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. Author manuscript; available in PMC: 2021 Jun 23.
Published in final edited form as: Genet Med. 2020 Jun 1;22(10):1673–1681. doi: 10.1038/s41436-020-0844-z

Table 2.

Overview of FOXC1 variant evaluation from ES data in 550 families with CAKUT, and for ES data of 100 negative control families with monogenic cause of SRNS.

Cohort CAKUT (N) CAKUT (%) SRNS (N) SRNS (%) OR p
1. Families with ES data 550 100
2. Families with rare FOXC1 variants (MAF <1%) 42 7.64% 1 1.00% 8.185 0.008
3. Families with rare FOXC1 variants determined to be pathogenica 8 1.45% 0 0% Infinity 0.616

CAKUT congenital anomalies of the kidney and urinary tract, ES exome sequencing, MAF minor allele frequency, OR odds ratio, SRNS steroid-resistant nephrotic syndrome.

a

The variants need to meet the following two criteria to be determined pathogenic. Criterion 1: High evolutionary conservation or functional severity prediction: a CADD score >20, OR be predicted to be deleterious by two of three in silico prediction tools, OR have a moderate to strong conservation at least to Xenopus tropicalis. Criterion 2: Allele frequency: the variant need to present in less than 20 heterozygous alleles in gnomAD.