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Angelman Syndrome Deletion Size: Does It Matter?

Deletion AS can be classified by the size of the deletion and where the deletion stops and starts.  There are multiple classes of Deletion AS (also referred to as types of deletions), but two are by far the most common. 

Class 1 deletions start at breakpoint 1 (BP1) in this figure below and end at breakpoint 3, for a total of about 6 million base pairs (6 Mb) deleted, while Class 2 deletions start at breakpoint 2 and extend to breakpoint 3 with about 5 million base pairs (5 Mb) deleted.   About half of individuals living with deletion AS have a Class 2 deletion, and about 40% have a Class 1 deletion.  Most of the remaining 10% living with deletion AS have a deletion that is larger, extending to breakpoints 4,5, or 6. Rarely, an individual has a smaller deletion that includes UBE3A.    

GeneReviews® [Internet]. Adam MP, Feldman J, Mirzaa GM, et al., editors. Seattle (WA): University of Washington, Seattle; 1993-2025.

Schematic drawing of chromosome region 15q11.2-q13 indicating the breakpoint regions BP1-BP6.

Large deletions (also called Class 3 or Class 4) 

Deletions larger than 7 Mb (most often Class 3 or Class 4 deletions) are rare but may be associated with more severe learning and developmental difficulties.   A small study of four individuals living with AS who have deletions larger than 7 Mb showed they had lower scores on developmental assessments of language, motor skills, daily living skills, and socialization skills (Sahoo et al, 2007).  Individuals living with deletions larger than 7 Mb may be less likely to walk independently (Varela et al, 2004).  More data from larger studies would be helpful to verify these findings. 

Class 1 and 2 deletions 

The Class 1 deletion includes four more genes than the Class 2 deletion. However, it is not clear whether missing these additional genes can cause more severe or different symptoms in AS.  Several studies have tried to understand this and have had conflicting results.   

Studies that evaluated the differences between individuals living with Class 1 and Class 2 deletions

When a gene is deleted, does that always cause symptoms or medical problems? 

No! Remember, humans typically have two copies of each gene.  For many genes, having just one copy is enough to prevent symptoms or medical issues.  For example, in neurotypical people, the brain typically only has one copy of UBE3A that is turned on, and that is fine! A person living with Deletion AS has no functional UBE3A in the brain.   

For many genes, as long as some functional protein is made, the exact amount of protein made can vary widely without causing any issues.  Often, one copy of a gene can make enough protein for the cells and body to function typically.  In addition, some genes have more than 2 copies, so missing one copy isn’t an issue.   

However, there are proteins that our cells and bodies need in an exact amount. For those genes, missing one copy of the gene may cause symptoms or medical issues.    

What do we know about the genes in Deletion AS?  

The genes deleted in Class 1 and Class 2 deletions are: 

GABRB3

GABRA5

GABRG3

OCA2

What about the genes that are deleted in a Class 1 deletion but not a Class 2 deletion?   

The genes deleted in Class 1 deletions, but NOT Class 2 deletions are: 

NIPA1

NIPA2

CYFIP1

GCP5 (TUBGCP5)

Do we know which genes cause the higher chance of seizures or more difficulties with speech and communication that may be seen in Deletion AS? 

Not for certain.  Given the currently available information, it is likely that missing the GABA genes contributes to the symptoms seen in Deletion AS (Frolich et al, 2019).  This is what led to clinical trials for alogabat in AS.   

Additional research is ongoing, including the development of a mouse model that has a deletion of all the genes seen in Deletion AS in humans, as well as a mouse model that has all the genes deleted EXCEPT FOR UBE3A, to better understand the role of these other genes in the symptoms and characteristics of Deletion AS.   

What’s the bottom line?  

Although individuals living with Deletion AS are also missing one copy of some or all the genes shown above, it is important to remember that loss of UBE3A causes the vast majority of symptoms of AS.  We know this because the primary symptoms of AS—developmental delays, limited or no verbal speech, seizures, balance difficulties—are seen in individuals living with all the AS genotypes.  There is significant overlap in the symptoms and the severity of the symptoms between an individual who lives with Mutation AS (which only affects UBE3A) and an individual who lives with Deletion AS.   

Class I and Class 2 deletions cause very similar symptoms and developmental delays.  If there is a difference between the groups, the difference is likely to be small, as multiple studies have not found the differences to be statistically significant (in other words, any differences seen between the groups could just be due to chance alone).  Because each individual living with AS is unique, knowing if a person has a deletion or if the deletion is Class 1 or Class 2 cannot be used to predict how a person will do.   

References: 

  1. Frohlich et al, 2019 https://pmc.ncbi.nlm.nih.gov/articles/PMC6482952/ 

  2. Keute et al, 2020 https://www.nature.com/articles/s41380-020-0858-6  

  3. Peters et al, 2012 https://pubmed.ncbi.nlm.nih.gov/21831244/:  

  4. Sadhwani et al, 2023 https://pmc.ncbi.nlm.nih.gov/articles/PMC8322148/ 

  5. Sadhwani et al, 2024 https://pubmed.ncbi.nlm.nih.gov/38879552/ 

  6. Sahoo et al, 2007 https://escholarship.org/uc/item/1928g0vm 

  7. Tan et al, 2011 https://pmc.ncbi.nlm.nih.gov/articles/PMC3563320/  

  8. Valente et al, 2013 https://pubmed.ncbi.nlm.nih.gov/23352739/  

  9. Varela et al, 2004 https://www.nature.com/articles/5201264 

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