No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>), or in Other Contactin-Associated Proteins or Contactins

<div><p>Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (<i>CNTNAP2</i>) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in <i>CNTNAP2</i> and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the <i>CNTN</i> or <i>CNTNAP</i> genes, including <i>CNTNAP2</i>, placing marked limits on the scale of their plausible contribution to risk.</p></div

Overall rare^* variant mutation burden: all genes.

<p>*rare variants were defined as follows: seen only in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 2% in this data, and less than 1% in all populations in the Exome Variant Server[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref038" target="_blank">38</a>] and SeattleSNP[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref039" target="_blank">39</a>] databases</p><p>Overall rare^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t001fn001" target="_blank">*</a>} variant mutation burden: all genes.</p

Rates of singleton^* mutations: all genes.

<p>*singleton mutations met the following criteria: seen only once in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 2% in this data, and less than 1% in all populations in the Exome Variant Server[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref038" target="_blank">38</a>] and SeattleSNP[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#pgen.1004852.ref039" target="_blank">39</a>] databases</p><p>Rates of singleton^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t002fn001" target="_blank">*</a>} mutations: all genes.</p

Location of all mutations of interest, i.e. rare and exclusive to cases or controls.

<p>Mutations were counted if missense, nonsense, splice site, or frameshift in <i>CNTNAP2</i> (in point of fact, all were missense). Variants in red are exclusive to cases; those in green, controls. Those predicted to be deleterious in SIFT are underlined in orange; in PolyPhen2, purple. Domain names and approximate locations from Bakkaloglu et al.,</p

Rates of mutation predicted deleterious^* by SIFT-or-PolyPhen2: all genes.

<p>*deleterious mutations were defined as “damaging” in SIFT and/or “possibly damaging” or “probably damaging” in PolyPhen2, as well as all nonsense and splice site mutations which were not evaluated by these programs but were regarded as deleterious intrinsically</p><p>Rates of mutation predicted deleterious^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t003fn001" target="_blank">*</a>} by SIFT-or-PolyPhen2: all genes.</p

Inheritance of mutations predicted deleterious^* by SIFT-or-PolyPhen2.

<p>*deleterious mutations were defined as “damaging” in SIFT and/or “possibly damaging” or “probably damaging” in PolyPhen2, as well as all nonsense and splice site mutations which were not evaluated by these programs but were regarded as deleterious intrinsically. Inheritance was a situation where recurrent mutations were counted more than once, because keeping only one instance of a variant and ignoring the rest would introduce arbitrary parent-of-origin bias</p><p>^†<i>CNTN6</i> and <i>CNTNAP4</i> each had one mutation that was confirmed to be de novo in whole blood</p><p>Inheritance of mutations predicted deleterious^{<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004852#t004fn001" target="_blank">*</a>} by SIFT-or-PolyPhen2.</p