Mutation 1717 1G-A homozygous

Question

Dear expert team,

our son has the above mutation. Are there possibly any insights in the context of a study by Vertex or others? Which class does this mutation belong to definitively (since I’ve seen it assigned to various classes), and if it is a splice mutation, what does that mean?

Your answer will be greatly appreciated. Many thanks in advance and kind regards.

Answer

Hello,

1717-1 G>A is a class 1 mutation of the CF gene CFTR — as you will see in a moment, there is NO ambiguous classification for this mutation. To avoid misunderstandings, this will be a long answer — thank you for your understanding and patience with this detailed text.

To understand the splice mutation, please imagine the CF gene as a book with several chapters (27 for CFTR), all of which need to be read in order to build the CF protein. Unlike in a typical book, the different chapters in our genotype are not located directly one after another; instead, two chapters are separated by something else, let us say an annoying ad that does not have anything to do with the actual story. With the CFTR gene, the proportion is shifted significantly in favor of the ads: ca. 200000 letters of the gene are ads (molecular biologists call them introns), and ca. 4500 letters are the actually important chapters that need to be read (molecular biologists call them exons). In order to find one’s way in the CFTR gene, only the exon positions are numbered: number 1717 is the first building block in exon 12 of the CFTR gene. The positions in the intron are indicated relative to that: 1717-1 translates into "a building block further ahead than 1717, i.e. the last building block in intron 11." 1717-1 G>A (we read this as "1717 minus 1 G to A") means: at this position in intron 11, there is supposed to be a G, but there actually is an A. In the case of your son, the mutation is homozygous, i.e. the A is present on the CFTR copy inherited from the mother as well as on that inherited from the father.

When reading, the cell does the following:

1. read out everything to the precursor messenger RNA, i.e. exons and introns in 204500 building blocks one after the other;

2. cut out intron and assemble exons to the messenger RNA that is 4500 building blocks long;

3. translate messenger RNA into protein — since three-letter groups of the messenger RNA describe one protein building block, the result is a CFTR protein ca. 1500 building blocks long.

In splice mutations, step 2 does not work (the cutting out of introns is called splicing). For it to work, the cell needs different signals, the most important ones of which are the building blocks on the first and the last two positions of the intron. With 1717-1 G>A, the information at the end of the intron is not recognizable — the cell does not know that this is where an intron ends and an exon begins. In 1993, Ann Harris and colleagues studied the messenger RNA from nasal polyps of patients with the 1717-1 G>A mutation (source: Human Molecular Genetics, 1993, Vol6 page 691): the messenger RNA is missing exon 11, the reading frame during the translation into the CFTR protein is shifted, a premature stop signal is used and the result is a shortened CFTR protein (only 566 building blocks long instead of the ca. 1500 of the functioning CFTR).

The confusion with the classification of splice mutations stems from the fact that there are many different splice mutations: positions further inside the intron are not used as consistently. If, for instance, the mutation occurs at position +5 further inside the intron, part of the precursor messenger RNA is processed correctly — unfortunately, this does not happen with a mutation on positions +1, +2, -1, and -2. Examples of splice mutations with such partially correct processing of the information are 2789+5G>A or 3272-26G>A — these mutations concern building blocks that lie 5 or 26 positions into the intron, and these are "not so important" for the splicing.

Unfortunately, I am currently not aware of any clinical studies focusing directly on 1717-1 G>A (e.g. to use the shortened transcript or a shortened protein with 566 building blocks resulting from it). According to the „clinicaltrails.gov“ database, there currently is a phase-2 pilot study that is testing the drug Ivacraftor® also in patients with the 1717-1 G>A mutation (web address: clinicaltrials.gov/ct2/show/study/NCT01685801). The short description of this clinical study does not contain any information on which mode of action Vertex suspects with Ivacraftor® and 1717-1 G>A — it remains to be seen whether the drug will be effective also in patients with 1717-1 G>A.

With best wishes, particularly for your son,

Frauke Stanke

25.11.2014