The two-year-old son of a Yemeni woman who sued the Trump administration to let her into the country to be with the boy has died.

The Council on American-Islamic Relations (Cair) announced that Abdullah Hassan died in UCSF Benioff children’s hospital in Oakland, where his father Ali Hassan brought him in October, to be treated for a genetic brain disorder. The boy’s mother, Shaima Swileh, remained behind in their home in Egypt. Hassan is a US citizen, as was his son. Swileh is not.

“We are heartbroken. We had to say goodbye to our baby, the light of our lives,” Ali Hassan was quoted as saying in a statement published Cair. A funeral was scheduled for Saturday.

Hassan lives in Stockton, California. He and Swileh moved to Egypt after marrying in war-torn Yemen in 2016. Swileh had been trying to get a visa since 2017, so the family could move to the US.

Shaima Swileh, right, stands with her husband Ali Hassan after she arrived at San Francisco international airport on 19 December. Photograph: Jeff Chiu/AP

Citizens from Yemen and four other mostly Muslim countries, along with North Korea and Venezuela, are restricted from entering the US under Donald Trump’s travel ban.

When the boy’s health worsened, Hassan went ahead to California to get their son help. As the couple fought for a waiver, doctors put Abdullah on life support.

“My wife is calling me every day wanting to kiss and hold her son for the one last time,” Hassan said, choking up at a news conference earlier this month.

He started losing hope and was considering ending his son’s suffering. But then a hospital social worker contacted Cair, which sued on 16 December, said Basim Elkarra, executive director of the group in Sacramento. The state department granted Swileh a waiver the next day.

“With their courage, this family has inspired our nation to confront the realities of Donald Trump’s Muslim ban,” said Saad Sweilem, a lawyer with Cair who represents the family. “In his short life, Abdullah has been a guiding light for all of us in the fight against xenophobia and family separation.”

Swileh held her son for the first time in the hospital on 19 December.