Medical InformationGenetic Mechanisms
GENETICS OF SCN1A
At least 70% of patients with Dravet syndrome have some type of SCN1A mutation. (1) While a mutation is not necessary for diagnosis, it is important to understand what DNA, genes, and mutations are. Each person has two copies of the SCN1A gene, one from each of our parents. Many Dravet mutations inactivate one copy of the gene, leaving only one functioning copy. This results in a condition called haplo-insufficiency,which means that one functioning copy is not sufficient to prevent seizures. Approximately 90% of Dravet mutations are ‘de novo’, meaning that they are not inherited from a parent, but rather are new mutations in the child.(1)”
What is DNA?
DNA is the set of instructions contained within each of our body’s cells. These instructions tell the cell how to build the proteins it needs to function. A strand of DNA is a long chain of 4 different nucleotides (abbreviated A, T, C, and G) strung together in a particular order, billions of nucleotides long. Because there is so much DNA in our cells, it is organized into 23 pairs of chromosomes (46 total), much like two sets of encyclopedias would be organized into 23 volumes each. When a sperm and an egg, each containing 23 chromosomes, combine, the result is 46 total chromosomes, organized into 23 matching pairs.
What is a gene?
The 23 pairs of chromosomes are further divided into smaller segments called genes. A gene is much like a chapter in an encyclopedia and codes for the production of a specific protein. Remember that a gene is a segment of DNA. Therefore, it is also a long chain of 4 different nucleotides strung together in a particular order. Because our cells have one copy of a gene from each parent, every cell has two copies of each gene.
Genes are read in groups of 3 nucleotides called codons. Each codon is translated into one of twenty amino acids, which are then strung together like beads on a necklace. The amino acids interact with each other based on their chemical properties just like magnetic beads would attract each other on a necklace if it were placed in a jewelry drawer. As the amino acids interact, the long chain folds on itself to form a very specific 3D shape. In the case of SCN1A, this 3D shape is an ion channel that functions as a gated channel in the membrane of neuronal cells, letting sodium ions into and out of the cell. This action allows electrical signals to propagate along neurons.
What is a mutation?
A mutation is a change in the sequence of nucleotides (abbreviated by the letters A, T, C, and G) within a gene. This change in the original sequence of DNA alters the sequence of amino acids, which may cause the chain to fold improperly and/or alter the functionality of the sodium ion channel. Dysfunctional sodium ion channels can result in improper electrical activity and seizures.
Although SCN1A has 160,000 nucleotides, the body edits this sequence of 160,000 down to about 6,000 in the final SCN1A gene that serves as the instructions for the sodium ion channel. (2) Still, with 6,000+ nucleotide positions, it is no wonder that most mutations reported in the literature have not yet been seen in another patient.
Remember that every cell actually contains two copies of SCN1A, one from each parent. Usually, only one copy is mutated, a condition termed “heterozygous.” (3) Most SCN1A mutations are “de novo,” meaning they are not inherited from either parent but rather occurred spontaneously in the patient. (4) Approximately 4% of the mutations seen in Dravet syndrome are inherited from parents, in which case the parent usually has fewer and less severe symptoms than the child in a phenomenon known as reduced penetrance. (1)
There are three main types of mutations: missense, nonsense, and insertions/deletions.
A missense mutation is a simple substitution of one nucleotide for another at a single location in a gene. This slight change in the sequence of nucleotides may result in zero or one changed amino acid in the long chain.
If a missense mutation occurs at a position that codes near the pore of the sodium ion channel, it is likely to significantly alter the ion channel’s function and cause a more severe case of SCN1A-related epilepsy such as Dravet syndrome. (5) If a missense mutation occurs at a less critical location on the gene, it may produce milder clinical symptoms or no symptoms at all. Approximately 47% of the mutations seen in Dravet patients are missense mutations. (1)
A missense mutation reported by a testing company may look like this:
Variant 1: Transversion G>T
Nucleotide Position: 4073
Codon Position: 1358
Amino Acid Change: Tryptophan>Leusine
Variant of Unknown Significance (heterozygous)
This says that the mutation was a substitution of T for G at the 4073rd nucleotide position (of 6000 in the final gene that is read). (6) Remember that nucleotides are read in groups of 3, called codons, so 4073 divided by 3 gives you the amino acid or codon position of 1358. The amino acid Leucine was substituted for the amino acid Tryptophan. The lab is unable to determine the significance because missense mutations can be associated with both mild and severe clinical presentations. The patient has only one copy of this mutation and is thus heterozygous. This real-life mutation is indeed in a pore region of the sodium ion channel, and this patient does have Dravet syndrome.
Nonsense mutations are similar to missense mutations in that one nucleotide is substituted for another. However, in the case of a nonsense mutation, that substitution causes the codon to be read as a “STOP” codon. The cell stops reading the gene at this point, and the protein is significantly shortened, or truncated. Nonsense mutations are usually associated with more severe SCN1A-related epilepsies such as Dravet syndrome. (5) Approximately 43% of mutations in Dravet syndrome are nonsense (truncation) mutations. (1) A nonsense mutation may be reported like this:
“The mutation c.3985C>T (heterozygous) resulting in a termination or stop codon at Arg 1329 was detected in exon 20 of the patient sample and is associated with Dravet syndrome.”
