What is a Mutation?

A mutation is a change in a person’s DNA. DNA is the long strand of instructions the body uses to make proteins and necessary substances for the body to function. The same set of DNA is contained in every single cell of a person’s body, and each cell reads only the segments of the long DNA strands that particular cell needs.

While DNA is often used in forensic science like a fingerprint, distinguishing between two suspects, it turns out only a small part of our DNA is different from one another’s. The genes (segments of DNA) for hair and skin color, for example, are unique to each individual, but most of our DNA is the same, or “conserved.” DNA containing genes for making bone marrow, tears, digestive enzymes, and neurons, for example, do not vary significantly among the human population.

Researchers have learned to read these conserved sections to find the exact sequence of “normal” instructions, and label the genes with specific names, such as “SCN1a” (Sodium Ion Channel, alpha-type subunit 1a). The SCN1a gene contains the instructions for building the sodium ion channels that allow charged chemicals into and out of our neurons, allowing electrical signals to move along the neuronal pathways throughout the body.

When an individual’s sequence of instructions is found to differ from that of the general population’s, it is called a mutation. There are several types of mutations, explained below:

Missense

A missense mutation is a simple change to one item in the gene.The gene may, for example have the following “letters” as instructions:

See the car and run

A missense mutation would involve the substitution of one “letter” for another, at any place in the gene:

See hhe car and run

Missense mutations result in incorrect “words” substituted somewhere within the DNA instructions. (Note that DNA is written in only the letters A, T, C, and G, rather than all 26 letters of the alphabet. Each group of 3 letters is called a codon instead of a “word,” and codes for a specific amino acid.)

Missense mutations may or may not change the overall result of the instructions: Sometimes the instructions are still interpreted correctly. Other times, the instructions may be entirely nonfunctional

Nonsense

A nonsense mutation is a more complex change to the genetic instructions. There are several types of nonsense mutations:

1. Deletion

A deletion is the removal of one “letter” from the genetic instructions. This results in a shift of the “reading frame,” making the instructions nonsense from the point of the deletion onward. If the “t” is deleted from “the” in the second word, the rest of the sentence becomes nonsense:

See hec ara ndr un

Deletions can involve 1 or many letters in the instructions. Some cases of entire gene deletions have been reported.

2. Insertion

Similarly, inserting an extra letter at any point will also cause a shift in the reading frame, making the instructions from that point onward nonsense.  Notice how inserting an extra “r” at the beginning of “the” makes the rest of the instructions nonsense:

See rth eca ran dru

3. Termination

The body reads the DNA instructions (gene by gene) in groups of 3 letters, and some “words” are signals of the end of the gene. Suppose “end” is the termination signal. Some mutations may form this “end” before the actual end of the gene, resulting in a shortened, or truncated, product, as the body will stop reading the gene at that point:

See the car end run

Mutation-Clinical Correlation

It is important to note that all types of SCN1A mutations have been associated with Dravet syndrome. While missense mutations are more common than nonsense mutations in the less severe areas of the spectrum (GEFS+, ICE-GTC, etc.), the type of mutation found cannot determine the resulting clinical picture at this time.

Also note that the SCN1A gene is over 80,000 “letters” long! This means that most mutations found are new, or not reported in the literature. As research continues and more mutations are identified, the likelihood of two patients’ mutations being identical increases.

One last thing to remember is that current technology does not always detect mutations. Mosaicism, intronic mutations, and large deletions are often not discovered by the simplest blood test. Up to 30% of patients diagnosed with Dravet syndrome have no detectable mutation. Further research will help us understand if these are cases of undetected mutations or a lack of mutations.

Understanding your Lab Report

After your child has had his/her blood test, you will receive a report from the lab that ran the test. It may say something like this:

This individual possesses one or more de novo DNA sequence variants whose significance is unclear or unknown. The specific variants have not been reported in the literature, though similar variants been observed in both disease-associated mutations and benign polymorphisms, precluding clear interpretation.

SCN1A Variant 1: Transversion G>T
Nucleotide Position: 4073
Codon Position: 1358
Amino Acid Change: Tryptophan > Leucine
DNA Variant Type: Variant of unknown significance (heterozygous)

What does this mean? Simply put, the written explanation means that the mutation (sequence variant) was not found in the parents (It is “de novo,” new to the individual). The particular mutation has not been reported in medical literature, but other similar (missense, nonsense, etc.) mutations in the same gene have been seen both in “affected” individuals (on the Dravet spectrum of disorders) and non-affected (“typical”) individuals. Thus they cannot say for sure whether the mutation is responsible for the seizures.

