Version May 2024
| Primary disease | Gene | Kidney phenotype |
| Alagille syndrome | JAGGED1, NOTCH2 | Cystic dysplasia |
| Apert syndrome | FGFR2 | Hydronephrosis |
| Bardet-Biedl syndrome | BBS1 | Cystic dysplasia |
| Beckwith-Wiedemann syndrome | Dysregulation of imprinting in chromosome 11p15.5 | Medullary dysplasia |
| Branchio-Oto-Renal syndrome (BOR) | EYA1, SIX1, SIX5 | Unilateral/bilateral agenesis/dysplasia, hypoplasia, collecting system anomalies |
| Campomelic dysplasia | SOX9 | Dysplasia, hydronephrosis |
| Cenani-Lenz syndrome | LRP4 | Agenesis, UPJO |
| DiGeorge syndrome | 22q11.2 deletions | Agenesis, dysplasia |
| Fraser syndrome | FRAS1, FREM2, GRIP1 | Agenesis, dysplasia |
| Hypoparathyroidism, sensorineural deafness, and renal anomalies (HDR) | GATA3 | Dysplasia |
| Kallmann syndrome | KAL1, SEMA3A | Agenesis |
| Mammary-Ulnar syndrome | TBX3 | Dysplasia |
| Meckel Gruber syndrome | MKS1, MKS3, NPHP6, NPHP8 | Cystic dysplasia |
| Nephronophthisis | CEP290, GLIS2, RPGRIP1L, NEK8, SDCCAG8, TMEM 67, TTC21B | Cystic dysplasia |
| Okihiro syndrome | SALL4 | Unilateral agenesis, VUR, malrotation, cross-fused ectopia |
| Pallister-Hall syndrome | GLI3 | Agenesis, dysplasia, hydronephrosis |
| Renal coloboma syndrome | PAX2 | Hypoplasia, VUR |
| Renal cysts and diabetes syndrome | HNF1b, TCF2 | Dysplasia, hypoplasia |
| Renal dysplasia, isolated (cystic or non-cystic) | DACH1, BICC1, CDC5L, NRIP1 | Dysplasia |
| Renal hypoplasia, isolated | BMP4, RET, DSTYK | Hypoplasia, VUR; DSTYK mutations also associated with UPJO |
| Renal tubular dysgenesis | Renin, angiotensinogen, ACE, AT1 receptor | Tubular dysgenesis |
| Rubinstein-Taybi syndrome | CREBBP | Agenesis, hypoplasia |
| Simpson-Golabi Behmel syndrome | GPC3 | Medullary dysplasia |
| Townes-Brock syndrome | SALL1 | Hypoplasia, dysplasia, VUR |
| Zellweger syndrome | PEX1 | Cystic dysplasia |
| Smith-Lemli-Opitz syndrome | DHCR7 | Renal hypoplasia, cysts, and aplasia |
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