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["Supplementary Table 16. Small CNVs Overlapping with DSD Genes versus CNVs in DECIPHER"]
["Gene","CNV Size (Kb) (This Study)","Size Range (Kb-Mb) (DECIPHER)","Smallest Size in DSD (DECIPHER)","Phenotype (DECIPHER)","Px with Urogenital Reproductive Anomalies","Total Px","XY","XX","not known","Total Gain","Total Loss"]
["AHRR","8.8-19.8","76.13 kb- 42.57 Mb","5.2 MB","hypospadias (1), adrenogenital syndrome (1), aplasia/hypoplasia of the breasts (1), uterine neoplasm (1), Cryptorchidism (1), Bilateral cryptorchidism (1), ureteral artesia  (1)",7,59,4,0,1,1,4]
["ANOS1 (KAL1)",7,"46.96 kb- 155.27 Mb","49.96 Kb","Micropenis (2), Hypospadias (2), Urethral valve (1), Bilateral cryptochidism (1), Cryptochidism (1), Azoospermia (1), Abnormality of the labia (1), Labial hypertrophy (1)",10,130,6,0,2,4,3]
["AR","8.4-190.5","443.41 kb- 155.27 Mb","443 KB","multiple renal cysts (1)",1,53,0,0,1,1,0]
["ARX",23,"1.7 kb- 155.27 Mb","1.8 Mb","Cryptorchidism (1), Abnormality of the labia (1), Labial hypertrophy (1)",3,80,3,0,0,2,1]
["ATRX","2.2-5.2","106.4 Kb-155.27 Mb","81 Mb","Genital hypolasia (1), Cryptorchidism (1), Primary ovarian failure (1), Labial hypertrophy (1)",4,67,3,1,0,0,2]
["AXIN1","2.1-12.7","431.82 kb-  14.44 Mb","11 Mb","Absent of nipples (1), renal cysts",1,32,0,1,0,0,1]
["BBS9",30,"58.8 Kb-58.02 Mb","22 Mb","bifid uvula (1), hydrocele testis (1)",2,13,1,1,0,0,2]
["BNC2","1.9-3.7","161.51 kb- 140.88 Mb","17 Mb"," Abnormality of the genital system (1), Urethrocele (1), hydronephrosis",2,37,0,2,0,2,0]
["CAMK1D",6,"326.84 kb- 46.13 Mb","2 Mb","Ureteral duplication (1), hydronephrosis",1,20,0,1,0,0,1]
["CHD7","2-11.4","8.3 Kb-146.06 Mb","37 Kb","Hypospadias (1), Abnormaility of the female genitalia (1), wide intermamillary distance (1)",3,22,1,2,0,1,2]
["CNTNAP3","95.7-374.0","1.07 Mb- 140.88 Mb","141 Mb"," Urethrocele (1)",1,17,0,1,0,1,0]
["CREBBP",5,"120 Kb-26.47 Mb","3.5 Mb (1 bp)","Hypoplastic labia majora (1), Bilateral cryptorchidism (1), Precocious puberty in females (1), Ovarian cysts (1), Hypospadias (1), Crytorchidism (1)",6,50,2,3,2,3,1]
["CTNNA3","6.6-92.2","21.24 kb- 29.60 Mb","28.5 Mb","Cryptorchidism (1)",1,51,1,0,0,0,1]
["CTNNB1","9.6-19.1 "," 437 Kb-43.15 Mb","5 Mb","Macroorchidism (1), gynecosmastia",1,13,0,0,1,0,1]
["CXCL12","6.9-8.1","46.13 Mb","none","none",0,1,0,0,0,0,0]
["DHRSX","1.1-48.8","21.47 kb-  155.27 Mb","346 Kb","Hypospadias (1), Male infertility (1), Cyptochidism (2)",4,103,3,0,1,3,1]
["DMD","1.1-17.4","15.9 Kb-155.27 Mb","155 Kb","Scrotal hypoplasia (1), Adrenal hypoplasia (1), Precocious menopause (1), Abnormalitly of labia (1), Cryptochidism (1), Labial hypertrophy (1)",6,125,5,1,0,3,3]
["EP300","3.1-3.6 ","138 Kb-42.82 Mb","18 Mb","Cryptorchidism (1),  Hypospadias (1), Micropenis (1)",3,21,2,0,0,1,0]
["ESR1","25-28","165.37 kb- 170.49 Mb","7.8 Mb","Abnormality of the testis (1), Delayed puberty (1), Cryptorchidism (1)",3,17,2,0,0,0,2]
["ESR2","1.5-12.8","15.58 kb- 22.87 Mb","none ","none",0,4,0,0,0,0,0]
