Children considering gender reassignment on the NHS are warned that puberty blockers carry risks and that their long-term effects are unknown, according to documents filed in a landmark case examining how the drugs are prescribed.

In January, the Observer reported that lawyers had filed papers in the high court as they prepared a judicial review against the Tavistock and Portman NHS Foundation Trust, which runs the UK’s only NHS Gender Identity Development Service (Gids), and NHS England.

Last Thursday, the court confirmed the review was proceeding, a decision that has dismayed the parents of some children but has been welcomed by those bringing the challenge.

“This whole area has needed serious examination for some time and I am delighted that the request for a judicial review has been granted,” said Susan Evans, a former nurse at the Tavistock, who has crowdfunded to bring the review.

Susan Evans, a former nurse with the Tavistock and Portman Trust, crowdfunded to bring the review. Photograph: Sam Tobin/PA

The claimants argue that children are too young to give informed consent to receive puberty blockers and want judges to make the decision.

But Polly Carmichael, the director of Gids, used her witness statement to defend the use of blockers. Carmichael argues: “The pausing of a puberty they do not want, in a birth-assigned sex they do not associate with, can be hugely beneficial in alleviating distress and can allow the young person to consider more widely what they may want for themselves without the pressure of further changes to their bodies.”

In papers submitted to court, Gids says that hormone blockers have been used for many years on adolescents who were born very small and benefit from delaying puberty.

The service insists children are told that “the length of time during which hormone-blocking treatment has been available is currently too short for any lifelong longitudinal study to be complete”.

A document shared with them states: “We do not know how blocker treatment will affect the bone strength, sex organ development or body shape in the long term or final adult height. There could be other long-term effects of blocker therapy that we do not know about.”

On Saturday night, a mother whose daughter was under the care of the Tavistock for almost seven years defended the service. “We were lucky that the guidelines changed around the time she turned 12 so that she could start blockers then, rather than wait until 16, which would, of course, have been way too late to prevent a damaging male puberty. Throughout all this time our clinicians at the Tavistock were endlessly supportive and kind, while at the same time sticking to the protocols and guidelines.”

The mother of another child said: “The blocker was safe and reversible and we are continuing to support his social transition and honestly think that if we had not had the help, support and guidance from Gids then I don’t know where we would be today.”

Gids said the decision to offer puberty blockers was “ultimately made by endocrinologists” independent of the service. Any decision to refer a child to an endocrinologist was taken only after a comprehensive assessment, it added.

In his witness statement, the Tavistock’s head, Paul Jenkins, confirmed that 30 clinicians had left the service in the past two years, a figure that he said was not out of line with “many other clinical services in the NHS”.

Jenkins said: “The nature of the work conducted at the trust and the pressure on waiting times (in common with many NHS services) means that staff at Gids often find themselves under pressure on a day to day basis.”

Critics accuse the service of failing to pay sufficient attention to other factors, such as social media or autism, which may influence a young person’s decision to transition.