3.3 TCF4 variants

3.3 TCF4 variants

First some basic facts about DNA. In DNA, there are four different kinds of nucleotides, which are adenine (A), guanine(G), thymine (T) and cytosine (C). Every three nucleotides together make up one 'codon' that codes for a specific amino-acid. There are 64 different codons, 61 encode amino acids and three are stop-codons that tell the cell where to stop translating. There are 20 different types of amino-acids, comparable to 20 different kinds of ingredients in a recipe. So, multiple codons can code for the same amino-acid. For example, there are four codons (GTT, GTC, GTA, GTG) that all code for the amino-acid valine.

Different kinds of DNA variants, also called mutations, have been described. If a change of nucleotide results in a codon which still codes for the same aminoacid, this is called a 'silent mutation'. When the change in a protein is such that it can't function properly, resulting in problems for the individual, these are called 'pathogenic'(causing disease). These are the most important possible variants:

Splice site
In the DNA, some parts of the nucleotides form codons that determine which amino-acids are used to make the protein, as described above. These parts are called exons. Exons can be short or long, but always are a multiple of 3 (because three nucleotides together code for one aminoacid). Other parts - before, after and in between the codons - are still made up of nucleotides, but these don't code for amino-acids; these bits are called 'introns'. The exons are numbered: the first is exon 1, then comes an intron, then the next exon (2), and so on. Mistakes in DNA can happen both in the intron and extron parts of DNA, and both can cause problems in the way proteins are put together. When the translation is made from DNA into protein, the introns get cut out or 'spliced out'. In case of a splice site mutation, a number of nucleotides in the specific site at which splicing takes place are inserted, deleted or changed, causing changes in the final protein which can cause problems in the functioning of the protein. 

Nonsense
A nonsense mutation is a change in the DNA that results in a stop codon where there should not yet be one. When this happens, the protein that is encoded by the DNA will be too short, incomplete and usually nonfunctional.

Frameshift
If a number of nucleotides is added or deleted that is not divisible by three, then this can change the 'reading frame' (the grouping of the codons), resulting in a completely different translation from what it was meant to be. The earlier in the sequence the deletion or insertion occurs, the more altered the protein. This is called a 'frameshift' variant. 

Missense
A 'missense' variant mutation is when a single nucleotide change results in a codon that codes for a different amino acid. Not every change results in a missense variant, because each aminoacid is encoded by several different codons. 

Deletions
A 'deletion' is a mistake in the DNA in which a part of a chromosome or a sequence of DNA is left out. Any number of nucleotides can be deleted, from just one to an entire piece of a chromosome. 

DNA mutations in Pitt-Hopkins
So what's up in the DNA of people with Pitt-Hopkins syndrome? Nearly all of the changes ('mutations') found in people with Pitt-Hopkins are unique. That means that nearly every person with Pitt-Hopkins whose DNA has been checked has a different variant. Most of the reported variants in people with Pitt-Hopkins syndrome are found between exons 7 and 19 on the long arm of the 18th chromosome. This part of the DNA codes for the protein 'Transcription Factor 4' (TCF4). These are the mutations that have been found:  

Most of the mutations found in people with Pitt-Hopkins are splice site, nonsense or frameshift variants.
In about 20% of individuals with Pitt-Hopkins, pathogenic missense variants are identified. Deletions within the gene ('intragenic') involving one or several exons of TCF4, that probably cause a shift in the reading frame, have been found in about 12% of published cases.^3,19,31–33 

The DNA mutations in people with Pitt-Hopkins are usually found in the 'bHLH domain', or basic helix-loop-helix domain, encoded by exon 18. The bHLH domain is a part of the protein which determines its shape. It is characterized by two curves (similar in shape to a spiral staircase) connected by a loop: that's where the name comes from. One TCF-4-protein usually works together with another TCF4 protein. It is the bHLH-domain that makes it possible for the two proteins to connect (which scientists call 'dimerizing'). So, if this part of the TCF-4-protein is non-functional, then TCF-4 can't do what it is supposed to do in many different parts of the body.