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. 2016 Jul 20;24(12):1715–1723. doi: 10.1038/ejhg.2016.86

Table 1. De novo CNVs in this cohort.

Sample Cytoband CNV (Candidate) genes Phenotypes Validation procedure Classification
DE21OSOUKBD100141 2q21.1 hg19 chr2:g.(131349899_131486169)_(131991166_132057166)dup Multiple incl. POTEJ, GPR148, AMER3, ARHGEF4, FAM168B, PLEKHB2 OA/TOF qPCR Uncertain – likely benign
DE12OSOUKBD100206 3p26.1 hg19 chr3:g.(8519329_8521841)_(8551649_8554052)dup LMCD1, LMCD1-AS1 OA/TOF, tracheomalacia qPCR Uncertain
SKZ_2111 7q35q36.3 hg19 chr7:g.(143820444_143839360)_(159119486_159138663)del Multiple incl. SHH, MNX1, SLC4A2 TOF, abnormally placed anus, hypospadias, ventricle septal defects FISH Pathogenic
SKZ_1810 SKZ_1810 8p22 11p14.3 hg19 chr8:g.(17613606_17625479)_(17613606 _17844353)dup hg19 chr11:g.(21600567_21853276)_(22015682_22016670)del FGL1, LFIRE1, MTUS1, PCM1 - OA/TOF, aplastic left lung, anencephaly, craniorachyschisis, kyphosis, ventricular septal defect, pulmonary stenosis, radial club hand, hypoplastic thumbs, horseshoe kidney, broad thorax OA/TOF, aplastic left lung, anencephaly, craniorachyschisis, kyphosis, ventricular septal defect, pulmonary stenosis, radial club hand, hypoplastic thumbs, horseshoe kidney, broad thorax MAQ assay MAQ assay Uncertain – likely benign Uncertain – likely benign
SKZ_1662 13q12.11 hg19 chr13:g.(22685293_22688792)_(22978753_22981935)del AK054845, LINC00540 OA/TOF, tracheal stenosis, abnormal sacrum and kidney abnormality MAQ assay Uncertain
SKZ_2111 16p13.11 hg19 chr16:g.(14985615_15156180)_(16289532_17000304)dup Multiple TOF, abnormally placed anus, hypospadias, ventricle septal defects MAQ assay Uncertain – likely pathogenic
SKZ_1307 21q22.2 hg19 chr21:g.(40099972_40100880)_(40152372_40154748)dup LINC00114 OA/TOF, anal stenosis and long toes and fingers MAQ assay Uncertain – likely benign

None of the parents had oesophageal atresia or trachea–oesophageal fistula. Therefore, main focus was on de novo CNVs. Depicted are the eight confirmed (with either qPCR or MAQ assay) de novo CNV out of 74 evaluated rare CNVs from the Erasmus MC – Sophia, Baylor College of Medicine and University of Bonn cohorts. qPCR/FISH/MAQ assay validation results are in Supplementary Figure 1. Chromosome region according to build hg19.