Structure of CNTNAP2 and NRXN1
(A) Schematic drawing of the genomic structure of CNTNAP2 with color coding for domain-coding exons and localization of mutations and deletions. Black bars represent deletions. Abbreviations are as follows: SP, signal peptide; DISC, discoidin-like domain; LamG, laminin-G domain; EGF, epidermal growth factor-like domain; FIB, fibrinogen-like domain; TM, transmembran region; PDZPB, PDZ-domain-binding site ; F1, family 1; P2, patient 2; Amish, homozygous mutation in the Amish population, published by Strauss et al. 36
(B) Schematic drawing of the genomic structure of α-NRXN1 and β-NRXN1 with color coding for domain-coding exons and localization of the mutation and deletion in patient 3, the deletion being represented by a black bar. Abbreviations are as follows: SP, signal peptide; LamG, laminin-G domain; EGF, epidermal growth factor-like domain; TM, transmembrane region; PDZPB, PDZ-domain-binding site.
(C) Schematic drawing of the domain structure of neurexins, CASPR2, and CASPR in humans and Drosophila. In contrast to CASPR, CASPR2 contains a PDZ-domain-binding site but lacks a PGY repeat region, rich in proline, glycine, and tyrosine residues. Both neurexin I and CASPR2/Nrx-IV contain PDZ-domain-binding sites at their intracellular C terminus but differ in the presence of discoidin-like and fibrinogen-like domains and in the order of laminin-G domains.

Nrx-IV Localizes to Synapses and Its Overexpression Reorganizes Synapse Architecture
(A) Presence of endogenous Nrx-IV at type 1b neuromuscular junctions (NMJs) of muscle 4, overlapping with active zones stained with nc82. White arrowheads point to Nrx-IV, labeling overlapping active zones.
(B) Synaptic terminal with increased bouton number and increased number of synaptic branches upon Nrx-I or Nrx-IV overexpression, stained with an anti-HRP marker and the nc82 antibody. The enlarged section depicts the increased density of active zones.
(C) Increased bouton number per μm² NMJ area in UAS-Nrx-I/ elav-Gal4; elav-Gal4/+ (dbElav:: Nrx-I) and elav-Gal4/+; UAS-Nrx-IV/ elav-Gal4 (dbElav:: Nrx-IV) versus control w1118 animals (contr. 1) and dbElav control animals (contr. 2).
(D) Quantitative analysis of increased active-zone density (number per μm² NMJ area) in neuronal Nrx-I and Nrx-IV overexpression.
(E) Increased number of synaptic branches in Nrx-I and Nrx-IV overexpression. Error bars indicate standard error of the mean. p values are related to the WT (control 1). Single asterisk, p < 0.008; double asterisk, p < 0.0003; triple asterisk, p < 0.0001.

Pedigrees and Results of Molecular Karyotyping
(A) Pedigree of family 1, with two affected children and homozygous deletion of CNTNAP2 affecting exons 2–9. Both parents are heterozygous carriers of the deletion. Results are from molecular karyotyping with Affymetrix 250K SNP arrays and analysis with the Genotyping Console 3.0.2 software (Affymetrix). The deletion-flanking SNPs in the 500K array of P1a are SNP_A-1991616 (145,562,641 Mb; UCSC Human Genome Browser version 18 [hg18]) and SNP_A-1991672 (146,730,410 Mb; hg18), with a maximal deletion size of 1,167,269 bp and a minimal size of 1,146,016 bp (Nexus software).
(B) Pedigree of P2, with one affected child. The patient harbors an in-frame 180 kb deletion affecting CNTNAP2 exons 5–8 and a splice-site mutation in the splice donor site of exon 11. Results of molecular karyotyping data from the Affymetrix 6.0 SNP array were analyzed with the Genotyping Console 3.0.2 software, showing a deletion from CN_1217185 (146,387,354 Mb; hg18) to SNP_A-4269862 (146,566,863 Mb; hg18). See Figure S1 for SNP copy-number profiles.
(C) Pedigree of P3, with a compound-heterozygous deletion of NRXN1 exons 1–4 and a stop mutation in exon 15. Results of molecular karyotyping data from the Affymetrix 6.0 SNP array were analyzed with the Genotyping Console 3.0.2 (Affymetrix), showing a 113 kb deletion between CN_864223 (51,001,003 Mb; hg18) and CN_864269 (51,113,677 Mb; hg18).
(D) Clinical pictures of P2, with a compound-heterozygous deletion and mutation in CNTNAP2 and of patient 3, with a compound-heterozygous deletion and mutation in NRXN1. Apart from a wide mouth in patient 3, no specific dysmorphisms are noted.

The Presynaptic Protein Bruchpilot Is Misregulated in Nrx-IV Knockdown Embryos and Larval Brains with Neuronal Overexpression of Nrx-I and Nrx-IV
(A and B) For quantitative evaluation, embryos have been assigned to one of three categories of bruchpilot (nc82) intensities: strong, moderate, and weak peripheral staining. (A) Images of strong and moderate central (ventral nerve cord, left panel) and peripheral (middle panel) presynaptic bruchpilot staining, representing the major fraction in WT and Nrx-IV knockdown embryos, respectively (UAS-Nrx-IV^RNAi/+; elav-Gal4/+ [Elav::RNAi Nrx-IV]). Note that peripheral and central synaptic staining of bruchpilot in the Nrx-IV knockdown embryos is diminished. Costaining with an anti-HRP marker, staining neuronal membranes, ensured the same focal plane in mutant and WT embryos. Arrowheads point to a specific identifiable synapse (the muscle 6/7 synapse). Bruchpilot staining of this synapse is depicted in insets in the middle panels. (B) Quantitative analysis of nc82 (anti-bruchpilot, synaptic active zones) labeling. Diagram shows mean with standard deviation.
(C) Representative pictures of bruchpilot staining in brains with neuronal overexpression of Nrx-I or Nrx-IV as a result of the following genotypes: WT, UAS-Nrx-I/ elav-Gal4; elav-Gal4/+ (dbElav:: Nrx-I) and elav-Gal4/+; UAS-Nrx-IV/ elav-Gal4 (dbElav:: Nrx-IV). Bruchpilot immunoreactivity is increased in both mutant conditions.
(D) Quantitative assessment of bruchpilot immunoreactivity in brains of genotypes shown in (C). The diagram shows the mean of normalized intensity with the standard error of the mean. p values in (B) and (D) are related to the WT, respectively. Single asterisk, p < 0.05; double asterisk, p < 0.01; triple asterisk, p < 0.0001.