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6 year oldJosé Filomeno dos Santos was removed months after a BBC investigation.
The $5bn (£3.7bn) fund has been mired in controversy since its 2011 launch.
This is the second of the former president's children to be dismissed by Mr Lourenço: Daughter Isabel dos Santos was removed as head of the country's state oil company Sonangol last year.
Billionaire Ms dos Santos is Africa's richest woman; it is not known how much her brother is worth.
Many of the children of the former president's children have government-linked roles.
Mr dos Santos stepped down after 38 years in power last year. Mr Lourenço, also known as JLo, succeeded him with a promise of cracking down on corruption.
He has also developed a reputation for pushing aside powerful figures associated with his predecessor.
JLo's decision to name Carlos Alberto Lopes, a former finance minister, as new chairman of the Fundo Soberano De Angola (FSDEA) on Wednesday came after an internal investigation into its workings.
It had been under increased scrutiny since it was revealed in the Paradise Papers leak that it had paid tens of millions in fees to a businessman who works closely with José Filomeno.
The Paradise Papers were a joint investigation between the BBC and other news outlets around the world into a leak of financial documents which throw light on the top end of the world of offshore finance.
In this case, it revealed Jean-Claude Bastos, sometimes also known as Jean-Claude Bastos de Morais, a Swiss-Angolan and close friend of the then president's son, was chosen as the fund's asset manager.
Mr Bastos was given responsibility for investing almost all of the fund's money, and was paid accordingly - earning more than $41m in just 20 months.
process". The firm was selected, it said, because of its "exemplary performance on previous mandates with the Angolan authorities".
The fund also said that giving near total control of investments to one asset manager was part of its policy for the first 18 months only.
In November 2017, Isabel dos Santos was fired as head of oil company Sonangol. She had dismissed criticism of her appointment to the head of Sonangol in 2016, later telling the BBC she had faced prejudice.
Angola is Africa's second-biggest oil producer.
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