Table 4.
Gene | hg19/GRCh37 | Genome reference | cDNA position | rs Number | Alternate DNA changes (Ref > Alt) | ΔAmino acida | CADD (Phred) | SIFT (Score) | PolyPhen-v2 (Score) | Used to predict |
---|---|---|---|---|---|---|---|---|---|---|
UGT2B7 | NC_000004.11:g.69962282G>A | NM_001074.2:g.90G>A | NM_001074.2:c.44G>A | – | – | – | 0.135 | Tolerated (0.110) | Benign (0.0310) | T:M1 |
UGT2B7 | NC_000004.11:g.69962349G>T | – | NM_001074.2:c.111G>T | rs1255338508 | – | p.(Met37Ile) | 0.004 | Tolerated (1.00) | Benign (0.0750) | T:M1 |
UGT2B7 | NC_000004.11:g.69962583C>T | NM_001074.2:g.391C>T | NM_001074.2:c.345C>T | rs1453130551 | – | – | 7.24 | – | – | T:M1 |
UGT2B7 | NC_000004.11:g.69962586G>C | – | NM_001074.2:c.348G>C | rs772560918 | – | p.(Met116Ile) | 0.121 | Tolerated (0.385) | Benign (0.00300) | T:M1 |
UGT2B7 | NC_000004.11:g.69962610A>G | – | NM_001074.2:c.372A>G | rs28365063 | – | p.(Arg124Ser) | 0.009 | – | – | t-MP |
UGT2B7 | NC_000004.11:g.69964232A>C | NM_001074.2:g.747A>C | NM_001074.2:c.722-726A>C | – | – | – | 2.37 | – | – | T:M1 |
UGT2B7 | NC_000004.11:g.69978319G>A | – | NM_001074.2:c.1455G>C | – | – | p.(Trp485*) | 36 | – | – | T:M1 |
UGT2B7 | NC_000004.11:g.69978334T>C | NM_001074.2:g.1516T>C | NM_001074.2:c.1470T>C | – | – | – | 0.005 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154360666C>T | – | NM_001145279.2:c.266C>T | rs199648369 | – | p.(Pro89Leu) | 21.4 | Deleterious (0) | Benign (0) | t-MP |
OPRM1 | NC_000006.11:g.154407714dup | NC_000006.11(OPRM1_v008):c.570-3247dup | NM_001145279.2:c.570-3247dup | rs101840062 | – | – | 1.25 | – | – | t-MP |
OPRM1 | NC_000006.11:g.154408673C>T | NC_000006.11(OPRM1_v008):c.570-2288C>T | NM_001145279.2:c.570-2288C>T | – | – | – | 5.66 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154412242delC | – | NM_001145279.2:c.1078delC | – | – | p.(Leu360Serfs*60) | 34 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154412881A>C | NC_000006.11(OPRM1_v008):c.1443 + 274A>C | NM_001145279.2:c.1443 + 274A>C | – | – | – | 4.67 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154414312T>C | NC_000006.11(OPRM1_v008):c.1443 + 1705T>C | NM_001145279.2:c.1443 + 1705T>C | – | – | – | 4.57 | – | – | t-MP |
OPRM1 | NC_000006.11:g.154414459G>A | – | NM_001145279.2:c.1443 + 1852G>A | – | – | p.(Val407Met) | 3.27 | Deleterious (0.0400) | Benign (0.00300) | t-MP |
OPRM1 | NC_000006.11:g.154414611G>A | NG_021208.2:g.87976G>A | NM_001145279.2:c.1443 + 2004 G>A | rs200646591 | – | – | 5.17 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154414678G>A | NC_000006.11(OPRM1_v008):c.1443 + 2071G>A | NM_001145279.2:c.1443 + 2071G>A | – | – | – | 14.8 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154428905C>A | – | NM_001145279.2:c.1444–10913C>A | rs1357614491 | C>T | p.(Ala396Asp) | 2.99 | Deleterious (0) | Benign (0.00900) | t-MP |
