More than two months after the Food and Drug Administration approved an expensive new gene therapy drug for a rare disease in children, the agency said it has major questions about the accuracy of some of the testing data. The FDA said Tuesday that the drug maker — AveXis, which is owned by Novartis — was aware of problems with the data and didn’t inform the agency until after the drug was approved.

The drug Zolgensma was approved in May to treat spinal muscular atrophy in children 2 and under. Children with the genetic mutation, which kills nerve cells in the spine, lose their ability to walk, eat and breathe. It affects about 1 in every 11,000 babies, and many die before turning 2.

The new drug, a type of gene therapy that fixes the mutation, has given hope to parents who often have few other options. With a price tag of $2.1 million, it is the most expensive drug in the world — the cost has been a major roadblock for patients who can’t get insurance to cover it.

Dr. Peter Marks, director of the FDA’s Center for Biologics Evaluation and Research, said Tuesday in a statement that AveXis manipulated some of the early data from testing in animals. That data was submitted as part of the drug’s application for approval.

“Ensuring truthful, complete and accurate data in product applications is a critical component of industry’s responsibility as they work to demonstrate the safety, purity and potency of biological products,” Marks said. “The submission of such truthful, complete and accurate data is also critical for the FDA to be able to protect the public health, and the law requires it.”

The FDA stopped short of pulling approval for the drug, saying that the agency “remains confident that Zolgensma should remain on the market,” and that all testing done in humans showed that the drug was safe and effective. The agency hasn't ruled out possible criminal or civil action against AveXis, according to the FDA statement.

“The idea that Novartis would go for approval of the most expensive drug in the history of the world and do it with data it knew to be inaccurate is an outrage and it could put patients in jeopardy,” David Mitchell, a cancer patient and founder of the advocacy group Patients For Affordable Drugs said via email.

In a statement provided to NBC News late Tuesday, Novartis said that AveXis became aware of the allegations and voluntarily told the FDA that the data was inaccurate, and that “at no time during the investigation did the findings indicate issues with product safety, efficacy or quality,” adding that that they “are fully confident in the safety, quality and efficacy of Zolgensma.”

One drug development expert said the case is unusual, but there should be no cause for alarm for patients.

"If I’m a parent, my major concern is the health of my child, and the FDA is reassuring me," Kenneth Kaitin, director of the Tufts Center for the Study of Drug Development, told NBC News. "The FDA is being transparent about it, and it has no impact on the value of that drug in treating a child."

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