go, the deputy said the light had just turned green," Cooper said.
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Both the deputy and the driver of the other vehicle were taken to a hospital, but injuries were believed to be minor.
The driver faces possible DWI charges related to the crash, Cooper said.
The incident was one of at least two crashes in the Houston area involving law enforcement vehicles this weekend.
In Montgomery County, five deputy constables were injured Saturday when the driver of a Tesla slammed into a deputy's cruiser, causing a chain-reaction crash.