We undertook a study of the 16p11.2 microdeletion/duplication region to investigate the role of common and rare genetic variation in 16p11.2 loci and risk for autism. Common and complex diseases such as autism can be due to genetic variation associated with a wide spectrum of allele frequencies 
. We hypothesized that common and/or rare functional variants in one or more genes in 16p11.2 may confer susceptibility to autism. To elucidate the potential role of 16p11.2 common genetic variation in autism, we analyzed existing SNP genotyping data from the following platforms: Affymetrix 5.0, Illumina 550 K, and Affymetrix 500 K microarrays. Our analysis identified a single nominal association with rs7193756 that resides in a LD block that contains the transmembrane protein C16orf54
and the quinolinate phosphoribosyl-transferase gene QPRT
. Overall, our association analyses indicate that common variation at 16p11.2 is not a major risk factor in autism. However, we cannot rule out the possibility that common (functional) variants not represented on the three commercially available microarrays may be associated with autism.
We also hypothesized that one or more genes residing within the 16p11.2 region harbor rare variants that increase risk for autism. In other studies, systematic mutation screening of genes initially identified through chromosomal, CNV, and/or resequencing analysis has led to the discovery of rare autism-associated variants/mutations in several genes, including NLGN3
at Xp22.3 
at 2p16.3 
at 22q13 
, and CNTNAP2
at 7q35 
. In the present study, we identified an initial significant association between a novel SEZ6L2
coding variant R386H and autism (p
is an intriguing candidate given the increased risk of clinical or subclinical epilepsy in autism (~20% of patients) 
is referred to as a seizure-related gene because a closely related ortholog, Sez-6
, is upregulated in response to seizure-inducing reagents in mouse neurons 
. The R386H substitution resides within a CUB domain that is found in functionally diverse developmental proteins such as Tolloid (involved in dorso-ventral patterning) and A5 (critical for targeting growing axons during nerve innervation) 
. Our expression studies of mouse and human SEZ6L2
in the developing embryo demonstrated high CNS-specific levels of brain expression, as would be expected for a neurodevelopmental disorder such as autism 
. Mice deleted for Sez6l2
do not show any obvious defects in development or behavior 
. However, mice deleted for all three SEZ
family members exhibit abnormal behavior that includes impaired motor coordination 
. It is possible that R386H may be necessary but not sufficient to produce autism and related disorders in some patients. Although the data presented here are insufficient to implicate a clear role for R386H in autism, follow-up investigations such as additional replication studies and functional experiments are warranted to evaluate its importance in disease risk.
Our screen for rare variants in seven additional genes identified several nucleotide substitutions of potential interest. The M225I substitution, predicted to affect protein function, was identified in the brain-specific synaptic vesicle-associated protein DOC2A (Double C2-Like Domain-Containing Protein, Alpha) that is thought to serve as a calcium sensor in neurotransmitter release 
. The M225I substitution is located between the two C2 domains, which interact with Ca2+
and phospholipids. Mice deleted for Doc2a
show alterations in synaptic transmission and long-term potentiation and exhibit learning and behavioral deficits that include an abnormal passive avoidance task 
. We also identified a DOC2A
promoter variant in another patient that is predicted to alter transcription factor binding sites for several brain-expressed genes.
In conclusion, we report an initial analysis of common and rare genetic variation in the 16p11.2 microdeletion/duplication region that is associated with ~1% of autism cases. The novel rare variants identified in this study represent an initial catalog of low frequency, putative functional risk factors in autism. We do not report compelling evidence for a role of either common or rare genetic variants in autism etiology. Our findings might be interpreted to suggest that deletion and/or duplication of multiple genes in the 16p11.2 interval is a more significant genetic risk factor for predisposition to autism, rather than molecular risk contributed by any one gene at this locus. Given that our choice of eight candidate genes was somewhat biased towards biological function, it is also possible that other genes or genomic features in the 16p11.2 region might contribute to autism. Although mutations associated with autism have been identified by screening as few as several hundred patients 
, one limitation of our study is the relatively small number of patients screened for rare variants. Additional studies in a larger number of patients for the genes examined here are warranted. In addition, the application of next-generation sequencing strategies to screen all genes and regulatory elements within the microdeletion/duplication may reveal more significant abnormalities.