Gene variant naming errors found in clinical genetics review

A systematic review of 52 scientific papers submitted to a leading clinical genetics journal over a two-year period has found pervasive inconsistencies in how gene mutations are reported, with none fully adhering to recommended standards for variant nomenclature.

The findings suggest that imprecise or non-standard naming of genetic variants may be contributing to difficulties in identifying relevant diagnostic evidence, with potential implications for rare disease diagnosis and clinical decision-making.

The work [1], led by Dr Peter Freeman, a geneticist at The University of Manchester, was published in Clinical Chemistry. The authors report that errors in variant naming were present across all manuscripts assessed, reducing the likelihood that genetic findings can be reliably identified in literature searches and clinical databases.

The researchers suggest this issue may help explain why a substantial proportion of rare diseases remain undiagnosed, including in countries with advanced genomic medicine services such as the UK.

Hospital geneticists often rely on published studies and curated databases, including ClinVar and the Leiden Open Variation Database (LOVD), to support diagnosis. However, inconsistent nomenclature can make it more difficult to retrieve relevant evidence, potentially slowing or limiting diagnostic conclusions.

Dr Freeman, whose research includes development of the VariantValidator tool for standardising variant descriptions, said that inconsistent reporting practices remain widespread across published literature.

He added that improved adherence to naming standards could make genetic data easier to locate in databases and literature searches, improving its usability in both clinical and research settings.

The authors also note that miscommunication arising from inconsistent variant naming has previously been linked to clinical misinterpretation in areas such as thrombophilia risk assessment and cystic fibrosis carrier status.

To address the issue, the researchers recommend wider adoption of standardised nomenclature guidelines, stronger enforcement during peer review, and greater use of structured data submission to public repositories.

They also highlight ongoing efforts, led in collaboration with professional bodies including the American College of Medical Genetics and Genomics (ACMG), to develop updated standards for variant reporting in clinical literature and databases.

The team suggest that improved consistency in genetic nomenclature could support more efficient use of diagnostic evidence and reduce the risk of missed or delayed diagnoses in rare disease cases.

More information online

1. Universal Presence of Gene/Variant Nomenclature Errors in Journal Manuscript Submissions published in Clinical Chemistry