Researchers Discover New Gene Variant Associated with Adult-onset Batten Initially Missed by Genetic Tests

A previously unidentified variant of a gene associated with adult-onset Batten disease (ANCL) was found in an affected family after initial genetic tests failed, highlighting the difficulties in diagnosing this condition despite advances in DNA sequencing technology, a new study shows. 

The case was described in the study, “Autosomal-dominant adult neuronal ceroid lipofuscinosis caused by duplication in DNAJC5 initially missed by Sanger and whole-exome sequencing,” published in the European Journal of Human Genetics.

Batten disease, also known as neuronal ceroid lipofuscinosis (NCL), comprises a group of rare inherited neuropsychiatric disorders in which each specific subtype is linked to mutations in a particular gene.

In adult-onset Batten disease, also known as Kufs disease, symptoms emerge around age 30. This particular form of the disease can be caused by mutations in several genes and can be particularly challenging to diagnose due to the variety of symptoms, including progressive epilepsy characterized by muscle spasms, motor disorders, and dementia. 

Despite recent advances in genetic testing, the gene variants associated with this form of the disease have yet to be identified in some families.

In an effort to improve genetic diagnosis for them, the Adult NCL Gene Discovery Consortium was established to bring together ANCL experts from the U.K., Europe, the U.S., Canada, and Australia.

Consortium members reviewed the clinical data of suspected ANCL cases, and those who were determined to have ANCL were subjected to DNA sequencing analysis of the candidate gene, as well as their entire genome by whole-exome sequencing (WES).

Genome refers to all the genes found in our DNA, and WES is a technique that examines the DNA sequence of all genes that provide instructions to make proteins (exome).

The researchers found a new genetic variant associated with ANCL that initial DNA sequencing had failed to find in a family affected by the disease.

The family included three affected people: the mother, diagnosed with ANCL at age 42, and who passed away at age 56; and her two sons, diagnosed at ages 31 and 34, both affected by seizures, memory loss, and physical disability.

Initial DNA sequencing to identify a candidate gene causing ANCL in both brothers failed, so they were sent for more detailed sequencing analysis. However, these tests “did not yield any functionally relevant candidate variant.”

By adjusting the search parameters, the team then identified a previously unknown gene variant in DNAJC5, the most prevalent gene for ANCL.

DNAJC5 provides instructions for making a protein called cysteine string protein alpha (CSP-alpha). This protein is found in the membranes of nerve cells and is responsible for recycling proteins involved in the transmission of nerve signals.

In this new gene variant — not listed in current genetic databases — a part of the DNA sequence of the DNAJC5 gene was duplicated, giving rise to an abnormal CSP-alpha protein that may be prone to aggregation.

To confirm the effects of this mutation on the CSP-alpha protein, the team conducted experiments to assess the localization and the characteristics of the abnormal protein in living cells.

Findings revealed that while the normal version of CSP-alpha was found in the cell membrane, its abnormal form was mostly present in the cytoplasm (liquid-like substance that fills the interior of cells), either in a diffuse or aggregated form.

“Our work demonstrates the limitations of Sanger sequencing [gene candidate sequencing] and WES in detection of even relatively small insertions and duplications and shows that analysis of next generation sequence data still requires an individualized approach and unique interpretations of the data,” the researchers wrote. “Continued reanalysis of the data with a team of experienced scientists may identify previously missed variants.”