["FAM167A-AS1 (C8orf12)","15.9-19.2","634.29 kb- 146.06 Mb","3.7 Mb","Cryptorchidism (2), Hypospadias (3), Vesicouteral reflux (2), Anal atresia (1), Ureteral artesia (1), Anteriorly placed anus (1)",10,73,6,5,0,3,8]
["FGD1",507,"3.8 Mb-155.27 Mb","3.9 Mb","Decreased testicular size (1), Micropenis (1), Enlarged penis (1), Macroorchidism (1), Cryptorchidism (1), Labial hypertrophy (1)",6,56,2,0,3,2,3]
["FGF7",139,"15.8-80 Mb","3.9 Mb","Early onset of puberty (1), Micropenis (1)",2,4,1,1,0,2,1]
["FGFR2","4-6","16.4-52 Mb","12 Mb","Vesicoureteral reflux (2), Abnormality of the labia (1), Ectopic anus (1), Cryptorchidism (1), Ambiguous genitalia, male (1), Hypospadias (1)",7,23,3,1,0,0,3]
["FLNA","10.7-22.9","23.3 Kb-155.27 Mb","507 Kb","Cryptorchidsim (3), Scrotal hypoplasia (1),  Recurrent urinary tract (1), Ovarian cysts (1) , Labial hypertrophy (1)",7,145,3,5,0,4,4]
["FLT1","2.4-11.4","3.2 Mb- 95.66 Mb","96 Mb","abnormal adrenal gland",1,7,0,0,0,0,0]
["FRAS1 ",11.5,"69.21 kb- 36.41 Mb","7 Mb","Cryptorchidism (1)",1,27,1,0,0,1,0]
["FRG1BP","121.4-345.2","372 Kb-55 Mb","none","none ",0,0,0,0,0,0,0]
["GATA4",7,"91.78 kb- 146.06 Mb","3.7 Mb","Cryptorchidism (2), Hypospadias (3), Vesicoureteral reflux (2), Ureteral artesia (1), Anteriorly placed anus (1)",9,77,6,3,1,2,8]
["GFRA1","18.3-22","308.83 kb- 52.34 Mb","6.7 Mb","Cryptorchidism (1)",1,17,1,0,0,0,1]
["GNRH1",64,"1.2-146 Mb","23 Mb","Cryptorchidism (1), Micropenis (1), Ureteral atresia (1), Anteriorly placed anus (1)",4,35,2,1,1,2,2]
["GRIP1 ","8.4-23.9","24.09 kb- 101.3Mb","none ","none ",0,12,0,1,0,0,1]
["HHAT",3,"42.12 kb- 104.25 Mb","71.6 Mb","Primary ovarian failure (1)",1,7,0,1,0,1,0]
["HSD17B3",7,"4.67 Mb- 140.88 Mb","7 Mb","Absent nipples (1), Wide intermamillary distance (1),  Hypoplastic genitalia (1), Urethrocele (1)",4,15,2,1,1,1,3]
["INSR","7-29.1","97.68 kb- 12.33 Mb","12 Mb","Abnormality of genitourinary system (1)",1,11,1,0,0,1,0]
["KANK1 ","4.1-32.1","34.7 Kb-140.88 Mb","5.7 Mb","Ambigious gentalia, female (2), Micropenis (1), Inappropriate sexual behavior (1), Vesicoureteral reflux (1), Abnormality of the genital system (1), Bilateral cryptochidism (2), Ectopic anus (2), Urethrocele (1)",10,109,5,6,1,1,11]
["KRAS","4.2-12.2","866 Kb-41.69 Mb","7 Mb","Cryptorchidism (1), Vesicoureteral reflux (1)",2,22,1,1,0,1,1]
["MOV10L1","4.6-10","457.12 kb- 42.82 Mb","1.1 Mb","Hypospadias (2), Micropenis (1), renal agenesis",3,91,3,2,0,1,4]
["MTHFR",31,"855.48 kb- 24.41 Mb","5.7 Mb","Cryptorchidism (2), Wide intermamillary distance (1), Hypospadias (1)",4,24,4,0,0,2,2]
["NLGN4X","1.5-4.8","47.5 Kb-155.27 Mb","2.9 Mb","Absent nipples (1), Gynecomastia (1), Micropenis (1),  Delayed puberty (1), Hypospadias (1), Male infertility (1), Cryptordism (2), Early onset of puberty (1), Azoospermia (1)",10,126,6,1,2,4,5]
["NOTCH1",4.371,"230.4 Kb-140.88 Mb","2.2 Mb","Cryptorchidism (1), Hypospadias (1), Micropenis (2), Urethrocele (1)",5,34,2,1,0,2,1]
["NOTCH2",29,"259.8 Kb-14.55 Mb","none","none ",0,13,0,0,0,0,0]
["NOTCH3","2.4-27","983.88 kb- 10.31 Mb","984 Kb","Gynecomastia (1), Percocious puberty in male (1)",2,12,2,0,0,1,1]
