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Supp. Figure S1. Sanger sequencing results of the pathogenic variants in ARID1A. Both forward (top) and reverse (bottom) sequencing results are shown for patients 26, 33 and 48. The peaks of the variant alleles are clearly lower for the nonsense variants (patient 26 and 33). The insert of patient 26 shows the Sanger sequencing results of DNA isolated from fibroblasts. The peak of the variant allele is almost as high as the wildtype allele, indicating a higher percentage of mosaicism in fibroblasts. For the frameshift variants in patients 48 and 25 the variant peaks are also consistently lower than wildtype peaks. As the variant in patient 25 is near the end of the sequenced fragment, the reverse sequence could not be interpreted at that location. A representative fragment downstream of the variant is shown in the insert, clearly displaying lower variant peaks than wildtype peaks.

Supp. Figure S2. Facial photographs per patient group

Supp. Figure S3. Pie-charts of the distribution of pathogenic variants in the SWI/SNF complex as published by Tsurusaki et al (left) and in our study (right). We did not include the SMARCA2-variants in this figure (see discussion).

Supp. Table S1. Characteristics of the variants extracted from the Exome Variant Server (EVS)

Supp. Table S2. Summary of the phenotype of the patients per patient group

Supp. Table S3. Variants in the EVS characterized as variants of unknown significance

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