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Table 3

Results of gene burden tests comparing the frequency of variants in BLK, KLF11, and PAX4 in a disease cohort with that in a population cohort

Variant typeGeneAllele count in MODY cohortAllele frequency in MODY cohortAllele count in population cohort (UK Biobank)Allele frequency in population cohort (UK Biobank)OR (95% CI)PPrior probabilityBFDP
Ultra-rare PTV BLK 4.10 × 10−4 14 3.77 × 10−5 10 (0.26–71) 0.09 0.2 0.71 
 KLF11 15 4.03 × 10−5 0 (0–39) 0.2 0.8 
 PAX4 1.61 × 10−5 0 (0–97) 0.2 0.8 
 HNF1A 15 6.11 × 10−3 8.07 × 10−6 762 (215–4,108) 1.37 × 10−30 0.2 1.20 × 10−9 
 HNF4A 1.22 × 10−3 5.38 × 10−6 228 (26–2,724) 2.79 × 10−6 0.2 0.03 
Ultra-rare missense variants BLK 4.10 × 10−4 141 3.79 × 10−4 1 (0.03–6.00) 0.6 0.2 0.82 
 KLF11 8.10 × 10−4 122 3.28 × 10−4 2.5 (0.3–9.0) 0.2 0.2 0.78 
 PAX4 8.10 × 10−4 84 2.26 × 10−4 3.6 (0.43–13.00) 0.1 0.2 0.70 
 HNF1A 21 8.56 × 10−3 102 2.74 × 10−4 31 (19–51) 1.70 × 10−23 0.2 5.80 × 10−38 
 HNF4A 14 5.70 × 10−3 83 2.23 × 10−4 26 (13–46) 4.41 × 10−15 0.2 1.20 × 10−25 
Variant typeGeneAllele count in MODY cohortAllele frequency in MODY cohortAllele count in population cohort (UK Biobank)Allele frequency in population cohort (UK Biobank)OR (95% CI)PPrior probabilityBFDP
Ultra-rare PTV BLK 4.10 × 10−4 14 3.77 × 10−5 10 (0.26–71) 0.09 0.2 0.71 
 KLF11 15 4.03 × 10−5 0 (0–39) 0.2 0.8 
 PAX4 1.61 × 10−5 0 (0–97) 0.2 0.8 
 HNF1A 15 6.11 × 10−3 8.07 × 10−6 762 (215–4,108) 1.37 × 10−30 0.2 1.20 × 10−9 
 HNF4A 1.22 × 10−3 5.38 × 10−6 228 (26–2,724) 2.79 × 10−6 0.2 0.03 
Ultra-rare missense variants BLK 4.10 × 10−4 141 3.79 × 10−4 1 (0.03–6.00) 0.6 0.2 0.82 
 KLF11 8.10 × 10−4 122 3.28 × 10−4 2.5 (0.3–9.0) 0.2 0.2 0.78 
 PAX4 8.10 × 10−4 84 2.26 × 10−4 3.6 (0.43–13.00) 0.1 0.2 0.70 
 HNF1A 21 8.56 × 10−3 102 2.74 × 10−4 31 (19–51) 1.70 × 10−23 0.2 5.80 × 10−38 
 HNF4A 14 5.70 × 10−3 83 2.23 × 10−4 26 (13–46) 4.41 × 10−15 0.2 1.20 × 10−25 

The frequency of ultra-rare (allele count = 1) PTV and missense variants in a MODY cohort (n = 1,227) was compared with the frequency in the UK Biobank population cohort (n = 185,898).

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