TABLE 3.
Genetic variants enriched in recurrent ADEH+ subjects showing the frequency of heterozygous (Ref/Alt) and homozygous (Alt/Alt) carriers within each ADRN phenotype group and the reference and alternate alleles (Ref/Alt) frequency in the TGP super-populations as reference
| Variant |
Frequency of carriers (Ref/Alt +Alt/Alt)a |
TGP Frequency |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene symbol | dbSNP ID | ADEH+ (n = 49) | ADEH− (n = 491) | NA (n = 237) | Amino acid change | AFR (Ref/Alt) | AMR (Ref/Alt) | EAS (Ref/Alt) | EUR (Ref/Alt) | SAS (Ref/Alt) |
| SIDT2 | rs142171036 | 8% | 0.4% | 0% | p. Arg710Cys | C: 100%/T: 0% | C: 100%/T: 0% | C: 100%/T: 0% | C: 99.9%/T: 0.1% | C: 100%/T: 0% |
| CLEC7A | rs16910526 | 28% +2% | 14.2% +1.2% | 10% +0.4% | Stop-gained | A: 98.9%/C: 1.1% | A: 96.3%/C:3.7% | A: 99.6%/C: 0.4% | A: 92.9%/C: 7.1% | A: 90.9%/C: 9.1% |
| rs140318683 | 2% | 0.8% | 0% | p. Leu183Phe | G: 100% A: 0% | G: 100%/A: 0% | G: 100%/A: 0% | G: 99.5%/A: 0.5% | G: 100%/A: 0% | |
| GSTZ1 | rs7972 | 26% +4% | 14.6% +0.8% | 11.2% +0.8% | p. Gly42Arg | G: 99.6%/A:.04% | G: 97.3%/A: 2.7% | G: 100%/A: 0% | G: 88.9%/A: 11.1% | G: 98.3%/A: 1.7% |
| TPSG1 | rs61587627 | 6% | 4.4% | 1.2% | p.Thr100Lys | G: 98.1%/T: 1.9% | G: 97.3%/T: 2.7% | G: 90.3%/T: 9.7% | G: 98.9%/T: 1.1% | G: 98.7%/T:1.3% |
| rs187607214 | 4% | 0.6% | 0% | p. Cys51 Tyr | C: 99.9%/T: 0.1% | C: 100%/T: 0% | C: 100%/T: 0% | C: 99.8%/T: 0.2% | C: 100%/T: 0% | |
| SP110 | rs372023963 | 2% | 0% | 0% | p. Thr628Met | NA | NA | NA | NA | NA |
| rs768938186 | 2% | 0% | 0% | p. Arg539Ter isoform b & d | NA | NA | NA | NA | NA | |
| rs149485401 | 6% | 1.2% | 0.8% | p. Gly483Arg isoform a & c | C: 100%/T: 0% | C: 99.1%/T: 0.9% | C: 100%/T: 0% | C: 98.1%/T: 1.9% | C: 100%/T: 0% | |
| RBBP8NL | rs200738153 | 14% | 3.2% | 1.6% | p. Leu267Pro | A: 99.9%/G: 0.1% | A: 99.7%/G: 0.3% | A: 100%/G: 0% | A: 99.2%/G: 0.8% | A: 99.8%/G: 0.2% |
| TRIM15 | rs34823152 | 26% | 7% +0.2% | 11.6% +0.4% | p. Leu235Val | C: 99.9%/G: 0.1% | C: 96.8%/G:3.2% | C: 99.8%/G: 0.2% | C: 95.1%/G: 4.9% | C: 98.9%/G: 1.1% |
| FRMD3 | rs4877747 | 16% | 4.4% | 2.8% | p. Asp485 Tyr | C: 99.9%/A: 0.1% | C: 97.0%/A: 3.0% | C: 93.1%/A: 6.9% | C: 97.6%/A: 2.4% | C: 96.0%/A: 4.0% |
Abbreviation: NA, variant not found in TGP.
If only one number is shown, it indicates only heterozygous carriers in each group; if two numbers are shown, then the first number is the frequency of heterozygous carriers, and the second number is the frequency of the homozygous carriers. Allele frequencies were obtained for Phase 3 release of TGP for five super-populations: AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), and SAS (South Asian). The frequencies were obtained from the Human (GRCh37.p13) genome on Ensembl.