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Table 3 Results of the intergenomic 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 SIFT MT dbSNP ExAC 1000 Genomes/EUR AF
Patients with ASD and mtDNA deletion (N = 10)
 P5 MGME1 T265I HET AR Likely pathogenic [37] 0.95 0.25 D rs76599088 0.007875 0.0044/0.0139
 P9 SUCLG1 G79D HET AR Uncertain significance 0.99 0 D n/d n/d n/d
Patients with ASD and without mtDNA deletion (N = 7)
 C-ASD1 MTO1 K321E HET AR Uncertain significance 1 0.001 D rs148667065 0.0000908 n/d
 C-ASD2 EARS2 R99Q HET AR Uncertain significance n/d 1 D n/d n/d n/d
Patients with MD and mtDNA deletion, without ASD (N = 7)
 C-MD1 WARS2 H151R HET AD/AR Uncertain significance 0.1 0.02 D rs150022801 0.001779 0.0008/0.003
 C-MD2 APEX1 R202P HET n/d Uncertain significance 0.6 0.01 P n/d 0.000008242 n/d
 C-MD3 ATP5A1 I173 V HET AR Uncertain significance 0.02 0.1 D n/d n/d n/d
 C-MD4 MTO1 V517 M HET AR Uncertain significance 0.03 0.1 D n/d n/d n/d
 C-MD5 C10orf2 N399S HET AR Pathogenic [38] 0.896 0.09 D n/d n/d n/d
C10orf2 A453Q HET AR Uncertain significance 0.053 0.27 D n/d n/d n/d
 C-MD6 MRPL3 S75 N HET AR Pathogenic [56] 0.8 0.34 D rs151331067  0.001606 0.0008/n/d
Healthy controls without mtDNA deletion (N = 6)
 C-H3 EARS2 S482 N HET AR Uncertain significance n/d 0.28 D n/d n/d n/d
 C-H4 SLC25A3 V219F HET AD Uncertain significance 0.62 0.001 D n/d n/d n/d
  1. Pathogenic, likely pathogenic, and rare variants of uncertain significance detected in the 10 mtdel-ASD cases and different comparison groups are presented (benign variations are not 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