Research Highlights

“Success in closing an important gap”

The transport of ions such as sodium, potassium and chloride in human cells is essential for survival. Professor Thomas Jentsch has been researching the various transport pathways for decades. Now he has discovered another disease gene that he and his team describe in the “American Journal of Human Genetics.”

Prof. Thomas Jentsch Foto: David Ausserhofer

Professor Jentsch, you’ve already discovered several ion channels and described their biological functions, identifying some of them as being involved in genetic diseases. And now you have some more news to share. What’s it about this time?
Thomas Jentsch: This time it’s not about an ion channel, but about the chloride/proton exchanger ClC-3. This exchanger is one of the nine members of the CLCN gene family that we discovered back in 1990. Until now, ClC-3 was the only member of the family for which no human disease-causing mutations were known. But now clinical colleagues brought twelve patients to our attention: Children with severe developmental disorders and mental disabilities, with whom exome sequencing had revealed mutations in this chloride transporter gene. Together with Michael Pusch from Genoa – a former coworker of mine – Maya Polovitskaya from my lab performed biophysical analyses on the mutant transporters. They confirmed their likely pathogenicity. These CLCN3 mutations lead to a broad spectrum of neurodegenerative or neurodevelopmental disorders associated with global development delay, intellectual disability, and structural brain abnormalities.

You’ve been in hot pursuit of ClC-3-related disease for a long time.
Yes, you could say that. We first suspected that CLCN3 was a disease gene in 2001. Back then, we detected severe neurodegeneration, that eventually led to the entire loss of an important brain structure, the hippocampus, in knock-out mice we had generated. Until now, however, there was no human disease correlate. It’s very satisfying to know that we’ve now closed this gap.

A whole spectrum of mutations

That’s pretty similar to a discovery you made last year. You then linked CLCN6 to another genetic form of neurodegeneration, a clinically severe form of lysosomal disease. What parallels do you see?
The symptoms are largely overlapping. With both CLCN3 and CLCN6 mutations, children have intellectual and motor deficits as well as morphological changes in the brain. Also, epilepsy can occur with mutations in either gene. In our work on CLCN6, we surprisingly found three unrelated children who carried exactly the same point mutation in the CLCN6 gene. This mutation, which was present in only one of the two copies (alleles) of the gene, led to the same, very severe phenotype in all three patients. In CLNC3, on the other hand, we were faced with a whole spectrum of mutations that led to diseases of varying severity. One pair of siblings exhibited a complete loss of ClC-3 function, which corresponds one-to-one to our mouse model. In this case, the mutation was present on both alleles and interrupts the synthesis of the transport protein – it can no longer perform any ion transport.

These siblings were the most severely affected patients. In other patients, the chloride transporter was mutated on only one of the two alleles, similar to what we had found for CLCN6; as a result, in these patients half of the transporters are normal, whereas the other half are mutant transporters in which only one amino-acid was changed. Rather than causing a loss of function, these mutated transporters displayed new, harmful functions. These can cause disease also when found in only one copy, in parallel to the normal transporter. In other words, the mutations are clinically dominant. Interestingly, in either CLCN3 or CLCN6 the dominant mutations increased the ion transport activity, particularly at the acidic pH values that are prevalent in intracellular compartments. These mutants lost the ‘brake’ by acidic pH that normally shuts down their activity in increasingly acidic compartments.

Disease symptoms not yet fully explained

But ultimately both lead to the destruction of nerve cells in the brain?
Yes, and in both genes, and by the way also in CLCN7, another focus of our work, both loss and gain of function lead to strongly overlapping disease symptoms – an astonishing finding that we still cannot really explain. Patients show neurodegeneration and/or impaired brain development, which cannot be easily distinguished in patients. CLCN3 mutations might also affect organs outside the nervous system, given that ClC-3, unlike ClC-6, is not only found in nerve cells, but probably in virtually all cells of the organism. However, neurological deficits and morphological brain changes are the cardinal symptom of those affected. What is astonishing is that the two transporters do not compensate each other; after all, they are located in very similar compartments within the cell, on organelles called endosomes.

These are small vesicles that take up substances from the outside, sort them, and transport some of them to lysosomes, where they are broken down. Viruses such as SARS-CoV-2 also can enter the cell via endocytosis. The entire endosomal-lysosomal pathway is very important for many cellular functions. Our aim is to clarify how these vesicles are influenced by CLC transporters and other ion channels and exchangers.

Target for new drugs identified

In previous studies, you demonstrated that mutations in other CLCN genes likewise lead to diseases.
Yes, CLCN7 causes a lysosomal storage disease and severe ossification, and CLCN5 causes kidney stones, just to name two examples. We also worked on potassium channels, and discovered that mutations in one of those channels cause (refers to mutations) epilepsy in humans. This work had identified an important target for new drugs. We also found that mutations in another potassium channel lead to deafness. This shows just how relevant ion channels and ion exchangers are for our health.

And you keep on discovering new ones. After identifying VRAC in 2014, you netted another previously unknown ion channel recently.
Two years ago, we successfully identified the gene for the acid-sensitive chloride ion channel ASOR. Although this channel is located in part on the same vesicles as CLCN exchangers, it does different things. We are actively investigating what exactly it does for the cell and the organism. I wouldn’t be surprised if it turns out that mutations in ASOR underlie human pathologies. So, this field continues to be extremely exciting.

The interview was conducted by Beatrice Hamberger and translated by Teresa Gehrs.


About the study
A dozen international partners, from Harvard Medical School, Consiglio Nazionale delle Ricerche and other institutions from a total of six countries, were involved in the study.

Anna R. Duncan et al (2021): „Unique variants in CLCN3, encoding an endosomal anion/proton exchanger, underlie a spectrum of neurodevelopmental disorders“, in “American Journal of Human Genetics” (AJHG), DOI: 10.1016/j.ajhg.2021.06.003

Prof. Dr. Thomas Jentsch
Department Physiology and Pathology of Ion Transport
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Physiology and Pathology of Ion Transport Lab
Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz-Association (MDC)
Phone +49 30 9406 2961

Silke Oßwald
Public Relations
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Phone +49 (0)30 94793 104



Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10
13125 Berlin, Germany
+4930 94793 - 100 
+4930 94793 - 109 (Fax)

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