OPRM1 | NC_000006.11:g.154429092dup | NC_000006.11(OPRM1_v008):c.1444-10726dup | NM_001145279.2:c.1444-10726dup | rs1319935018 | – | – | 0.796 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154430035A>T | NC_000006.11(OPRM1_v008):c.1444-9783A>T | NM_001145279.2:c.1444-9783A>T | – | – | – | 0.162 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154439693G>A | NC_000006.11(OPRM1_v008):c.1444-125G>A | NM_001145279.2:c.1444-125G>A | – | – | – | 1.01 | – | – | t-MP |
OPRM1 | NC_000006.11:g.154439699C>T | NC_000006.11(OPRM1_v008):c.1444-119C>T | NM_001145279.2:c.1444-119C>T | – | – | – | 2.38 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154439986_154439987delCT | NC_000006.11(OPRM1_v042):c.*130_*131del | NM_001145279.2:c.*130_131delCT | – | – | – | 9 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154440143delT | NG_021208.2:g.241572delT | NM_001145279.2:c.*287delT | – | – | – | 9.15 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154440379T>A | NG_021208.2:g.113744T>A | NM_001145279.2:c.*523T>A | rs1252162127 | – | – | 9.57 | – | – | T:M1 |
OPRM1 | NC_000006.11:g.154567680C>G | NG_021208.2:g.241046C>G | NM_001005803.1:c.246 + 45C>G | – | – | – | 6.36 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87138569G>A | NG_011513.1:g.208996C>T | NM_000927.4:c.3489 + 22C>T | – | G>C, G>T | – | 1.84 | – | – | t-MP |
ABCB1 | NC_000007.13:g.87144642C>A | – | NM_000927.4:c.3187G>T | rs761914266 | – | p.(Gly1063Cys) | 35 | Deleterious (0) | Probably damaging (0.996) | t-MP |
ABCB1 | NC_000007.13:g.87144644T>C | – | NM_000927.4:c.3185A>G | – | – | p.(Lys1062Arg) | 17.5 | Tolerated (0.185) | Benign (0.0250) | T:M1 |
ABCB1 | NC_000007.13:g.87165761A>C | NG_011513.1:g.181804T>G | NM_000927.4:c.2481 + 13T>G | – | – | – | 2.39 | – | – | t-MP |
ABCB1 | NC_000007.13:g.87175444C>T | NG_011513.1:g.172121G>A | NM_000927.4:c.1726-104G>A | – | – | – | 9.3 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87178819C>T | – | NM_000927.4:c.1570G>A | – | – | p.(Val524Ile) | 28.3 | Deleterious (0) | Probably damaging (0.818) | T:M1 |
ABCB1 | NC_000007.13:g.87179086G>A | NG_011513.1:g.168479C>T | NM_000927.4:c.1554 + 81C>T | rs2235035 | – | – | 0.167 | – | – | t-MP |
ABCB1 | NC_000007.13:g.87179342G>T | – | NM_000927.4:c.1379C>A | – | – | p.(Thr460Asn) | 18.8 | Tolerated (0.0900) | Benign (0.0165) | T:M1 |
ABCB1 | NC_000007.13:g.87179361C>T | – | NM_000927.4:c.1360G>A | – | – | p.(Asp454Asn) | 32 | Deleterious (0.0100) | Probably damaging (0.782) | T:M1 |
ABCB1 | NC_000007.13:g.87179532T>C | – | NM_000927.4:c.1305A>G | – | – | p.(Thr435=) | 0.033 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87183666dup | NG_011513.1:g.163912dup | NM_000927.4:c.828-405dup | rs5885589 | insAA, insAAA, insAAAAA | – | 3.26 | – | – | t-MP |
ABCB1 | NC_000007.13:g.87214505A>C | NG_011513.1:g.133060T>G | NM_000927.4:c.286 + 323T>G | – | A>C, A>T | – | 1.04 | – | – | t-MP |
ABCB1 | NC_000007.13:g.87214740G>T | NG_011513.1:g.132825C>A | NM_000927.4:c.286 + 88C>A | – | – | – | 4.11 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87214994A>G | – | NM_000927.4:c.120T>C | – | – | p.(Phe40=) | 15.7 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87229912C>T | NG_011513.1:g.117653G>A | NM_000927.4:c.-7 + 159G>A | – | – | – | 11.4 | – | – | T:M1 |
