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Table 4 Results of the ASD-NGS panel

From: Mitochondrial dysfunction and autism: comprehensive genetic analyses of children with autism and mtDNA deletion

Patient ID Gene Mutation Zygosity Inheritance Clinical relevance Polyphen2
Patients with ASD and mtDNA deletion (N = 10)
 P1 FOXP2 A280T HET AD Uncertain significance 0.99
 P2 RAI1 V1565M HET AD Uncertain significance 0.845
AUTS2 L433P HET AD Uncertain significance 1
 P3 TSC2 K22N HET AD Uncertain significance 1
CHD7 Fs HET AD Pathogenic [38] n/d
 P4 RELN L496P HET AD/AR Uncertain significance 0.98
KATNAL2 R1382S HET AR/AD Uncertain significance 0.99
 P6 ZNF804A A1108T HET n/d Uncertain significance 1
 P7 RAI1 G1070R HET AD Uncertain significance 0.99
 P8 DHCR7 W119* HET AR Pathogenic n/d
NHS R409Q HET XLD Uncertain significance 1
 P10 PDE10A P477A HOM AR/AD Uncertain significance 0.99
Patients with ASD and without mtDNA deletion (N = 7)
 C-ASD1 SHANK2 A1129P HET n/d Uncertain significance 0.86
 C-ASD2 PON3 S820N HET n/d Uncertain significance 1
NRXN1 S820N HET AR Uncertain significance 0
CNTNAP2 Y716C HET n/d Uncertain significance 0.9
 C-ASD3 SCN2A L577I HET AD Uncertain significance 0
 C-ASD4 NLGN4X Q89H HET XLD Uncertain significance 0.99
 C-ASD6 GNA14 Y287C HET n/d Uncertain significance 1
Healthy controls (N = 6)
 C-H1 ZNF804A A1108T HET n/d Uncertain significance 1
NIPBL R765K HET AD Uncertain significance 0.001
 C-H2 ZNF804A A1108T HET n/d Uncertain significance 1
 C-H3 RELN A150V HET AD/AR Uncertain significance 0.974
Patient ID SIFT MT dbSNP ExAC 1000 Genome/ EUR AF  
Patients with ASD and mtDNA deletion (N = 10)
 P1 0.23 D n/d 0.000008278 n/d  
 P2 0.02 P rs368106957 0.0001819 0.0002/0  
n/d D n/d 0.0002025 n/d  
 P3 0.42 P n/d n/d n/d  
n/d D n/d n/d n/d  
 P4 0.02 D n/d n/d n/d  
0.14 P rs148791504 0.0009651 0.0016/n/d  
 P6 0.16 P rs112183442 0.02529 0.0158/0.0457  
 P7 0.01 D rs370633684 0.0004679 0.0004/0.00077  
 P8 0.12 P rs11555217 0.0007 n/d  
0.31 P n/d 0.00002282 n/d  
 P10 1 P rs61733392 0.004515 0.0024/0.006  
Patients with ASD and without mtDNA deletion (N = 7)
 C-ASD1 0.29 D rs377255888 0.00004137 n/d  
 C-ASD2 0 D rs139856535 0.002787 0.0016/n/d  
0.33 D rs80293130 0.0002235 0.0002/n/d  
0.18 D n/d 0.00008303 n/d  
 C-ASD3 0.91 D n/d n/d n/d  
 C-ASD4 0.1 D n/d n/d n/d  
 C-ASD6 1 D rs61755085 0.001506 0.0014/0.004  
Healthy controls (N = 6)
 C-H1 0.16 P rs112183442 0.02529 0.0158/0.0457  
0.64 D rs185678374  0.0005529 0.0004/n/d  
 C-H2 0.16 P rs112183442 0.02529 0.0158/0.0457  
 C-H3 0.01 n/d n/d 0.000008245 n/d  
  1. The detected rare variants of the 10 mtdel-ASD cases, in ASD patients without a mtDNA deletion, and in healthy controls are presented (only pathogenic, likely pathogenic variations and variations with uncertain significance variations are shown)
  2. P mtdel-ASD patient, non-mtdel-ASD ASD patient without mtDNA deletion, MD patient with mitochondrial disease, H healthy control individual, HET heterozygous, AR autosomal recessive, AD autosomal dominant, n/d no data, SIFT sorting intolerant from tolerant prediction database, MT mutation t@ster prediction database, D disease causing according to mutation t@ster prediction, P polymorphism according to mutation t@ster prediction, ExAC allele frequency data from exome aggregation consortium, 1000 Genomes allele frequency data from 1000 Genomes project, EUR AF allele frequency in the European Super Population of the 1000 Genomes project
  3. *The symbol of the non sense mutation in protein level