This says that the nucleotide C was replaced with a T at position 3985, which resulted in the amino acid Arginine being replaced with a stop codon at position 1329. (3985 nucleotides, read in groups of 3, correspond to 1329 amino acids.) Only one of the two copies of SCN1A in the patient is mutated (heterozygous), as is usually the case. “Amber,” “Opal,” and “Ochre” may appear on your report and are some of the names for stop codons. The lab can be fairly confident this mutation is disease-producing because of the high correlation between truncation mutations and Dravet syndrome.
This same mutation may be reported by another lab like this
This report does not specify the nucleotide position, but it identifies the amino acid position as 1329, and the asterisk (*) next to the amino acid position indicates a stop codon. Again, the lab is confident this mutation will result in Dravet syndrome.
Sometimes, one or more nucleotides are deleted from the gene. If one nucleotide is inserted or deleted, the reading frame of codons is shifted, and every amino acid is incorrect from that point on. This results in a nonfunctional sodium ion channel.
If a group of 3 nucleotides is inserted/deleted, only one codon is added/missing, respectively, and the protein may still be functional depending on the location of that insertion or deletion.
Large segments of DNA may be inserted or deleted, up to and including the entire SCN1A gene. These mutations have varying phenotypes, and account for roughly 2-3% of Dravet mutations. (5)(1)
When the mutation occurs in the sperm, the egg, or very soon after fertilization, all of the daughter cells derived from the growing embryo will be positive for the mutation. This is the case for most mutations found in Dravet syndrome. (1)
However, if the mutation occurs later in the development of the embryo, only the cells descended from the mutated cell will carry the mutation. The cells descended from the non-mutated cells of the embryo will remain healthy. This patient would be classified as “mosaic” for the mutation. The later the mutation took place, the lower the percentage of cells descended from the mutated cell, and the lower the “% mosaicism” or “mosaic load.” (This is a broad generalization: In reality, the degree of specialization of the cells at the time of mutation plays a significant role in where the mutated cells are concentrated in the patient’s body and what the ultimate mosaic load is.) One study reported that SCN1A mutations with 12-25% mosaic load were potentially pathogenic, with reduced penetrance, meaning not all who carried the mutation in mosaic form exhibited signs or symptoms. (5)
What about SNP’s?
Mutations are actually a natural phenomenon that has been occurring in humans for thousands of years. Most changes in DNA sequence have little to no bearing on the final protein products because they occur in regions that are edited out during gene processing, or their location in the final protein does not alter its function. In fact, many members of the healthy population have variants in their genes that are shared with a significant percentage of the population. Because these variants have no obvious clinical symptoms, they are called Single Nucleotide Polymorphisms (SNP’s) and are not considered mutations. Your lab report may include these SNP’s, but their presence is not considered a positive SCN1A test.
What does this mean for the patient?
Researchers and epileptologists are learning more about the role SCN1A mutations play in Dravet syndrome and related epilepsies every day. At this point, it is clear that SCN1A mutations of any kind can be responsible for Dravet syndrome. However, because some SCN1A mutations are present in healthy individuals, too, there are probably many factors that determine the severity of symptoms that result from the mutation. SCN1A mutations are helpful in supporting a clinical diagnosis. Remember, roughly 30% of patients with Dravet syndrome have no detected mutation, and a mutation is not required for diagnosis.
Is it all bad news?
No! There is so much active research on SCN1A and related epilepsies that scientists are uncovering new knowledge and potential places for therapy every year. The fact that an epilepsy syndrome like Dravet can be traced to a root cause, despite many unknown factors and modifiers, is wonderful news and gives us hope that a cure is possible.
- 2012. Xu XJ, Zhang YH, Sun HH, Liu XY, Jiang YW, Wu XR. Genetic and phenotypic characteristics ofSCN1A mutations in Dravet syndrome. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2012 Dec;29(6):625-30
- 2015. Brunklaus A, Ellis R, Stewart H, Aylett S, Reavey E, Jefferson R, Jain R, Chakraborty S, Jayawant S, Zuberi SM. Homozygous mutations in the SCN1A gene associated with genetic epilepsy with febrile seizures plus and Dravet syndrome in 2 families. Eur J Paediatr Neurol. 2015 Feb 21
- 2003. Nabbout R, Gennaro E, Dalla Bernardina B, Dulac O, Madia F, Bertini E, Capovilla G, Chiron C, Cristofori G, Elia M, Fontana E, Gaggero R, Granata T, Guerrini R, Loi M, La Selva L, Lispi ML, Matricardi A, Romeo A, Tzolas V, Valseriati D, Veggiotti P, Vigevano F, Vallée L, Dagna Bricarelli F, Bianchi A, Zara F. Spectrum ofSCN1Amutations in severe myoclonic epilepsy of infancy. Neurology. 2003 Jun 24;60(12):1961-7
- 2015. Meng H, Xu HQ, Yu L, Lin GW, He N, Su T, Shi YW, Li B, Wang J, Liu XR1, Tang B, Long YS, Yi YH, Liao WP . TheSCN1AMutation Database: Updating Information and Analysis of the Relationships among Genotype, Functional Alteration, and Phenotype. Hum Mutat. 2015 Jun;36(6):573-80
Special thanks to DSF Board Member, Nicole Villas for putting together this informative guide.
Parents or family members with additional questions may contact DSF Scientific Advisory Board member, Dr. Miriam Meisler
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