Table 2. Pathogenicity analysis of variants at loci associated with elevated micronucleus levels.
| Mouse genomic location | Nearest gene | Consequence | Log P value | GERP Score | Grantham classification | Grantham score | SIFT class | Lowest SIFT score | EnsEMBL VEP class | EnsEMBL aa change | AA Change | Nuc Change |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr8:33576360-33576360 | Tex15 | A > T | 12.48026273 | −1.05 | Radical | 110 | Tolerated | 0.4 | Downstream gene variant; missense variant | R/S | R1939S | A5817T |
| chr8:33268792-33268792 | Wrn | G > A | 12.45662832 | −3.07 | Radical | 145 | Tolerated | 0.3 | Missense variant | S/L | S1021L | C3062T |
| chr8:33557389-33557389 | Tex15 | A > C | 12.43606688 | 3.19 | Radical | 110 | Tolerated | 0.44 | NMD transcript variant; downstream gene variant; missense variant | S/R | S160R | A478C |
| chr8:33557366-33557366 | Tex15 | G > T | 12.4319775 | 3.14 | Radical | 205 | Tolerated | 0.13 | NMD transcript variant; downstream gene variant; missense variant | C/F | C152F | G455T |
| chr8:33546343-33546343 | Tex15 | C > G | 12.42405548 | 3.56 | Nonconservative | 60 | Deleterious; tolerated | 0.02 | NMD transcript variant; missense variant | A/G | A94G | C281G |
| chr17:34804124-34804124 | Cyp21a1 | A > G | 8.239597012 | 0 | Nonconservative | 64 | Deleterious | 0.01 | Downstream gene variant; missense variant; upstream gene variant | V/A | V71A | T212C |
| chr17:34711526-34711526 | Tnxb | G > A | 8.198665514 | 4.53 | Radical | 125 | Deleterious; tolerated | 0.05 | Missense variant | G/R | G397R | G1189A |
| chr17:34711722-34711722 | Tnxb | G > A | 8.188940007 | −9.05 | Conservative | 29 | Deleterious | 0.02 | Missense variant | R/H | R462H | G1385A |
| chr17:34713138-34713138 | Tnxb | T > A | 8.185003889 | −2.37 | Radical | 113 | Tolerated | 0.21 | Missense variant | L/Q | L550Q | T1649A |
| chr17:35161042-35161042 | Prrc2a | T > G | 8.088956801 | 4.11 | Conservative | 15 | Deleterious | 0.02 | Downstream gene variant; missense variant; upstream gene variant | M/L | M249L | A745C |
| chr11:69236603-69236603 | Gucy2e | C > G | 7.758017279 | −9.38 | Radical | 125 | Tolerated | 0.46 | Missense variant; upstream gene variant | G/R | G15R | G43C |
| chr10:121667433-121667433 | D930020B18Rik | T > C | 7.543972828 | 0.726 | Radical | 155 | Tolerated | 0.85 | Missense variant | F/S | F75S | T224C |
| chr11:69047870-69047870 | Aurkb | T > C | 7.224042226 | 2.01 | Radical | 155 | Tolerated | 0.74 | Missense variant; upstream gene variant | F/S | F45S | T134C |
| chr11:69134001-69134001 | Aloxe3 | G > A | 6.687629704 | 3.92 | Conservative | 56 | Deleterious | 0.01 | NMD transcript variant; missense variant; upstream gene variant | G/S | G341S | G1021A |
| chr11:69107564-69107564 | Per1 | C > T | 6.656511366 | 2.92 | Nonconservative | 64 | Deleterious | 0.01 | Downstream gene variant; missense variant | A/V | A1014V | C3041T |
| chr9:109061596-109061596 | Atrip | A > T | 5.330403284 | −0.969 | Radical | 113 | NMD transcript variant; downstream gene variant; missense variant; synonymous variant; upstream gene variant | L/Q | NA | NA | ||
| chr9:109073661-109073661 | Atrip | T > A | 5.271500634 | 0.625 | Radical | 152 | Deleterious | 0.03 | NMD transcript variant; downstream gene variant; missense variant; splice region variant; upstream gene variant | D/V | NA | NA |
| chr9:109432436-109432436 | Fbxw16 | A > G | 5.023943697 | 0 | Radical | 155 | Tolerated | 0.56 | Missense variant | F/S | F454S | T1361C |
| chr2:30174134-30174134 | D2Wsu81e | C > T | 4.890540776 | 4.1 | Radical | 125 | Tolerated | 0.34 | Downstream gene variant; missense variant | G/R | G373R | G1117A |
| chr2:30174134-30174134 | D2Wsu81e | C > T | 4.890540776 | 4.1 | Radical | 125 | Tolerated | 0.34 | Downstream gene variant; missense variant | G/R | G373R | G1117A |
| chr2:29702527-29702527 | Rapgef1 | G > T | 4.806085521 | 1.45 | Conservative | 24 | Deleterious; tolerated | 0.02 | NMD transcript variant; missense variant | Q/H | Q510H | G1530T |
| chr2:29702527-29702527 | Rapgef1 | G > T | 4.806085521 | 1.45 | Conservative | 24 | Deleterious; tolerated | 0.02 | NMD transcript variant; missense variant | Q/H | Q510H | G1530T |
| chr2:29788325-29788325 | Coq4 | G > T | 4.571110541 | 0 | Radical | 102 | Tolerated | 0.32 | NMD transcript variant; missense variant; upstream gene variant | R/L | R14L | G41T |
| chr9:109060491-109060491 | Atrip | T > G | 3.712727076 | 0.625 | Conservative | 15 | Deleterious; tolerated | 0.03 | NMD transcript variant; downstream gene variant; missense variant; upstream gene variant | M/L | M688L | A2062C |
| chr5:148288927-148288927 | Mtus2 | C > A | 3.699186538 | 0 | Radical | 110 | NMD transcript variant; missense variant; synonymous variant | S/R | NA | NA | ||
| chr5:148288935-148288935 | Mtus2 | T > C | 3.692862836 | 0 | Radical | 145 | NMD transcript variant; missense variant; synonymous variant | L/S | NA | NA | ||
| chr9:109058117-109058117 | Trex1 | G > C | 3.215586866 | −1.25 | Radical | 125 | Tolerated | 0.18 | Downstream gene variant; missense variant | R/G | R269G | C805G |
Shown are the top five scoring variants at each of the seven genome-wide significant loci ranked by –log10 P-value. See Materials and Methods for a description of the approach used for variant annotation.