["NR0B1","4.9-5.6","1.21 Mb- 155.27 Mb","6.7 Mb","adrenal hypoplasia, precocious menopause (1), Labial hypertrophy (1)",2,76,1,1,0,0,2]
["NR5A1 ",18,"3.18 Kb-140.9 Mb","16.7 Mb","unilateral renal agenesis (1), urethrocele (1)",2,10,0,2,0,2,0]
["NR5A2","1.1-4.5","1.77 Mb- 104.25 Mb","72 Mb","Primary ovarian failure (1)",1,11,0,1,0,1,0]
["OCA2","2.4-29.3 ","583.2 Kb- 7.7 Mb","540 Kb","hypoplasia of penis (1), cryptorchidism (2), scrotal anomaly (1), male external genitalia anomaly (2), hypospadias (1), aplasia of the testis (1) , ureteral duplication (1)",9,18.8,7,0,1,5,3]
["PBX1","1.2-7.1","275.89 kb- 104.25 Mb","876 Kb","Vesicoureteral reflux (1), Cryptorchidism (1), Ectopic anus (1), Micropenis (1), renal dysplasia",4,14,1,1,null,1,1]
["PCDH17",6.653,"4.83 Mb- 95.66 Mb","4.8 Mb","Urinary incontinence (1)",1,17,1,0,0,1,0]
["PCSK1",24.8,"147 kb- 13.31 Mb","13 Mb","Cryptorchidism (1)",1,12,1,0,0,0,1]
["PDGFRA","2.9-18.8","173.88 kb- 29.20 Mb","12 Mb","Anteriorly placed anus (1)",1,9,0,1,0,1,0]
["PIP5K1B","1.7-4.1","212.78 kb- 140.88 Mb","12.6 Mb","Wide intermamillary distance (1),  Urethrocele (1)",2,25,1,1,0,1,1]
["POR",15,"1 Mb- 35.4 Mb","2.6 Mb","Precocious puberty (1) ",1,18,1,0,0,1,0]
["PTCH1","3.7-16.4","5.3 Kb-140.88 Mb","8.9 Mb","Hypoplastic genitalia (1), Cryptorchidism (1),  Urethrocele (1)",3,18,2,1,0,1,2]
["PTPN11","16.4-37","29.8-101.30 Mb","none (1 bp)","cryptorchidism (1), wide intermammalary distance",1,4,0,0,0,0,0]
["RAF1","3.9-13.6","145.06 kb- 39.59 Mb","145 Kb","Aplasia of testes (1), Micropenis (1), Wide intermamillary distance (1)",3,22,1,1,0,2,0]
["ROCK2","28.1-42.2","524.74 kb- 89.01 Mb","34 Mb","Micropenis (1)",1,16,1,0,0,1,0]
["SHOX","41.5-41.7","32.02 kb- 155.27 Mb","61.7 Kb","Vaginal atresia (1), Male hypogonadism (1), Abnormality of the testis (1),  Male infertility (1), Cryptorchidism (1), Azoospermia (1)",6,130,4,0,2,4,2]
["SNRPN","14.8-36.5","4.09 kb- 79.78 Mb","4.4 Mb","Abnormality of male external genitalia (1), Hypospadias (1), Ureteral duplication (1), Aplasia of the testes (1), Abnormality of male external genitalia (1),Cryptorchidism (1), Abnormality of the scrotum (1)",7,194,7,0,1,5,3]
["SOS1",18,"10.3 Kb-89.01 Mb","27.2 Mb","kidney anomaly (1)",1,18,0,0,0,0,0]
["SOX9","1.6-6","836 Kb-66.75 Mb","none","none ",0,6,0,0,0,0,0]
["SRD5A2",6.9,"253.91 kb- 89.01 Mb","254 Kb","Anal atresia (1), Micropenis (1)",2,15,2,0,0,2,0]
["SUPT3H","9.8-10","117.85 kb- 170.49 Mb","none (531 Kb)","none (1 - adrenal glands anomalies, multiple renal cysts, renal agenesis)","0 (1)",0.7,0,0,0,0,0]
["TGFB1",4.015,"72.32 Kb","none ","none ",0,1,0,0,0,0,0]
["TP63","1.4-11.8","29.72 kb- 104.32 Mb","1.9 Mb","Supernumerary nipples (1)",1,27,2,1,0,2,1]
["VAMP7","1.5-94 ","147.30 kb- 155.27 Mb","5 Mb","Precocious menopause (1), Ovarian cysts (1), Primary ovarian failure (1)",3,81,0,3,0,0,3]
["WNT2",6,"562.18 kb- 44.49 Mb","43 Mb","Anal artresia (1), Urethral Stricture (1)",2,23,1,0,0,1,0]
["WWOX","1.8-148.2","32.98 kb- 29.95 Mb","33 Kb","Precocious puberty in females (1), Hydocele testis (1), Vesicoureteral reflux (1), Inverted nipples (1)",4,32,1,3,0,2,2]

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