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Court told main suspect in Krystal Fraser's disappearance was alleged father of her child

Krystal Fraser was pregnant when she disappeared in June 2009. (Supplied: Victoria Police)

A witness has told the coronial inquest the primary suspect in the case of missing Pyramid Hill woman Krystal Fraser had allegedly been having an affair with the heavily pregnant woman. 

Ms Fraser, who had an intellectual disability, was 23 and just days away from giving birth to a boy she had named Ryan when she disappeared on June 20, 2009.

A police investigator had previously told a coronial inquest that he considered Peter "PJ" Jenkinson, from Gunbower, the primary suspect.

Witness Denise Jones's husband, Stephen Jones, had been good friends with Mr Jenkinson before Mr Jones took his life in the winter of 2010.

Ms Jones claimed her husband stopped speaking to Mr Jenkinson after the primary suspect was questioned by police several weeks after Ms Fraser's disappearance.

"Steve was just gutted, he just could not believe what he was hearing because none of the family, nobody knew about it," Ms Jones told the inquest.

The inquest heard Mr Jenkinson attempted to visit Mr Jones with his new girlfriend, Nguyen, and their baby, but Mr Jones walked out of his home with a gun and told his former friend to leave.

"Steve, when it came to it, he was straight down the line. He didn't muck around," Ms Jones said.

Mr Jones's daughter, Shannon Connolly, told the inquest that as a teenager she remembered overhearing Mr Jenkinson tell her father he wanted Ms Fraser to get rid of the baby.

"He didn't want it but she did," she said.

Search for Krystal

A friend of Mr Jones, Susan McGillvray, took the stand on Friday, telling the court Mr Jones had become "possessed" with finding evidence of Ms Fraser's remains.

She claimed he had shown her a bag of clothing that appeared to contain something that looked like a stained shirt with stab holes in it.

"I asked Steve, 'Why do you tell me these things, why do you get me involved?'"

"And he said, 'You're a good person, you'll do what's right with this information'.'"

On another occasion, Mr Jones visited her shop crying and emotional, the court heard.

"He said, 'I told him, I told Pete, not the baby'," Ms McGillvray said.

"He was a very loving family man and very protective of children, and this had really upset him."

Two years ago, Ms McGillvray met with Ms Fraser's family.

"I mentioned to the mother the type of shirt that looked like was in the bag, and she said Krystal didn't have a shirt like that," she said.

Ms McGillvray revealed she now wished she had probed her friend further.

"I wished I'd asked a lot more questions because I've got kids and I'd want to know where they were," she said.

Mr Jenkinson is scheduled to appear at the inquest next week.

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