Table 2.
Best-ranked models
| Gene Name | OMIM Phenotype No. | Known Mendelian Disease Inheritance | Best Model (Lowest FET P) | ||
|---|---|---|---|---|---|
| Clinical Group/Inheritance Model/Collapsing Model | P Value (Fisher Exact Test) | OR [95% CI] | |||
| Known Mendelian nephropathy genes | |||||
| PKD1 | 173900 | Dominant/multiple | Mendelian or congenital CKD/dominant/ultrarare, deleterious predicted | 1.6×10−55 | 29.45 [19.5 to 44.8] |
| PKD2 | 613095 | Dominant/multiple | Mendelian or congenital CKD, dominant/rare, protein-truncating | 5.6×10−26 | >352 [56 to >13164] |
| COL4A5 | 301050 | X-linked dominant/multiple | Mendelian or congenital CKD/dominant/rare protein-truncating | 4.7×10−12 | >155 [21 to >6512] |
| COL4A4 | 203780/141200 | Autosomal dominant and recessive | All cases/dominant/ultrarare non-benign/LIMBR50 | 1.0×10−5 | 8.53 [3.1 to 23.7] |
| COL4A3 | 104200/203780/141200 | Autosomal dominant and recessive | All cases/dominant/ultrarare deleterious predicted | 3.1×10−5 | 7.92 [2.8 to 22.2] |
| No prior associations with Mendelian nephropathy | |||||
| SLC17A1 | NA | Not previously reported | AURORA only/dominant/rare missense-only | 3.15×10−6 | 4.8 [2.5 to 9.0] |
| CPT2 | 255110/600649/608836 | Autosomal recessive | All cases/dominant/rare missense-only/MTR50 | 4.0×10−7 | 4.50 [2.4 to 8.5] |
| SCLT1 | NA | Not previously reported | CUMC only/dominant/rare, nonbenign/MTR50 | 2.0×10−6 | 8.25 [3.5 to 19.7] |
To calculate OR and 95% CI for undefined events due to zero-cell counts we force a single count to zero cell and specify greater (>) than resulting OR and undefined 95% CI. Gene names are italicized. FET, Fisher Exact Test.