TABLE II.
Seventeen Rare CNVs Identified and Validated in 15 Patients With Isolated Posterior Urethral Valves
| Locus | Genomic coordinates | Size (bps) | Type | Study subject ID | DECIPHER patients with overlapping CNVs & kidney & urinary tract anomalies | Gene(s)/transcript(s) |
|---|---|---|---|---|---|---|
| 1p35.1 | 33,543,972‥33,625,417 | 81,446 | Het Del | 5 | ADC; TRIM62 | |
| 1p34.1 | 46,557,405‥46,649,046 | 91,642 | Het Del | 7 | PIK3R3; RP11-322N21.2; RP4-533D7.5; TSPAN1 | |
| 1p31.1 | 82,947,889‥83,089,454 | 141,566 | Dupl | 12 | 266358: Hydronephrosis | Intergenic |
| 1q21.3 | 152,651,029‥153,284,782 | 633,754 | Dupl | 10 | C1orf68; KPRP; LCE1A; LCE1B; LCE1C; LCE1D; LCE1E; LCE1F; LCE2A; LCE2B; LCE4A; LCE6A; IVL; RP1-13P20.6; SMCP; SNORA31; SPRR1B; SPRR2A; SPRR2B; SPRR2D; SPRR2E; SPRR2F; LELP1; PRR9; RP1-140J1.1; LOR; PGLYRP3 | |
| 2p14–15 | 63,936,936‥64,110,691 | 173,756 | Dupl | 11 | ACA59; UGP2 | |
| 3p25.3 | 10,253,823‥10,332,468 | 78,646 | Dupl | 4 | 1876: Horseshoe kidney | GHRL; IRAK2; TATDN2 |
| 3q23 | 139,162,298‥140,231,134 | 1,068,837 | Dupl | 8 | 250665: Renal hypoplasia | 7SK; AC048346.1; CLSTN2; NMNAT3; RBP1; RBP2; RP11-13L2.2; RP11-166D18.1; RP11-31966.1; RP11-31966.3; RP11-442N1.1; RP11-442N1.2; RP11-68L1.1; RP11-68L1.2 |
| 3q28 | 191,907,021‥191,947,455 | 40,435 | Dupl/Tripl* | 9 | 256994: Hydronephrosis | FGF12 |
| 4q35.2 | 187,444,387‥187,593,959 | 149,573 | Dupl | 6 | 2384: Hypospadias, Micropenis 267301: Hypospadias | FAT1; MTNR1A |
| 6p22.3 | 16,446,643‥16,853,607 | 406,965 | Dupl | 3 | AL137003.1; ATXN1; RP1-151F17.1 | |
| 6q24.1 | 140,776,223‥142,206,247 | 1,430,025 | Dupl | 13 | 288262: Hydronephrosis | 7SK; AL356137.1; RP11-551A11.1; RP11-63E9.1; RP3-46062.2 |
| 12p13.2 | 10,874,088‥11,029,515 | 155,428 | Dupl | 14 | 266262: Hydronephrosis | CSDA; PRR4; RP13-81N3.2; TAS2R10; TAS2R7; TAS2R8; TAS2R9 |
| 16p13.12 | 13,938,976‥14,372,873 | 433,898 | Dupl | 2 | 264947: Hypospadias | CTA-276F8.2; CTD-2135D7.2; CTD-2135D7.3; CTD-2135D7.4; CTD-2135D7.5; ERCC4; MKL2; YRNA |
| 17q23.1–23.2 | 58,113,570‥60,325,665 | 2,212,096 | Het Del | 1 | 276114: Hypospadias 287822: Hypospadias | AC002994.1; AC008158.1; AC018628.1; AC079005.1; APPBP2; BCAS3; BRIP1; C17orf64; C17orf82; CA4;CTD-2319I12.1; HEATR6; INTS2; MED13; NACA2; PPM1D; RP11-15E18.1; SCARNA20; TBX2; TBX4; U6; USP32; Y_RNA; snoU13 |
| 18q21.31 | 56,018,908‥56,110,489 | 91,582 | Dupl | 8 | NEDD4L | |
| 20q13.2–13.31 | 52,395,038‥56,373,484 | 3,978,447 | Het Del | 15 | 251098: Hydronephrosis 278520: Male hypogonadism | AC005220.3; AC006076.1; AL117380.1; AL117380.2; AL121914.1; AL133232.1; AURKA; BCAS1; BMP7; C20orf43; CASS4; CBLN4; CSTF1; CTCFL; CYP24A1; DOK5; FAM209A; FAM209B; FAM210B; GCNT7; MC3R; MTRNR2L3; PCK1; PFDN4; PMEPA1; RAE1; RBM38; RN5S487; RP11-380D15.3; RP11-560A15.3; RP11-560A15.4; RP4-718J7.4; RP4-800J21.3; RP4-813D12.2; RP4-813D12.3; RP5-1010E17.1; RP5-1010E17.2; RP5-843L14.1; RP5-897D18.1; SPO11; TFAP2C; U3; U4atac; U6; YRNA; ZBP1; snoU13 |
| 21q22.11 | 31,523,734‥31,545,654 | 21,921 | Het Del | 14 | 286121: Hypospadias, Micropenis 288278: Micropenis | CLDN17 |
Het Del, heterozygous deletion; Dupl, duplication; Tripl, Triplication.
Bolded genes are highlighted in the figures and/or discussion section.
Coordinates (hg19) predicted using PennCNV.
*
CNV predicted as duplication by both algorithms was determined to be copy-number 4–5 (most likely a triplication) via qPCR.