Three NHS Genetics Labs Fail to Share Variant Data Vital for Rare Disease Diagnosis

An investigation published by The BMJ has found that three of England’s seven NHS genetics laboratories are failing to routinely share vital information about genetic variants in public databases, a gap that experts and families warn could be prolonging uncertainty for patients with suspected rare diseases and delaying access to diagnosis, treatment, and care. The findings, based on freedom of information responses provided by the laboratories at the start of 2026, reveal that variant sharing across the NHS genomic service is inconsistent, incomplete, and in some cases entirely absent, despite a formal requirement that has been in place since 2024.

England’s genomic diagnostics are coordinated through seven NHS Genomics Laboratory Hubs, or GLHs, each responsible for clinical genomics services in its region, including genetic testing, molecular diagnosis, treatment planning, and counselling for families affected by inherited conditions. Since 2024, these hubs have been required under guidance from the Association for Clinical Genomic Science, the professional body representing clinical genomics scientists in the United Kingdom, to submit the variants they identify to public databases such as ClinVar. That guidance is explicit about why the obligation matters: prompt and accurate molecular diagnosis is crucial for targeting treatment and optimising patient care, and it is therefore described as the professional responsibility of the clinical genomics community to ensure that data is shared appropriately and responsibly.

ClinVar, maintained by the US National Center for Biotechnology Information, functions as a shared clinical evidence base for variant interpretation. When a laboratory identifies a change in a patient’s DNA, the clinical significance of that change, whether it is pathogenic, benign, or of uncertain significance, depends on the accumulated evidence from every patient in whom it has previously been observed. Each new submission strengthens the collective ability to interpret variants accurately, supports the reclassification of variants as knowledge evolves, and feeds directly into research on rare disease. When laboratories withhold their findings from this shared pool, they create structural blind spots that selectively limit the evidence available to every other diagnostic service, clinician, and researcher who depends on it.

The freedom of information responses indicate that three of the seven hubs, the South East hub led by Guy’s and St Thomas’ NHS Foundation Trust, the South West hub led by North Bristol NHS Trust, and the North East and Yorkshire hub led by The Newcastle upon Tyne Hospitals NHS Foundation Trust, are not routinely submitting variants to ClinVar. The laboratories point to good intentions and say they lack the necessary staff and technology to meet the requirement, adding that they intend to implement it as soon as possible. Even among the four hubs that are routinely submitting, the investigation found significant backlogs of variants that remain unsubmitted, along with inconsistencies and gaps in what has been shared.

For families affected by rare genetic conditions, the consequences of this fragmented data landscape are not abstract. Sophie Muir, whose son’s variant in the CACNA1C gene, associated with a severe multisystem disorder, was not picked up through NHS testing, describes the effect of inconsistent submission practices on the diagnostic pathway. ClinVar, she explains, functions as the shared clinical evidence base on which variant interpretation depends, and uneven participation creates blind spots that selectively limit the evidence available for rare disease diagnosis, variant reclassification, and research. Muir, who chairs the rare disease charity the Timothy Syndrome Alliance, argues that the failure amounts to a betrayal of the public investment in genomic medicine.

Other clinicians and researchers echo that concern. Jack Underwood, a forensic psychiatry registrar, observes that there is a loop that is broken when variants are not submitted to ClinVar, a reference to the feedback cycle through which each diagnosed patient’s data helps interpret the next. Professor John Sayer, an expert in rare inherited kidney diseases, is more direct, warning that patients ultimately are missing out because this is not happening. In a field where a single confirmed molecular diagnosis can end a diagnostic odyssey lasting years or even decades, and where treatment decisions, surveillance regimes, and family planning all hinge on accurate variant interpretation, the absence of shared evidence translates directly into prolonged uncertainty and delayed care.

The laboratories themselves cite practical constraints as the principal reason for the delay. Staffing was the issue most frequently mentioned in the freedom of information responses, reflecting the chronic workforce pressures that have affected NHS laboratory services across the board. Some hubs also blamed the time taken to develop the policies needed to govern submission, alongside technology and infrastructure issues that complicate the extraction and formatting of variant data for external databases. Those hubs that have not yet implemented routine ClinVar submissions say they plan to do so this year, suggesting that the gap, while significant, may be transitional rather than permanent.

Yet the explanations have done little to reassure critics who see the problem as symptomatic of something larger. Clare Turnbull, Professor of Cancer Genetics at the Institute of Cancer Research in London, frames the delay in variant sharing as part of a wider issue of lagging NHS information technology systems hobbling progress and innovation in genomic medicine. The United Kingdom invested heavily in the 100,000 Genomes Project and built the NHS Genomic Medicine Service on the promise that publicly funded sequencing would generate a continuously improving knowledge base. When the laboratories at the sharp end of that service cannot feed their clinically interpreted findings back into shared databases, the value of that national investment is diminished for every patient who follows.

The question of stewardship is central to the criticism. Muir points out that the GLHs are generating clinically interpreted data within a publicly funded system, and that public funds are going in to pay for genetic testing that is then not being shared. Sayer agrees that variant sharing maximises the value of the public investment in genetic testing and adds a further ethical dimension: knowing someone’s genetics is privileged information, and if a patient has consented to their data being used for the greater good, then failing to allow that information to be shared betrays the patient’s trust. Consent, in other words, is being given on the understanding that participation in genomic medicine is collective, an understanding that the current submission failures undermine.

For Muir and families like hers, the stakes are measured in time that rare disease patients do not have. The diagnostic odyssey for a rare genetic condition frequently involves years of inconclusive tests, and every variant that sits unsubmitted in a laboratory backlog is evidence that could have shortened that journey for another child. We do not have time on our side, she says, noting that families, children, researchers, clinicians, patient advocacy organisations, and the life sciences sector all need this data. The BMJ investigation makes clear that the technical requirement to share variant data exists, that the professional guidance is unambiguous, and that the remaining obstacles are organisational rather than scientific. Whether the three non-compliant hubs deliver on their stated intention to implement routine submissions this year will determine whether England’s genomic medicine service can close a gap that, until now, has been quietly limiting the power of one of the most ambitious publicly funded healthcare data systems in the world.

Subject of Research: NHS genomic laboratories' inconsistent sharing of genetic variant data in public databases for rare disease diagnosis

Article Title: NHS labs fails to share data vital for diagnosis and care of rare diseases

Article References: NHS labs fails to share data vital for diagnosis and care of rare diseases. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: NHS, genomics, rare diseases, ClinVar, genetic variants, variant interpretation, Genomics Laboratory Hubs, The BMJ, data sharing, molecular diagnosis, patient advocacy, genetic testing