Table 2. Top 30 Amish-specific putative damaging exonic missense variants by prevalence in affected individuals.
| Chr. | Position | Ref | Alt | dbSNP 138 | Gene | #BP1 | # Well | 1000G freq. | EVS freq. |
| chr8 | 39521389 | T | C | rs147445686 | ADAM18 | 13 | 8 | . | 0.0023 |
| chr8 | 37692704 | G | A | rs113270504 | GPR124 | 13 | 9 | 0.011 | 0.017 |
| chr6 | 42146043 | A | G | rs200275941 | GUCA1A | 12 | 7 | . | . |
| chr1 | 40020020 | C | A | rs79473113 | LOC728448 | 10 | 8 | . | . |
| chrX | 65835841 | A | G | rs73221529 | EDA2R | 10 | 10 | 0.0024 | 0.007 |
| chr19 | 14164629 | C | T | rs75841596 | PALM3 | 9 | 11 | 0.017 | . |
| chr2 | 61413761 | C | A | rs200746889 | AHSA2 | 8 | 1 | . | 0.00015 |
| chr8 | 120430415 | G | A | Novel | NOV | 8 | 5 | . | . |
| chr9 | 5164252 | C | T | Novel | INSL6 | 8 | 7 | . | . |
| chr1 | 1387499 | T | A | rs199583997 | ATAD3C | 8 | 8 | . | 0.0018 |
| chr18 | 76335864 | G | A | rs149637223 | LOC100132713 | 8 | 10 | . | . |
| chr1 | 27661952 | C | T | rs150461998 | TMEM222 | 8 | 10 | 0.0096 | 0.009 |
| chr16 | 25238420 | G | A | rs117255669 | AQP8 | 7 | 1 | 0.0087 | 0.017 |
| chr19 | 9067237 | T | G | rs201826382 | MUC16 | 7 | 3 | . | . |
| chr2 | 96907615 | A | C | Novel | LOC285033 | 7 | 3 | . | . |
| chr16 | 48204130 | C | T | rs60681475 | ABCC11 | 7 | 4 | 0.0078 | 0.011 |
| chr6 | 84925066 | A | G | rs147915749 | KIAA1009 | 7 | 4 | 0.00091 | 0.003 |
| chr6 | 84904604 | G | C | rs17790493 | KIAA1009 | 7 | 4 | 0.0179 | 0.019 |
| chr19 | 9059827 | A | G | rs76869876 | MUC16 | 7 | 4 | 0.0046 | 0.006 |
| chr3 | 172365793 | C | T | Novel | NCEH1 | 7 | 5 | . | . |
| chr11 | 48267242 | G | A | rs145684951 | OR4X2 | 7 | 5 | . | 0.0002 |
| chr2 | 163302901 | C | T | rs78247304 | KCNH7 | 7 | 5 | . | . |
| chr11 | 55798414 | G | T | rs142890517 | OR5AS1 | 7 | 5 | . | 7.70E-05 |
| chr17 | 3195777 | A | T | rs149826123 | OR3A1 | 7 | 6 | 0.0037 | 0.004 |
| chr7 | 120911438 | G | A | rs138155176 | C7orf58 | 7 | 6 | 0.00092 | 0.0017 |
| chr22 | 26937139 | C | T | rs117701840 | TPST2 | 7 | 6 | 0.0041 | 0.005 |
| chr12 | 110566907 | A | G | rs34684319 | IFT81 | 7 | 6 | 0.014 | 0.0145 |
| chr10 | 75860740 | A | G | rs71579374 | VCL | 7 | 7 | 0.00046 | 0.0009 |
| chr1 | 1269071 | A | G | rs376489341 | TAS1R3 | 7 | 8 | . | 7.70E-05 |
| chr19 | 12429782 | G | A | rs112896133 | ZNF563 | 7 | 8 | 0.0041 | 0.0088 |
Exonic missense variants, identified in 50 subjects with WGS, were filtered by <2% allele frequency in 1000 Genomes, EVS and 54 HapMap WGS. Functional impact was assessed by consensus of Polyphen2 and SIFT.