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Table 2

Population frequency of variants in BLK, KLF11, and PAX4 published as MODY causing

GeneVariantAllele count/total alleles in gnomAD v2.1.1Allele frequency in gnomAD v2.1.1Allele count in ancestry with maximum frequency/ total alleles in the ancestryMaximum 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 21  
 p.E548Rfs*112 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 21  
 c.1108-2A>G 21  
HNF4A p.Q255* 42  
 p.R141* 43  
GeneVariantAllele count/total alleles in gnomAD v2.1.1Allele frequency in gnomAD v2.1.1Allele count in ancestry with maximum frequency/ total alleles in the ancestryMaximum 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 21  
 p.E548Rfs*112 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 21  
 c.1108-2A>G 21  
HNF4A p.Q255* 42  
 p.R141* 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.

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