Table 2.
Population frequency of variants in BLK, KLF11, and PAX4 published as MODY causing
| Gene | Variant | Allele count/total alleles in gnomAD v2.1.1 | Allele frequency in gnomAD v2.1.1 | Allele count in ancestry with maximum frequency/ total alleles in the ancestry | Maximum allele frequency in a single ancestry in gnomAD v2.1.1 (ancestry) | Reference no. for variants |
|---|---|---|---|---|---|---|
| BLK | p.A71T | 3,281/282,812 | 0.012 | 420/10,368 | 0.041 (Ashkenazi Jewish) | 7 |
| KLF11 | p.Q62R | 25,823/282,778 | 0.091 | 1,497/10,370 | 0.144 (Ashkenazi Jewish) | 9 |
| p.T220M | 1,207/282,762 | 4.27 × 10−3 | 1,098/24,958 | 0.044 (African/African American) | 9 | |
| p.A347S | 36/282,304 | 1.28 × 10−4 | 17/35,410 | 4.80 × 10−4 (Latino/Admixed American) | 9 | |
| PAX4 | p.R31L | 105/250,972 | 4.18 × 10−4 | 102/30,616 | 0.003 (South Asian) | 44 |
| p.R164W | 14/282,800 | 4.95 × 10−5 | 3/24,948 | 1.2 × 10−4 (African/African American) | 8 | |
| p.R192H | 2,214/282,856 | 7.83 × 10−3 | 2,182/19,946 | 0.109 (East Asian) | 8 | |
| HNF1A | p.P447L | 3/249,186 | 1.20 × 10−5 | 1/20,812 | 4.81 × 10−5 (Finnish European) | 21 |
| p.V380Sfs*4 | 0 | 0 | 0 | 0 | 21 | |
| p.E548Rfs*112 | 0 | 0 | 0 | 0 | 21 | |
| p.R131Q | 1/251,390 | 3.98 × 10−6 | 1/113,698 | 8.80 × 10−6 (non-Finnish European) | 21 | |
| c.1768 + 1G>A | 0 | 0 | 0 | 0 | 21 | |
| c.1108-2A>G | 0 | 0 | 0 | 0 | 21 | |
| HNF4A | p.Q255* | 0 | 0 | 0 | 0 | 42 |
| p.R141* | 0 | 0 | 0 | 0 | 43 |
Allele frequency taken from gnomAD v2.1.1. The table provides coding variants reported before 2016 that are reported to cause MODY, as the release of ExAC (26) that year meant for variants published since then investigators have had access to a large control population as part of their screening process. The HNF1A and HNF4A variants included here for comparison are those from the original articles used in the LOD score calculations in Table 1.