From Gene to Protein:

DNA’s importance in forming the sodium ion channel

Now that you have some knowledge about what a mutation is, let’s look more closely at the details. Recall that sodium ion channels are the openings in the outer cell membrane that lets ions, electrically charged chemicals, into and out of the neuron. What does a mutation in a patient’s DNA have to do with the functionality of their sodium ion channels?

The creation of a sodium ion channel within our cells is broken down into three steps:

1. DNA is read
2. An amino acid chain is formed
3. The chain is folded to make a 3-dimensional structure

1. Reading the DNA

Recall that DNA is the long chain of instructions contained inside each of the body’s cells. The chain is essentially made of 4 chemicals known as nucleotide bases. They are Adenine, Thymine, Guanine, and Cytosine, usually abbreviated as A,T,G, and C, respectively. The sequence of the 4 bases determines how the instructions will be read and what the body will use produce with them.

Because DNA is such a long chain of instructions containing millions of bases, in humans it is organized into more manageable chunks of data much like a set of encyclopedias. Each individual encyclopedia is known as a chromosome, and contains a portion of the total DNA. Humans have 46 total chromosomes, made of 2 sets of 23 chromosomes: 23 from the mother, and 23 from the father. Each chromosome is further divided into smaller segments of DNA known as genes. A gene would correspond to a topic in one encyclopedia: it is a very small segment of the total information contained in the set. A specific gene such as SCN1a may contain anywhere from 1,000 to 10,000 bases.

2. Forming the Amino Acid Chain

When the cell needs a substance for structural, chemical, or other cellular improvements, it unravels the DNA in the gene containing the instructions for that particular substance. (Imagine the cell selecting the right encyclopedia, opening it up, and finding the particular topic it needs within the book.) The cell reads that small subset of instructions by grouping the nucleotide bases into groups of 3, called codons. They are called codons because they “code” for one of 20 specific amino acids, which the cell then strings together much like a long necklace made of beads. Each set of 3 nucleotide bases codes for one of the 20 amino acids, or may instead be a “start” or “stop” codon, signaling the cell to start or stop reading the gene at that point.

3. The Final Product: A Protein such as the Sodium Ion Channel

After the cell has read the gene and made the string of beads (amino acids) according to the specific directions contained in the gene, it then folds the string of amino acids in upon itself to create a specific 3-dimensional structure known as a protein. This structure may be used for cellular support, enzymatic function, or a variety of other uses. The protein is folded in a very specific way according to the chemical interactions between the amino acid “beads” on the chain. Some of the amino acids are attracted to each other, some repel each other, and some are attracted in groups to each other. The attractions determine what the overall structure will look like and how it will function.

The SCN1a gene instructs the cell to make a 3-dimensional protein with a sort of tube-like appearance called a sodium ion channel. The cell then transports this tube-like structure to the membrane, where it is embedded and functions like a pore with a gate allowing charged chemicals into and out of the cell.

Its structure is extremely important, because its tube-like quality and gate allow only specific chemicals into and out of the cell. Additionally, the pore region of the sodium ion channel has an overall polarity due to the amino acid beads that formed the tunnel in the first place. If the pore region is malformed, it is quite possible that the chemicals that are supposed to be allowed into and out of the cell may not be allowed to pass through, or may pass through in the wrong amounts.

The Sodium Ion Channel and Seizures

Recall that the brain transmits electrical and chemical signals along a network of specialized cells called neurons. Neurons are rich in the pores (sodium ion channels) that allow chemicals to pass into and out of the cell, allowing the brain’s signals to propagate throughout the brain and body.

Usually, the brain sends out discrete signals that create an action potential (brief disruption in the balance of the charge inside a cell compared to the charge outside a cell) that passes in a fraction of a second, then allows the cell to return to its resting state. This disruption in the balance of charge is attained by sending charged chemicals (sodium, Na+, for example) into or out of the cell through ion channels such as the sodium ion channel.

When a mutation in the DNA that coded for the construction of the sodium ion channel causes a structural difference that the ion channel does not function properly, two things can happen:

1. The neurons may become hypoexcitable, or not easily excited. The signal is stopped because the cell fails to allow the chemicals into/out of the cell that would propagate the signal.
2. The neurons may become hyperexcitable, or too easily excited. The signal may indeed pass, but the ion channel may allow too much of the charged chemicals into/out of the cell, maintaining an “excited” state even after the signal should have passed and the cell should have returned to its normal state.

Seizures are often described as an “electrical storm” within the brain. The hyperexcitability of neurons with mutated sodium ion channels is easily correlated to this electrical storm. However, hypoexcitability can also be associated with seizures in a more complicated model involving other chemicals called neurotransmitters.