Table 4 |. Gene Prioritization (GPS) for the genes across the four loci identified with genome-wide significance.
Shown are genes across the four loci, for which we found any relevant evidence: (i) blue: gene contains at least one credible set variant that was protein-altering (missense, non-mediated decay, NMD, or altered splicing; Supplementary Table 6A, information obtained from VEP49); (ii) orange: the gene’s expression shows a modulation by any of the signal’s credible set variant (expression quantitative trait loci, eQTL, in NephQTL50 or GTEx v851; Supplementary Table 6B), (iii) gene shows a kidney phenotype in mouse or human (MGI52, OMIM53; Supplementary Table 7A&B). The full GPS shows all genes overlapping the four loci (Supplementary Table 8) and the online version is searchable and customizable (i.e. the weights per column can be altered) to re-sort the table reflecting other preferences (www.genepi-regensburg.de/rapiddecline).
| Any credible set variants in gene | eQTL-modulated expression by any credible set variant | Evidenced kidney phenotype | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Weight | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| Locus name | Locus no. | Gene | Chromosome | Distance to 1st signal variant | #credible set variants in gene | Gene Priority Score | Missense | NMD | Altered splicing | NephQTL glomerulus | NephQTL tubulointerstitium | GTEx v8 kidney tissue | GTEx v8 any other tissue | In mice (MGI) | In human (OMIM) |
| [UMOD-PDILT] | 1 | UMOD | 16 | 0 | 10 | 2 | |||||||||
| [UMOD-PDILT] | 1 | PDILT | 16 | 2,846 | 1 | 1 | |||||||||
| [WDR72] | 2 | WDR72 | 15 | 0 | 37 | 2 | |||||||||
| [PRKAG2] | 3 | PRKAG2 | 7 | 0 | 16 | 2 | |||||||||
| [PRKAG2] | 3 | GALNTL5 | 7 | 246,675 | 0 | 1 | |||||||||
| [OR2S2] | 4 | OR2S1P | 9 | 75,251 | 0 | 1 | |||||||||
| [OR2S2] | 4 | GNE | 9 | 276,506 | 0 | 1 | |||||||||
| [OR2S2] | 4 | CD72 | 9 | −319,507 | 0 | 1 | |||||||||
Locus name=Nearest gene(s), stated in brackets to distinguish from gene or protein names, #credible set variants in gene region=#variants in the 99% credible set overlapping the gene’s region, Gene Priority Score=Cumulative score (here: weighing all categories equally; see Supplementary Table 8 for all genes in locus regions and online version for customization of weights), Blue section: gene contains ≥1 credible set variant overlapping the gene with relevant function (yes=blue/no=white); Orange section: locus/signal contains ≥1 credible set variant that modulates gene expression (yes=orange/no=white) in NephQTL glomerulus, NephQTL tubulointerstitium, GTEx v8 kidney tissue or GTEx v8 any tissue;Green section: gene shows a kidney-related phenotype (yes=green/no=white) in MGI Mouse kidney phenotype or OMIM Human kidney phenotype.