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Comprehensive analysis tool for SYNGAP1 genetic mutations
Supporting both patient education and professional clinical analysis
This information is for educational purposes only and should not replace professional medical advice. Always consult with qualified healthcare professionals for medical decisions.
This tool helps parents understand genetic test results for SYNGAP1 mutations. DNA contains instructions for making proteins - think of it like a recipe book. When there's a change (mutation) in the SYNGAP1 gene, it can affect how the SYNGAP1 protein works, which may impact brain development and function. This tool shows you where the change occurs and what it might mean, but it's designed to complement - not replace - discussions with your geneticist or medical team.
Supports: c.* (coding), p.* (protein - provides more detailed mutation analysis) notation with 1-letter or 3-letter amino acids
This tool covers 95%+ of common HGVS notation patterns and follows official standards. If your mutation cannot be parsed, please contact SYNGAP Global Network to report the issue.
Quick Examples:
Changes in exons directly affect the protein recipe - like using wrong ingredients in a cake.
Usually don't affect protein since introns are cut out. But sometimes can mess with the cutting process.
SYNGAP1 gene showing 19 exons with mutation location marked
Genes are like recipes written in DNA for making proteins. When a gene is read, it produces a copy called RNA, which is then turned into a protein.
This visualization shows how your mutation affects the SYNGAP1 protein sequence (1,343 amino acids).
Learn the fundamentals
Understand exons & introns
Types & effects
The specific gene
What are the four letters in the DNA alphabet?
Which parts of genes contain the actual protein instructions?
Click on any mutation type above to learn how it affects the DNA sequence and protein production.
Which type of mutation is most likely to completely change the protein?
Child with SYNGAP1 mutation
Most SYNGAP1 mutations are de novo (new mutations not inherited from parents)
Most SYNGAP1 mutations are:
SYNGAP1 Syndrome is caused by a variant on the SYNGAP1 gene located on chromosome 6p.21.32. The human body is made of trillions of cells, each containing 23 pairs of chromosomes (46 total), with each chromosome containing thousands of genes.
SYNGAP1 encodes a protein crucial for synaptic plasticity and learning. It acts as a GTPase-activating protein (GAP) that regulates Ras signaling at synapses, essential for proper brain development and function.
Most SYNGAP1 mutations are de novo (new mutations), though familial cases with autosomal dominant inheritance have been reported. Mosaicism, where some cells carry the mutation while others don't, can occur and may result in milder symptoms.
A gene is like a book containing chapters. The SYNGAP1 gene has 19 chapters (exons) separated by cover pages (introns). These chapters contain the information used to create the SYNGAP1 protein, which is then used by the brain.
Bigger exons are statistically more likely to have mutations, like longer chapters having more chances for typos.
No single exon of the SYNGAP1 gene is linked to a specific neurodevelopmental disorder. Mutations causing these disorders can occur in any exon, and it's usually the type of mutation and which protein region is affected that matter most.
Some studies suggest that mutations in exons 1-4 might cause milder symptoms, but this isn't a strict rule.
Research Note: This pattern is not guaranteed and more research is needed to confirm any exon-specific severity patterns.
When evaluating SYNGAP1 mutations, focus on the type of mutation (missense, nonsense, frameshift) and which protein domains are affected rather than the specific exon number. There is no clear pattern connecting specific exons to certain disease features.
A single nucleotide error in just 4,029 characters can lead to SYNGAP1 syndrome. This is truly a minimal "bad luck event" considering the entire human genome has around 3 billion nucleotides.
But it's not just the 4,029 coding nucleotides: The complete SYNGAP1 gene contains 37,881 total characters including introns. While intron mutations are less likely to cause problems, they can still disrupt the gene reading process.
Understanding how DNA creates proteins is essential to understanding mutations. Think of it as a three-step recipe-making process:
When there's a mutation in the SYNGAP1 gene, it can change the recipe for making the SYNGAP1 protein. Even tiny changes can make the protein work poorly or not at all, leading to the symptoms of SYNGAP1 syndrome.
Genome testing is preferred even if more expensive, as intron mutations can sometimes affect protein creation by disrupting the gene reading process.
Think of DNA as a sentence made of letters. Mutations are like typos:
One letter is swapped for another
Can change one amino acid or sometimes do nothing
One or more letters are lost
Removing whole codons (3 letters) keeps reading frame intact, but removing 1-2 letters shifts the frame
Extra letters are added
Shifts the reading frame, changing all downstream amino acids
A section of DNA is copied and inserted next to the original
Can cause gene dosage imbalance or frameshift if not in multiples of 3
Messes up the 3-letter "word" system
Usually causes severe protein problems
Accidentally creates an early "stop" signal
Creates shortened, usually non-functional protein
Below is the complete amino acid sequence of the SYNGAP1 protein (1,343 amino acids). Click or hover over any letter to see detailed information.
Most amino acids can be created by multiple different codon combinations. This is called the "genetic code redundancy." When a DNA change occurs but still produces the same amino acid, it's called a synonymous or "silent" mutation.
Use our DNA Decoder to analyze specific SYNGAP1 mutations and get detailed explanations.
>99% certainty of disease causation
90-99% certainty of disease causation
10-90% uncertainty range
VUS classifications may need to be reassessed every few years as new evidence becomes available.
1-10% chance of pathogenicity
<1% chance of pathogenicity
Detailed analysis of missense mutations with structural and functional predictions
A missense mutation is a single nucleotide change that results in a codon that codes for a different amino acid, potentially affecting protein function.
Visit SynGAP Missense ServerUse our clinical-grade DNA Decoder to analyze specific SYNGAP1 variants and generate reports.
Initializing 3D viewer...
Click on the structure to see residue details
Use our comprehensive tools to understand how mutations affect both sequence and structure.