Supplementary Table 1. Summary of Clinical Characteristics and Genotypes Compared to Reported

Supplementary Table 1. Summary of clinical characteristics and genotypes compared to reported patients with overlapping CNVs and renal anomalies.

Total RefSeq Entriesc in patients DECIPHER and in this study and Renal Extra-renal CNV literature patients with genes in minimal Case Phenotype anomalies Locus and coordinatesa CNV type and coordinates in reported patients Phenotypes type overlapping CNVs and overlap region in relatives urinary tract anomalies compared to DECIPHER/literat ure patients UBE2J1, RRAGD, ANKRD6, LYRM2, MDN1, CASP8AP2, GJA10, BACH2, MIR4464, 6q15q16.1 1 VUR ADHD Dup MAP3K7, (90,112,800-96,421,497) MIR4643, CASC6 EPHA7, TSG1, MANEA-AS1, MANEA

7q31.1 FOXP2 138 VUR Speech delay Del (113,823,505-114,134,615)b PDXDC1, MIR1972-2, MIR1972-1, NTAN1, RRN3, MIR6511B-1, 2141: abnormal kidney. Dup: 14,944,560-16,305,736 MIR3180-4, 250060: bladder defect. Del: 14,944,560-16,305,736 16p13.11 NPIPA5, MPV17L, 75 VUR Del 993: renal agenesis, Dup: 15,504,454-17,409,257 (14,960,247-16,210,889) C16orf45, ureteral atresia KIAA0430, Sanna-Cherchi et al., Dup: 15.03-15.80 MIR6506, NDE1, 2012: renal MIR484, MYH11, hypodysplasia FOPNL, ABCC1, ABCC6

156 VUR Mother Hypertension Dup 19p13.3 249482 : VUR Del: 2,977,780-5,187,666 DOHH, FZR1, duplex encephalopathy (3,445,313-4,020,426) . C19orf71, kidney and + Learning 258067 :VUR. Del: 3,259,054-5,450,303 MFSD12,HMG20B, bed wetting difficulties GIPC3, TBXA2R, 273505: Hydronephrosis Del: 2,415,448-4,936,950 CACTIN-AS1, CACTIN, PIP5KiC, TJP3, APBA3, MRPL54, RAX2, MATK, ZFR2, Risheg et al., 2013: ATCAY, NMRK2, 1.renal agenesis Del: 3.37-4.506b DAPK3, MIR637, 2. hydronephrosis Del: 3,814,392-4,605,977b EEF2, SNORD37, PIAS4, ZBTB7A

SYN2, TIMP4, PPARG, TSEN2, 258291 and 260758: Dup: 11,171,653-12,099,656 C3orf83, MKRN2, 3p25.1p25.2 renal dysplasia 27 PUV Dup RAF1, TMEM40, (11,932,005-12,874,890) 615: Micropenis and Dup 12,615,855-12,760,917 CAND2, RPL32, aplasia of testes SNORA7A

9p24.2p24.1 SLC1A1, SPATA6L 184 PUV Del (4,390,991-4,606,385) COX10, CDRT15, HS3ST3B1, MGC12916,CDRT7, 17p12 123 PUV Del CDRT8, PMP22, (14,041,754-15,390,352) MIR4731, TEKT3, CDRT4, TVP23C

Isidor et al., 2010: 3 SULF1, SLCO5A1, Congenital unrelated patients PRDM14, NCOA2, Del: minimal deleted region 70,326,013-71,052,779*. hypothyroidism 8q13.2q13.3 Hydronephrosis TRAM1, 18 PUV Dup + Left (70,063,994-72,748,846) LOC286190, Del and mutations involving EYA1 associated with hydrocoele Abdehak et al., 1997; LACTB2, XKR9, branchio-oto-renal syndrome (OMIM 113650) Orten et al., 2008 EYA1 PSMA1, PDE3B, 11p15.2 CYP2R1, CALCA, 142 PUV Dup (14,535,952-15,200,169) CALCB, INSC

SLC31A2, FKBP15, SLC31A1, CDC26, PRPF4, RNF183, 9q32 77 PUV Dup WDR31, (114,937,474-115,348,530) BSPRY,HDHD3, ALAD, POLE3, C9orf43, RGS3 IDS, CXorf40A, MAGEA9B, MAGEA9, HSFX2, Xq28 40 PUV Dup 3875: Renal dysplasia. Dup: 148,486,388-148,971,029 HSFX1,TMEM185 (148,339,952-149,013,489) A, MAGEA11 MAGEA8, Cxorf40B Paternal LRGUK, SLC35B4, greatgrand- AKR1B1, 7q33 88 MCDK (L) father Dup AKR1B10, (133,477,997-134,039,874) solitary AKR1B15, BPGM kidney TBC1D31, FAM83A, MIR4663, 8q24.13 93 DK (L) Del C8orf76, ZHX1, (124,231,161-124,421,591) ATAD2

KIRREL (NEPH1), CD1D, CD1A, CD1C, CD1B, 1q23.1 CD1E, OR10T2, 15 MCDK (L) Dup (156,158,148-156,847,101) OR10K2, OR10K1, OR10R2, OR6Y1, OR10X1, OR10 Z1

85 MCDK (L) Macrocephaly + Del/Dup 17q12 Chr17: ZNHIT3, Neurocognitive (31,889,664-33,323,678) MYO9, PIGW, and and Dup GGNBP2, neurobehaviour 22q11.21 DHRS11,MRM1, problems (17,277,228-18,635,160) LHX1,AATF, MIR2909, ACACA,C17orf78, TADA2A, DUSP14, SYNRG, DDX52, MIR378J, HNF1B, YWHAEP7 Chr22: DGCR6, PRODH, DGCR5,DGCR9, DGCR10,DGCR2,D GCR11,DGCR14,TS SK2,GSC2,LOC100 652736, SLC25A1, CLTCL1, HIRA, MRPL40, C22orf39, UFD1L, CDC45, CLDN5, LINC00895, SEPT5, SEPT5-GP1BB, GP1BB, TBX1, GNB1L, C22orf29, TXNRD2, COMT, MIR4761, ARVCF, TANGO2, MIR185, DGCR8, MIR3618,MIR1306, TRMT2A, RANBP1, ZDHHC8, LOC388849, LOC284865, LINC00896, RTN4R, MIR1286 FAM169B, IGFR1, MIR4714, hydronephro- 15q26.3 PGPEP1L, SYNM, 169 Dup ureterosis (R) (96,505,470-97,823,818) TTC23, LRRC28, HSP90B2P

DRD5, SLC2A9, hydronephro- 72 Dup 4p16.1(9,356,195-9,688,100) WDR1 ureterosis (R)

hydronephro- 177 Dup XYY ureterosis (L) a start and end positions are based on UCSC genome build hg18 except Case 40 and 138 which are based on build hg19 b start and end positions are based on UCSC genome build hg19 c list includes genes and non-coding RNAs (microRNA (MIR)) in chromosomal region using UCSChg18 (http://www.genome.ucsc.edu).

*Coordinates from whole-genome oligonucleotide array CGH (probe co-ordinates) Isidor et al, 2010

ADHD= Attention deficit hyperactivity disorder

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