TABLE 3.

The pathogenic CNVs in this study are matched with the records in the Decipher database for same mutation types (duplication/deletion).

Fetus ID	CNV-CMA	Band	Chromosome coordinate	Chromosome	Start	End	Duplication/deletion	CNV size (bp)	Decipher ID	Variant	Duplication/deletion	Sex	Size	Pathogenicity/contribution	Inheritance	Phenotype(s)-renal/kidney/neph/glom	Phenotype(s) -other	CNV syndromes
P77	46, XX, arr[hg19] 4p16.1(8, 212, 173-8, 437, 267) × 1	4p16.1	Chr4: 8, 212, 173–8, 437, 267	Chr4	8, 212, 173	8, 437, 267	Deletion	225094	287892	Chr4: 71, 553–8, 732, 736	Deletion	46XX	8.66 Mb	Pathogenic	De novo constitutive	Renal cyst	Ventricular septal defect; intrauterine growth retardation; choroid plexus cyst	NA
P77	46, XX, arr[hg19] 4p16.1(8, 212, 173-8, 437, 267) × 1	4p16.1	Chr4: 8, 212, 173–8, 437, 267	Chr4	8, 212, 173	8, 437, 267	Deletion	225094	307768	Chr4: 71, 552–18, 839, 648	Deletion	46XY	18.77 Mb	Pathogenic full	De novo constitutive	Abnormality of the renal pelvis, penile hypospadias	Umbilical hernia; external ear malformation; cataract, hypertelorism, iris coloboma; abnormal eyelid morphology, depressed nasal bridge, epicanthus, micrognathia, preauricular skin tag, short philtrum, up slanted palpebral fissure; fifth finger distal phalanx clinodactyly; aplasia/hypoplasia of the corpus callosum, hypoplasia of the corpus callosum; prominent protruding coccyx	NA
P77	46, XX, arr[hg19] 4p16.1(8, 212, 173-8, 437, 267) × 1	4p16.1	Chr4: 8, 212, 173–8, 437, 267	Chr4	8, 212, 173	8, 437, 267	Deletion	225094	326600	Chr4: 72, 447–11, 175, 255	Deletion	46XX	11.10 Mb	Pathogenic full	De novo constitutive	Chronic kidney disease	Severe intrauterine growth retardation	NA
P82	46, XX, arr[hg19] 7q36.2 (153, 529, 677-153, 763, 852) × 3	7q36.2	Chr7: 153, 529, 677–153, 763, 852	Chr7	153, 529, 677	153, 763, 852	Duplication	234175	368657	Chr7: 152, 306, 254–159, 118, 566	Duplication	46XX	6.81 Mb	Pathogenic	De novo constitutive	Renal dysplasia	Ventricular septal defect; intrauterine growth retardation; spinal dysraphism	NA
P82	46, XX, arr[hg19] 9p24.1p23 (8, 959, 747-9, 058, 856) × 1	9p24.1p23	Chr9: 8, 959, 747–9, 058, 856	Chr9	8, 959, 747	9, 058, 856	Deletion	99109	253970	Chr9: 2, 146, 330–9, 663, 533	Deletion	46XY	7.52 Mb	Pathogenic	De novo constitutive	Abnormality of the kidney, horseshoe kidney	Intellectual disability	NA
P16	46, XY, arr 8p23.2(2, 350, 511-2, 734, 916) × 3	8p23.2	Chr8: 2, 350, 511–2, 734, 916	Chr8	2, 350, 511	2, 734, 916	Duplication	384405	253970	Chr8: 487, 644–18, 600, 102	Duplication	46XY	18.11 Mb	Pathogenic	De novo constitutive	Abnormality of the kidney, horseshoe kidney	Intellectual disability	NA
P16	46, XY, arr 8p23.2(2, 350, 511-2, 734, 916) × 3	8p23.2	Chr8: 2, 350, 511–2, 734, 916	Chr8	2, 350, 511	2, 734, 916	Duplication	384405	278296	Chr8: 1, 765, 533–6, 939, 296	Duplication	46XX	5.17 Mb	Pathogenic	De novo constitutive	Ectopic kidney	Aplasia/hypoplasia of the nipples; hypertension; hypothyroidism; abnormal facial shape, reduced number of teeth; delayed speech and language development, global developmental delay, poor motor coordination; joint laxity, spinal canal stenosis	NA
P10	46, XX, dup(10p12.31, 20.76-21.00, 242K)	10p12.31	Chr10: 20, 760, 000–21, 000, 000	Chr10	20, 760, 000	21, 000, 000	Duplication	240000	354979	Chr10: 1, 48, 325–24, 786, 291	Duplication	46XY	24.64 Mb	Pathogenic full	De novo constitutive	Abnormality of the ureter, renal hypoplasia	Heart murmur; long eyelashes, prominent forehead; global developmental delay	NA