ABCB1 | NC_000007.13:g.87230159C>A | NG_011513.1:g.117406G>T | NM_000927.4:c.-95G>T | – | – | – | 13.1 | – | – | T:M1 |
COMT | NC_000022.10:g.19929314C>T | NG_011526.1:g.25800C>T | NM_006440.3:c.13C>T | – | – | – | 12.2 | Deleterious (0.0600) | Benign (0.0618) | T:M1 |
COMT | NC_000022.10:g.19951173G>A | – | NM_000754.3:c.374G>A | rs759305975 | – | p.(Arg125His) | 25.2 | Deleterious (0.0100) | Probably damaging (1.00) | t-MP |
COMT | NC_000022.10:g.19951174C>T | – | NM_000754.3:c.375C>T | rs1223964672 | – | p.(Arg125=) | 23.6 | – | – | T:M1 |
COMT | NC_000022.10:g.19957537G>A | NG_011526.1:g.33275G>A | NM_000754.3:c.*1278G>A | – | – | – | 10.1 | – | – | T:M1 |
CYP2D6 | NC_000022.10:g.42522312T>C | NG_008376.3:g.8682G>A | NM_000106.5:c.*75 + 189G>A | rs116390392 | – | – | 2.19 | – | – | T:M1 and t-MP |
CYP2D6 | NC_000022.10:g.42528224G>A | NG_008376.3:g.2775C>T | NM_000106.5:c.-1426C>T | rs28588594 | – | – | 1.33 | – | – | t-MP |
t-MP toxicologically inferred metabolizer phenotype, CADD Combined Annotation Dependent Depletion
aExon positions are as follows: UGT2B7 NM_001074.2:c.-46_721 (exon 1), NM_001074.2:c.722_870 (exon 2), NM_001074.2:c.871_1002 (exon 3), NM_001074.2:c.1003_1090 (exon 4), NM_001074.2:c.1091_1310 (exon 5), 1311_*251 (exon 6); OPRM1 NM_001145279.2:c.-523_-1 (exon 1), NM_001145279.2:c.1_145 (exon 2), NM_001145279.2:c.146_569 (exon 3), NM_001145279.2:c.570_922 (exon 4), NM_001145279.2:c.923_1443 (exon 5), NM_001145279.2:c.1444_*738; ABCB1 NM_000927.4:c.-493_-331 (exon 1), NM_000927.4:c.-330_-7 (exon 2), NM_000927.4:c.-6_68 (exon 3), NM_000927.4:c.69-117 (exon 4), NM_000927.4:c.118_286 (exon 5), NM_000927.4:c.287_338 (exon 6), NM_000927.4:c.339_530 (exon 7), NM_000927.4:c.531_702 (exon 8), NM_000927.4:c.703_827 (exon 9), NM_000927.4:c.828_999 (exon 10), NM_000927.4:c.1000_1113 (exon 11), NM_000927.4:c.1114_1224 (exon 12), NM_000927.4:c.1225_1350 (exon 13), NM_000927.4:c.1351_1554 (exon 14), NM_000927.4:c.1555_1725 (exon 15), NM_000927.4:c.1726_1887 (exon 16), NM_000927.4:c.1888_2064 (exon 17), NM_000927.4:c.2065_2211 (exon 18), NM_000927.4:c.2212_2319 (exon 19), NM_000927.4:c.2320_2397 (exon 20), NM_000927.4:c.2398_2482 (exon 21), NM_000927.4:c.2482_2685 (exon 22), NM_000927.4:c.2686_2786 (exon 23), NM_000927.4:c.2787_2927 (exon 24), NM_000927.4:c.2928_3084 (exon 25), NM_000927.4:c.3085_3282 (exon 26), NM_000927.4:c.3283_3489 (exon 27), NM_000927.4:c.3490_3636 (exon 28), NM_000927.4:c.3637_*380 (exon 29); COMT NM_000754.3:c.-249_-92 (exon 1), NM_000754.3:c.-91_-1 (exon 2), NM_000754.3:c.1_289 (exon 3), NM_000754.3:c.290_483 (exon 4), NM_000754.3:c.484_615 (exon 5), NM_000754.3:c.616_*1239; CYP2D6 NM_000106.5:c.-90_180 (exon 1), NM_000106.5:c.181_352 (exon 2), NM_000106.5:c. 353_505 (exon 3), NM_000106.5:c.506_666 (exon 4), NM_000106.5:c.667_843 (exon 5), NM_000106.5:c.844_985 (exon 6), NM_000106.5:c.986_1173 (exon 7), NM_000106.5:c.1174_1315 (exon 8), NM_000106.5:c.1316_*75 (exon 9)