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Supp. Figure S1. ATRX and MAGT1 mutations. A. Single nucleotide deletion in ATRX. B. Chromosome X array with MAGT1 CNV (enlarged in inset). C. Position of ATRX single nucleotide deletion in exon 36 and MAGT1 CNV in intron 3 which contains an alternative splice site and overlaps 3’UTR of isoform 2, UCSC, hg18. D. Schematic diagram of the ATRX gene (not to scale). The blue horizontal line represents exon 36. The mutation discovered in this study is indicated with an arrow. The principal domains, the zinc finger motif (ADD) and the highly conserved helicase motif, are indicated as are the conserved P box (P) and a glutamine-rich region (Q). Total number of mutations in ADD, helicase and the C terminus is indicated by numbers inside circles. A total of 6 different constitutional mutations have previously been reported near the C-terminus of ATRX, all of which lead to protein truncation [Gibbons et al., 2008].

Supp. Figure S2. RT-PCR products for MAGT1 gene. C1 and C2 are controls.

Supp. Figure S3. ATG4 RNA (A) and protein (B) expression. C = controls.

Supp. Table S1. Summary of clinical findings

Supp. Table S2. Summary of genetic investigations

Supp. Table S3. Analysis of genetic variants detected by exome sequencing

Supp. Table S4. Candidate chromosome X variants

Supp. Table S5. Primers used for Sanger sequencing

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