Table 3.
Identified genomic disorders and likely pathogenic copy number variants
| ID | COU Category | CNV | CNV Size (Mb) | Type | GD-CNV | Dosage-Sensitive Genes | CAKUT (Human) | Sex | FHX | Consanguinity | Additional Genitourinary Phenotype | Extrarenal Phenotype |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P74a | UVJO | chr1: 145415279-145763815 | 0.349 | DEL | 1q21.1 susceptibility locus for TAR syndrome | RBM8A | M | N | N | |||
| P84 | UVJO | chr1: 145415279-145748587 | 0.333 | DUP | 1q21.1 TAR syndrome region duplication | RBM8A | M | N | N | VUR | ||
| P30a | UPJO | chr1: 146496480-147415562 | 0.919 | DEL | 1q21.1 recurrent microdeletion | F | N | U | ||||
| P15 | UPJO | chr7:144702944-148544434 | 3.841 | DEL | 7q36.1 deletion | CUL1, EZH2 | M | U | U | |||
| P26 | COU-NOS | chr15: 30918893-32404534 | 1.486 | DEL | 15q13.3 microdeletion syndrome | F | N | U | ||||
| P60 | COU-NOS | chr15:23684690-28557995 | 4.873 | DUP | 15q11.2 Prader–Willi/Angelman (type 1) reciprocal duplication | M | N | U | ||||
| P11 | UPJO | chr16: 29675050-30199897 | 0.525 | DEL | 16p11.2 deletion | PRRT2 | TBX6 | M | Y | U | VUR, KHD | Bifid thumbs |
| P44 | UVJO | chr16: 15460510-17564653 | 2.104 | DEL | 16p13.11 recurrent microdeletion | MYH11 | M | N | U | |||
| P45 | UVJO | chr16:14960412-16357072 | 1.397 | DUP | 16p13.11 duplication | MYH11 | M | N | U | Preauricular appendix | ||
| P67 | UVJO | chr16: 14947324-16359036 | 1.412 | DEL | 16p13.11 recurrent microdeletion | MYH11 | M | N | U | LUTM (phimosis) | Growth retardation | |
| P76 | COU-NOS | chr16: 15460510-17353355 | 1.893 | DEL | 16p13.11 recurrent microdeletion | MYH11 | M | N | N | Perthes disease | ||
| P04a | COU-NOS | chr17: 34851067-36293050 | 1.442 | DEL | RCAD deletion | ACACA, HNF1B | HNF1B | M | N | N | VUR, KHD | |
| P10 | COU-NOS | chr17: 34797485-36340198 | 1.543 | DEL | RCAD deletion | ACACA, HNF1B | HNF1B | M | N | N | Facial dysmorphism, pervasive developmental disorder | |
| P19 | UPJO | chr17: 34842442-36104994 | 1.263 | DEL | RCAD deletion | ACACA, HNF1B | HNF1B | M | N | U | KHD | |
| P37 | UPJO | chr17: 29051270-30377236 | 1.326 | DEL | NF1 microdeletion syndrome | NF1, SUZ12 | F | N | U | Neurofibromatosis type I | ||
| P46 | UVJO | chr22: 20706073-21386101 | 0.680 | DEL | DiGeorge A-D, DiGeorge B-D, DiGeorge C-D, DiGeorge C-E | M | Y | U | Mild grandular hypospadia, high arched palate, slight antimongolioid slant | |||
| P70 | UPJO | chr22: 18893888-20307511 chr22: 20706073-21571022 |
2.279 | DEL | DiGeorge A-B, DiGeorge A-D, DiGeorge C-D, DiGeorge A-D, DiGeorge B-D, DiGeorge C-E | DGCR8 | M | N | N | Facial dysmorphism, syndactyly, growth retardation | ||
| P47 | UPJO | chrX: 71693492-72092398 | 0.399 | DUP | Triple X | HDAC8 | F | N | U | |||
| P69 | UVJO | chrX: 149638017-155004401 | 5.366 | DEL | Xq28 rett syndrome | SLC6A8, MECP2, NSDHL, F8, L1CAM, ABCD1, MTM1, RAB39B, FLNA, DKC1, IKBKG, AVPR2 | NAA10, NSDHL, CCNQ, DKC1 | F | N | N | Interatrial defect | |
| P54 | UPJO | chr2: 60679700-66798661 | 6.119 | DUP | WDPCP | F | N | U | ||||
| P16 | UVJO | chr2: 141072471-142888527 | 1.816 | DUP | LRP1B | F | N | U | ||||
| P23 | UPJO | chr9: 137320857-137630692 | 0.310 | DUP | COL5A1 | F | N | U | ||||
| P52 | COU-NOS | chr14: 31495110-33293979 | 1.799 | DEL | HECTD1, ARHGAP5, AKAP6 | F | Y | U |
COU, congenital obstructive uropathy; CNV, copy number variants, GD, genomic disorder; CAKUT, congenital anomalies of the kidney and urinary tract; FHX, family history; UVJO, ureterovesical junction obstruction; DEL, deletion; TAR, thrombocytopenia-absent radius; M, male; N, no; DUP, duplication; VUR, vesicoureteral reflux; F, female; U, unknown; UPJO, ureteropelvic junction obstruction; COU-NOS, congenital obstructive uropathy—not otherwise specified; Y, yes; RCAD, renal cysts and diabetes; LUTM, lower urinary tract malformation; KHD, kidney hypodysplasia.
a
Individual also carries a single nucleotide variant.