We are often contacted by patients with Fabry-related conditions who have intronic mutations in their genetics. Therefore, we would like to turn our and your attention back to intronic mutations:

Intronic mutations are an even broader topic. If you ask the Fabry experts, they usually explain that intronic mutations cannot do anything because there is no information in the introns. The answer is that simple and that wrong.

If you want to read the details and have access to Pubmed: https://pubmed.ncbi.nlm.nih.gov/28497172/ (“Deep intronic mutations and human disease”, direct at Springer: https://link.springer.com/article/10.1007/s00439-017-1809-4, Human Genetics volume 136, pages 1093–1111; 2017)

Briefly and simplified: on the one hand, there is also regulatory information in the introns that has an influence on enzyme production. On the other hand, certain sequences of the DNA sequence are used to determine between the introns and exons. If a new exon start is created by mutation in the intron, then the gene is read incorrectly (even if the “original” exons are all correct).

Unfortunately, most gene tests do not pay attention to intronic mutations at all, these areas are not analysed at all. But at the latest, if lyso-GB3-values or enzyme activity are abnormal, one has to search for the cause, which can then lie in the intron.

See also the article on intronic mutations on our website.

Various publications attempt to prove the apathogenicity of the controversial mutations. Some of them describe rather individual cases and are therefore not statistically reliable. Others refer to previous publications when making their statements. If you now look at the sources where the original statements with evidence come from, you will very often find two studies from 2003:

• Yasuda: “Fabry disease: characterisation of alpha-galactosidase A double mutations and the D313Y plasma enzyme pseudodeficiency allele”.
• Froissart: “Fabry disease: D313Y is an alpha-galactosidase A sequence variant that causes pseudodeficient activity in plasma”.

Both authors worked closely together, i.e. the studies are not independent! The studies show altered biochemical and physical properties of the modified enzyme. However, they then assume that these changes have no effect on the cellular level. But already in this study, disturbed processes in the cells are detected, which were later further investigated in studies on another controversial mutation. There it was shown that these changes lead to so-called ER stress (ER = endoplasmic reticulum). This ER stress is the cause of cell malfunction and even cell death. (see also Unfolded Protein Response)

Another point is the so-called ER stress, more about this in our blog entry:
Fabry as a lysosomal storage disease, is there possibly more to it.
(Source e.g. https://doi.org/10.1101/2022.09.27.509714)

I.e. the statements on apathogenicity are often not reliable or even wrong.

Therefore, most authors add that due to the small number of cases and various open questions, apathogenicity cannot necessarily be proven and further research is necessary.

Important Research that is made impossible by the deliberate filtering out of the controversial mutations in the gene laboratory.

Example:

A publication from 2020 also refers to these two studies to prove apathogenicity.

In this publication (“An expert consensus document on the management of cardiovascular manifestations of Fabry disease”, Linhart et al. 2020) it was written: “As a cautionary example, the p.Asp313Tyr change results in a serum pseudodeficiency of AGAL-A activity and is not disease-causing. Similarly, a number of GLA variants previously thought to be disease-causing (e.g. p.Arg118Cys) have been shown to be of uncertain significance or likely benign. “(This is followed by a citation)

We have traced back the sources until we reached the original source:

In turn, the Varsome database cites Yasuda’s study as a source to prove pathogenicity.

There are five classifications regarding the pathogenicity of mutations/variants:

• pathogenic – causing disease
• likely pathogenic – probably causing disease
• uncertain significance
• likely benign
• benign

In Germany the Genetic Diagnostics Commission has decided that laboratories should only report pathogenic and likely pathogenic variants in their findings. Variants of unclear significance can be mentioned in the findings. Benign and probably benign variants should no longer be reported.

Since there are a large number of benign variants in genetics, it seems perfectly understandable to filter them out.

But who determines whether a variant is pathogenic or not? And what about the variants where scientists do not agree (=unclear significance)? And who does the classification?

The classification can and must be done by each laboratory/doctor/centre itself. There are ACMG (American College of Medical Genetics) guidelines for this. However, these guidelines are under discussion, e.g. for Fabry itself. They also leave considerable room for interpretation. For example, the D313Y variant is classified by laboratories as “likely benign”. With other studies as a reference, this variant can also be classified as “likely pathogenic” (see e.g. Varsome database).

The literature situation is currently inconclusive; more recent work points to pathogenic factors. Nevertheless, some variants (such as the D313Y or A143T) have been reclassified as benign by some laboratories/centres and are now not even reported.

So, on the one hand, the stipulation of the Genetic Engineering Commission and the decision of doctors and laboratories is incomprehensible, because this actively keeps patients away from diagnosis and therapy. On the other hand, it also impairs research or even prevents it altogether.

We continue to fight for the controversial mutations, but the fight is severely and systematically hindered.