Table 4. Gene Prioritization Within Genome-Wide Significant Loci.
| Gene | Score | Expression FPKM, Mean (SD) | TWASa | PASCAL P Value | Mouse Model, P Valueb | |||
|---|---|---|---|---|---|---|---|---|
| Retina, Macular | Retina, Peripheral | Retinal Pigment Epithelium or Choroid, Macular | Retinal Pigment Epithelium or Choroid, Peripheral | |||||
| rs11184959 on chromosome 1:106 777 024-107 851 213 | ||||||||
| PRMT6c | 2 | 3.57 (0.77) | 3.61 (0.96) | 1.41 (0.86)d | 2.39 (0.46)d | 0 | 0.599 | 5.37 × 10−5 |
| NTNG1 | 0 | 1.95 (0.79) | 1.66 (0.73) | 0.72 (0.24) | 0.97 (0.27) | 0 | 0.628 | NA |
| rs2839127 on chromosome 21:47 099 280-48 073 550 | ||||||||
| LSSd | 4 | 8.11 (2.44)e | 2.36 (1.02)e | 3.19 (0.88) | 3.51 (1.1) | 6f | 1.44E-03g | 8.13 × 10−6 |
| PCNTd | 2 | 2.43 (0.36)d | 1.59 (0.43)e | 1.84 (0.84) | 1.26 (0.19) | 1 | 0.010g | NA |
| SPATC1L | 2 | 1.23 (0.49) | 1.23 (0.34) | 2.24 (0.5) | 2.07 (0.6) | 30f | 2.98E-04g | NA |
| YBEY | 2 | 2.59 (1.12) | 2.13 (0.25) | 2.27 (0.61) | 2.18 (0.67) | 37f | 0.015g | NA |
| PCBP3c | 2 | 6.75 (1.17) | 5.92 (1.78) | 0.51 (0.26)d | 0.24 (0.13)c | 0 | 0.010g | NA |
| MCM3AP | 1 | 3.75 (0.51) | 3.11 (0.76) | 3.01 (0.56) | 2.81 (0.56) | 2 | 0.021g | NA |
| C21ORF58 | 1 | 0.49 (0.14) | 0.49 (0.15) | 0.14 (0.13) | 0.11 (0.08) | 1 | 0.010g | NA |
| FTCD | 1 | 0.04 (0.04) | 0.01 (0.02) | 0 (0.01) | 0 (0) | 0 | 2.93E-04g | NA |
| DIP2A | 1 | 1.8 (0.48) | 1.74 (0.53) | 0.67 (0.18) | 0.61 (0.11) | 6f | 0.059 | >.99 |
| PRMT2 | 1 | 4.92 (0.93) | 4.17 (0.39) | 4.39 (0.88) | 4.32 (1.14) | 5f | 0.197 | NA |
| COL6A1d | 1 | 4.62 (1.38)e | 2.76 (1.24)e | 24.76 (10.71) | 36.51 (14.39) | 0 | 0.701 | NA |
Abbreviations: C21ORF58, chromosome 21 open reading frame 58; COL6A1, collagen 3 type VI alpha 1 chain; DIP2A, disco interacting protein 2 homolog A; FPKM, fragments/reads per thousand base-pairs of transcript per million reads of the respective gene; FTCD, formimidoyltransferase 1 cyclodeaminase; LSS, lanosterol synthase; MCM3AP, minichromosome maintenance complex component 3 associated protein; NA, not applicable; NTNG1, netrin G1; PASCAL, Pathway scoring algorithm; PCBP3, poly(RC) binding protein 3; PCNT, pericentrin; PRMT2, protein arginine methyltransferase 2; PRMT6, protein arginine methyltransferase 6; SPATC1L, spermatogenesis and centriole associated 1–like; TWAS, transcriptome-wide association study; YBEY, YbeY metalloendoribonuclease.
Number of nominally significant TWAS results of 43 total possible results for gene over all tissues in Genotype-Tissue Expression project; number of tissues with significant local expression quantitative trait loci according to the expression quantitative trait loci.
Combined Retinal Morphology phenotype P value according to the International Mouse Phenotyping Consortium (http://www.mousephenotype.org/); NA indicates that no knockout mouse model is available or investigated for the respective gene.
Nominally significant differential expression between the central and peripheral retinal pigment epithelium or choroid.
Nominally significant differential expression between the central and peripheral retinal pigment epithelium.
Nominally significant differential expression between the central and peripheral retina.
More than 5 nominally significant TWAS results for gene over all tissues in Genotype-Tissue Expression project (https://www.gtexportal.org/home/).
Significant PASCAL gene score; statistically significant combined retinal morphology phenotype P value according to the International Mouse Phenotyping Consortium (http://www.mousephenotype.org/).