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Table 2 Diagnostic copy number variants identified among patients undergoing next-generation sequencing-based multi-gene panel testing for suspected skeletal dysplasia

From: Diagnostic utility of next-generation sequencing-based panel testing in 543 patients with suspected skeletal dysplasia

Study ID Phenotype Chrom Event Copy number OMIM morbid gene(s) Size category Minimum size (bp) Classification
324 Hypotonia, developmental delay, blue sclera. Family history of OI. Consanguinity reported 9 Loss 0 TMEM38B Intragenic 241 Pathogenic
247 Macrocephaly, short stature, thin tubular bones, small thorax 6 Loss 1 CUL7 Intragenic 458 Likely pathogenic
096 Skeletal dysplasia consistent with Stickler syndrome or brachyolmia 1 Loss 1 COL11A1 Intragenic 827 Likely pathogenic
435 Short stature, dysmorphic facies X Loss 1 SHOX Single gene 20,429 Pathogenic
460 Short stature, markedly reduced limb length, scoliosis, chronic musculoskeletal pain X Loss 0 SHOX Single gene 20,429 Pathogenic
226 Short stature, markedly reduced limb length. Father with short limbs X Loss 1 SHOX Single gene 324,729 Pathogenic
516 Short stature, dysmorphic facies, speech delay 20 Loss 1 BMP2, MCM8, FERMT1 Multigenic 827,196 Pathogenic
454 Disproportionated short stature, hypermobility, delayed bone age, abnormal epiphyses 15 Loss 1 ADAMTS17, CHSY1, IGF1R MEF2A, CERS3, LINS1, ALDH1A3 Multigenic 3,343,316 Pathogenic
456 Disproportionate short stature 15 Loss 1 ADAMTS17, CHSY1, IGF1R, MEF2A, CERS3, LINS1, ALDH1A3 Multigenic 3,764,795 Pathogenic
257 Rhizomelic short stature, relative macrocephaly X Loss 1 SHOX, ARSL, CSF2RA, XG, NLGN4, Multigenic 5,774,581 Pathogenic
540 Rhizomelic short stature, relative microcephaly, difficulty pronating and supinating arms. Family history if similar features in two first-degree relatives and others X Loss 1 SHOX, ARSL, CSF2RA, XG, NLGN4, STS Multigenic 6,683,360 Pathogenic
023 Multiple congenital anomalies including skeletal abnormality of the radius and abnormal hands 18 Gain 3 Whole chromosome Aneuploidy N/A Pathogenic
233 Short stature, possible reduced femur length, coarse facial features X Loss 1 Whole chromosome Aneuploidy N/A Pathogenic
  1. Bolded font represents the genes included on the multi-gene panel received by this patient that are encompassed within the CNV (see Additional file 3)