Table 3.
Top 25 ranked genes across all groups and models
| Gene Name | Clinical Group | Best Model (Lowest FET P) | ||
|---|---|---|---|---|
| Inheritance Model/Collapsing Model | P Value (Fisher Exact Test) | OR [95% CI] | ||
| PKD1 | Mendelian or congenital CKD | Dominant/ultrarare, deleterious-predicted | 1.6×10−55 | 29.5 [19.5 to 44.8] |
| PKD2 | Mendelian or congenital CKD | Dominant/rare, LOF | 5.6×10−26 | 352.3 [56.1 to 13163] |
| COL4A5 | Mendelian or congenital CKD | Dominant/rare, LOF | 4.7×10−12 | 155.4 [21.5 to 6512] |
| CPT2 | All cases | Dominant/rare, missense/MTR50 | 4.0×10−7 | 4.5 [2.4 to 8.5] |
| AHDC1 | APOL1 cases | Dominant/rare | 5.91×10−7 | 14 [5 to 37.9] |
| SCLT1 | CUMC only | Dominant/rare/MTR50 | 2.0×10−6 | 8.2 [3.2 to 22.7] |
| SLC17A1 | AURORA only | Dominant/rare, missense | 3.15×10−6 | 4.8 [2.5 to 9] |
| TNFAIP6 | Glomerular neph. | Dominant/rare | 4.23×10−6 | 10.8 [3.7 to 33.6] |
| SLC9A2 | Glomerular neph. | Dominant/rare, missense/LIMBR50 | 5.04×10−6 | 4.4 [2.3 to 8.2] |
| ALDH1L2 | Glomerular neph. | Dominant/rare/LIMBR50 | 5.09×10−6 | 6.6 [2.9 to 14.9] |
| COL4A4 | All cases | Dominant/ultrarare/LIMBR50 | 1.01×10−5 | 8.5 [2.9 to 30.3] |
| PAX7 | Unknown or other | Dominant/rare, missense/LIMBR50 | 1.04×10−5 | 5.5 [2.6 to 10.5] |
| EFEMP2 | CUMC only | Dominant/rare, missense/MTR50 | 1.52×10−5 | 6.8 [2.7 to 18.1] |
| BAG3 | Hypertensive neph. | Dominant/rare/MTR50 | 1.73×10−5 | 8.5 [3.3 to 19.2] |
| RPS6KL1 | Glomerular neph. | Dominant/rare, missense/MTR50 | 2.06×10−5 | 6.1 [2.6 to 13.9] |
| KRTAP1 to 5 | COL4A3/4/5 cases | Dominant/rare, missense | 2.15×10−5 | 30.6 [7.2 to 98.8] |
| PDIA4 | All cases | Dominant/rare/MTR50 | 2.43×10−5 | 4.4 [2.1 to 9.3] |
| JPH1 | AURORA only | Dominant/rare, missense | 2.67×10−5 | 4.1 [2.1 to 7.7] |
| GNPNAT1 | All cases | Dominant/rare, missense | 2.71×10−5 | 27.4 [3.8 to 1193.7] |
| CREBRF | Unknown or other | Dominant/rare/LIMBR50 | 2.78×10−5 | 22.9 [5.2 to 99.7] |
| ANXA2 | CUMC only | Dominant/ultrarare, deleterious-predicted | 2.91×10−5 | 18.8 [3.7 to 181] |
| TUBA1C | Hypertensive neph. | Dominant/ultrarare, deleterious-predicted | 2.98×10−5 | 94.4 [7.5 to 4770] |
| GEMIN2 | PKD1/2 cases | Dominant/rare/LIMBR50 | 3.04×10−5 | 78.4 [11.3 to 469] |
| COL4A3 | All cases | Dominant/ultrarare, deleterious-predicted | 3.05×10−5 | 7.9 [2.6 to 28.4] |
| TMEFF1 | Tubulo-interstitial | Dominant/rare | 3.72×10−5 | 17.3 [4.7 to 53.2] |
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. Three genes that had high numbers of likely artifactual variants have been excluded. FET, Fisher Exact Test; LOF, loss of function; neph, nephropathy.