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The church, with a congregation of about 150, is located off of NW Maynard Road.
The Rev. Carla Gregg-Kearns, senior pastor, said two wooden signs cut into the shape of a comma and painted in rainbow colors have been posted back-to-back in the ground at the church's entrance for about a year.
Gregg-Kearns said the comma is used throughout the United Church of Christ as an expression of their belief that God is still speaking.
"It's the way that we let folks know that we're welcoming of the lesbian, gay, bisexual, transgender, queer community," she said. "So it's an important piece of who we are."
The church reported the incident to Cary Police, but there are no surveillance cameras in the area that would have caught the vandal who is believed to have struck sometime between Thanksgiving Day and Sunday.
Gregg-Kearns said the church didn't feel threatened by what happened but said it sent a targeted message. She said the church member who made the signs is repainting the marred one with hopes to have it back up by Sunday.
"Having that part attacked in that sort of way, I think, made me feel it was a core piece of who we are that somebody was trying to send a message about," she said. "That it's something that they want erased or that they don't want to see."