| Gene | Disease OMIM | Chromosome | Renal phenotype | Extrarenal phenotype | References |
| AGT | RTD | 1p42 | Reduced number of proximal tubules, short proximal tubules without brush border, atrophic loops of Henle and collecting ducts, closely packed glomeruli, marked thickening and disorganization of interlobular and preglomerular arteries | Large low-set ears, limb-positioning defects, arthrogryposis, lung hypoplasia, skull ossification defects | [29, 45] | AGTR1 | RTD | 3p24 | Similar to AGT phenotype, PUV | Similar to AGT phenotype | [29, 45, 46] | AGTR2 | — | Xq22-q23 | UPJ obstruction, megaureter, MCDK hydronephrosis, PUV | — | [38–41, 47] | ACE | RTD | 17q23.3 | Similar to AGT phenotype renal hypodysplasia, PUV | Similar to AGT phenotype | [29, 45, 46] | BMP4 | — | 14q22-q23 | Renal hypodysplasia | Cleft lip, microphthalmia | [48] | | | | | | | BMP7 Dlx5/Dlx6 p63 | SHFM #603273
| 3q27 | Urethral malformations | Split-hand/split-foot malformation | [49] | CDC5L | — | 46XX,t(6; 19) (p21; q13.1)
| Multicystic kidney dysplasia | — | [50] | Eya1 | BOR #113650
| 8q12 | Unilateral or bilateral renal agenesis renal hypodysplasia, VUR | Deafness, ear malformations branchial cysts | [51] | Fras1/ Fram2 | Fraser syndrome | 4q21 13q13. 3 | Renal agenesis/hypodysplasia | Ear and heart defects, syndactyly cryptophthalmos | [21, 51, 52] | FoxC1 | — | 6p25 | CAKUT | — | [53] | Gata3 | HDR syndrome #146255
| 10pter | Renal dysplasia | Hypoparathyroidism sensorineural deafness | [54] | HNF1β/ TCF2 | MODY5 #606391 RCAD #137920 GCKD #609886
| 17q12 | Renal hypodysplasia, cysts | Diabetes | [20, 55, 56] | Pax2 | Renal-coloboma syndrome
| 10q24 | Renal hypoplasia, VUR | Optic nerve coloboma branchyal cysts | [34, 57, 58] | Ren | RTD | 17q23.3 | Similar to AGT phenotype | Similar to AGT phenotype | [29, 45] | Ret | Renal agenesis #191830
| 10q11.2 | Absence of the kidney and ureter | Hirschsprung disease | [37] | Robo2 | — | 3p12.3 | VUR | Limb and facial defects | [44, 59–61] | Six2 | — | 2p16-p15 | Renal hypodysplasia | — | [48] | Slit2 | — | 4p15.2 | Hydroureter, supernumerary UBs | — | [59] | Umod | MCDK2 | 16p12.3 | Cysts in distal tubules and collecting ducts, renal dysplasia | — | [62, 63] | Upk3A | — | 22q13.31 | Renal agenesis/hypodysplasia | Facial and limb defects | [64, 65] | Usf2 | — | 46XX t(6;19) (p21; q13.1)
| Multicystic kidney dysplasia | — | [66] | XPNPEP3 | NPHP-like nephropathy | 22q13.2 | Renal cysts and dysplasia | — | [67] |
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AGTR: angiotensin II receptor type 1, AGTR2: angiotensin II receptor type 2, ARPKD: autosomal-recessive polycystic kidney disease, ADPKD: autosomal-dominant polycystic kidney disease, UPJ: ureteropelvic junction, VUR: vesicoureteral reflux, PUV: posterior urethral valves, UPJ: ureteropelvic junction, MCDK: multicystic dysplastic kidney, PUV: posterior urethral valve, RTD: renal tubular dysgenesis, RCAD: renal cysts and diabetes, MODY: maturity-onset diabetes, GCKD: glomerulocystic kidney disease, and NPHP: nephronophthisis, X-prolyl aminopeptidase (aminopeptidase P) 3, putative.
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