Table 2.

Pathogenic SNVs in 35 known genes identified in 62 families with CAKUT by Whole-Exome Sequencing

Family ID	Gene	Sex	Ethnicity	Renal phenotype	Genome build	Chr: position	Nucleotide change	Amino- acid change	Other organ defects	Seen in CMG	ESP EA/AA	CADD score	Frequency in ExAc	Number of LOF in ExAc	Family segregation	Comment
1	PAX2	M,F	Spanish	RHD	Hg19	10: 102509528	c.70delG	p.G24fs	Optic nerve coloboma (previously undiagnosed)	no	N/R N/R	35	0	5	Yes; multiple individuals, AD	Known pathogenic variant, impacts medical management
2	HNF1B	M	Mixed Caucasian and African Caribbean	CRD	Hg19	17: 36070584	c.1132dupC	p.Q378fs	Gout, elevated LFTs (recent diagnosis) and increased echogenicity of pancreas (not noted prior to WES)	no	N/R N/R	35	0	0	De novo by WES and Sanger	Novel pathogenic variant, impacts medical management
3	EYA1	F	AA	VUR, MCDK	Hg19	8: 72183988	c.867+5G>A	n/a	No	no	N/R N/R	16.61	0	4	De novo by WES and Sanger	Known recurrent pathogenic variant in BOR; MCDK in this patient with VUR likely due to this variant, impacts medical management

AA African American; AD, autosomal dominant, BOR; Branchio-oto-renal syndrome; CADD, Combined Annotation Dependent Depletion; Chr, chromosome ; CMG, Center for Mendelian Genomics; CRD, Cystic renal dysplasia; ESP, Exome Sequencing Project; ExAc, Exome Aggregation Consortium ; LFT, liver function tests; LOF, loss-of-function; MCDK, Multicystic dysplastic kidney; N/R, none reported, RHD, Renal hypodysplasia; VUR, Vesicoureteral reflux.