Table 1.

Genetic causes of a kidney dysplasia phenotype

	Kidney phenotype	Extrarenal phenotype	Mode of inheritance	Incomplete penetrance	Variable expressivity	Type of variant	Literature
EYA1	KHD, cystic dysplasia, unilateral/bilateral kidney agenesis, hydronephrosis, kidney malrotation, VUR	BOR syndrome 1, conductive/sensorineural deafness, preauricular pits, branchial anomalies, external ear anomalies, facial nerve palsy, arched palate, (congenital cataracts reported once)	AD	Yes	Yes	SNV, indel, CNV	Hwang, 2013, Kidney Int Heidet, 2017, J Am Soc Nephrol Unzaki, 2018, J Hum Gen Abdelhak, 1997, Nat Genet
GATA3	KHD, cysts, VUR, FSGS, single kidney	HDR syndrome, hypoparathyroidism with hypocalcemia, deafness, uterine anomalies	AD	Yes	Yes	SNV, CNV	Hwang, 2013, Kidney Int Heidet, 2017, J Am Soc Nephrol Belge, 2017, NDT Muroya, 2001, J Med Genet Van Esch, 2000, Nature
GREB1L	KHD, unilateral/bilateral kidney agenesis, VUR, pelvic kidney, megaureter, duplex ureter	Uterine malformations	AD	Yes	Yes	SNV, indel	De Tomasi, 2017, AJHG Sanna-Cherchi, 2017, AJHG Brophy, 2017, Genetics
HNF1B	KHD, multicystic dysplasia, single kidney, UPJO, hyperuricemia, hypomagnesemia, oligomeganephronia	Diabetes mellitus (MODY5), uterine malformations, pancreas hypoplasia/agenesia, elevation of liver transaminases, MRKHS	AD	Yes	Yes	SNV, indel, CNV	Hwang, 2013, Kidney Int Heidet, 2017, J Am Soc Nephrol Bekheirnia, 2017, Genet Med Bingham, 2002, Genet Med Edhill, 2008, NDT Ishiwa, 2019, Pediatr Nephrol Nakayama, 2010, Pediatr Nephrol Thomas, 2011, Pediatr Nephrol Ulinski, 2006, J Am Soc Nephrol Madariga, 2013, CJASN Horikawa, 1997, Nat Genet
PAX2	KHD, cystic dysplasia, oligomeganephronia, single kidney, VUR, horseshoe kidney	Optic nerve anomalies, retinal coloboma, morning glory syndrome, hearing loss	AD	Yes	Yes	SNV, indel, CNV	Hwang, 2013, Kidney Int Heidet, 2017, J Am Soc Nephrol Bekheirnia, 2017, Genet Med Ishiwa, 2019, Pediatr Nephrol Thomas, 2011, Pediatr Nephrol Madariga, 2013, CJASN Taranta, 2007, Clin Nephrol Sanyanusin, 1995, Nat Genet
PBX1	KHD, oligomeganephronia, horseshoe kidney, single kidney, duplex ureter, VUR	Developmental delay, hypotonia, ear malformations, deafness, heart defects, cryptorchidism, bone malformations, mild fascial dysmorphism	AD	unknown	Yes	SNV, CNV	Heidet, 2017, J Am Soc Nephrol Le Tanno, 2017, J Med Genet
SALL1	KHD, VUR, dystopic kidney	Townes-Brocks syndrome, dysplastic ears, bifid thumbs, triphalangeal thumbs, anorectal malformations, sensorineural hearing loss, facial nerve palsy, external ear anomalies, heart defects, microcephaly, developmental delay	AD	No	Yes	SNV, CNV	Hwang, 2013, Kidney Int Unzaki, 2018, J Hum Gen Kohlhase, 1998, Nat Genet
Large CNVs (e.g. 1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2)	KHD, CAKUT	Diverse	n/a	unknown	unknown	CNV	Bekheirnia, 2017, Genet Med Sanna-Cherchi, 2012, AJHG Verbitsky, 2019, Nat Genet Haller, 2018, PNAS Lopez-Rivera, 2017, NEJM

Note: For detailed information on the cited references please refer to Supplementary data.

Abbreviations: AD, autosomal dominant; BOR, branchiootorenal syndrome (OMIM #113650); indel, short insertion/deletion; HDR, hypoparathyroidism, sensorineural deafness, and renal dysplasia (OMIM #146255); KHD, kidney hypodysplasia; MRKHS, Mayer-Rokitansky-Kuster-Hauser syndrome (OMIM %277000); SNV, single nucleotide variant; UPJO, ureteropelvic junction obstruction.