P47	46, XX, arr 16p11.2(29, 634, 212-30, 154, 740) × 1	16p11.2	Chr16: 29, 634, 212–30, 154, 740	Chr16	29, 634, 212	30, 154, 740	Deletion	520528	301482	Chr16: 29, 673, 954–30, 198, 600	Deletion	46XY	524.65 kb	Pathogenic partial	Unknown	Hydronephrosis, unilateral renal agenesis	Duodenal stenosis	16p11.2 deletion syndrome (Phenotype: abnormality of the face; feeding difficulties in infancy; intellectual disability; pointed chin)
P47	46, XX, arr 16p11.2(29, 634, 212-30, 154, 740) × 1	16p11.2	Chr16: 29, 634, 212–30, 154, 740	Chr16	29, 634, 212	30, 154, 740	Deletion	520528	370503	Chr16: 29, 656, 684–30, 190, 568	Deletion	46XY	533.88 kb	Pathogenic	Unknown	Renal dysplasia, unilateral renal agenesis	Global developmental delay; tracheomalacia	16p11.2 deletion syndrome (Phenotype: abnormality of the face; feeding difficulties in infancy; intellectual disability; pointed chin)
P47	46, XX, arr 16p11.2(29, 634, 212-30, 154, 740) × 1	16p11.2	Chr16: 29, 634, 212–30, 154, 740	Chr16	29, 634, 212	30, 154, 740	Deletion	520528	331267	Chr16: 29, 652, 360–30, 190, 593	Deletion	46XY	538.23 kb	Likely pathogenic	De novo constitutive	Abnormality of the kidney	Abnormality of coordination, autistic behavior	16p11.2 deletion syndrome (Phenotype: abnormality of the face; feeding difficulties in infancy; intellectual disability; pointed chin)
P47	46, XX, arr 16p11.2(29, 634, 212-30, 154, 740) × 1	16p11.2	Chr16: 29, 634, 212–30, 154, 740	Chr16	29, 634, 212	30, 154, 740	Deletion	520528	283293	Chr16: 29, 622, 757–30, 177, 916	Deletion	46XY	555.16 kb	Pathogenic	De novo constitutive	Hydronephrosis	Failure to thrive; abnormality of the thumb, hypoplasia of the radius, lower limb hypertonia, radial club hand; hypertonia; broad-based gait, global developmental delay; decreased fetal movement	16p11.2 deletion syndrome (Phenotype: abnormality of the face; feeding difficulties in infancy; intellectual disability; pointed chin)
P45	46, XX, arr 22q11.21(18, 923, 623-19, 008, 108) × 3	22q11.21	Chr22: 18, 923, 623–19, 008, 108	Chr22	18, 923, 623	19, 008, 108	Duplication	84485	304917	Chr22: 17, 029, 055–37, 959, 706	Duplication	46XX	20.93 Mb	Pathogenic	Unknown	Axial malrotation of the kidney	Patent ductus arteriosus after birth at term; iris coloboma, posterior capsular cataract; high palate, prominent nasal bridge, short nose, small anterior fontanelle, smooth philtrum; hypoplastic toenails; polyhydramnios	22q11.2 duplication syndrome (Phenotype: intellectual or learning disability, developmental delay, slow growth leading to short stature, and hypotonia)
P46	46, XX, arr 22q11.22(22, 314, 463-22, 550, 078) × 3	22q11.22	Chr22: 22, 314, 463–22, 550, 078	Chr22	22, 314, 463	22, 550, 078	Duplication	235615	304917	Chr22: 17, 029, 055–37,959,706	Duplication	46XX	20.93 Mb	Pathogenic	Unknown	Axial malrotation of the kidney	Patent ductus arteriosus after birth at term; iris coloboma, posterior capsular cataract; high palate, prominent nasal bridge, short nose, small anterior fontanelle, smooth philtrum; hypoplastic toenails; polyhydramnios	22q11.2 duplication syndrome (Phenotype: intellectual or learning disability, developmental delay, slow growth leading to short stature, and hypotonia)

CNV, copy number variation; NA, not available.