ClinVar Miner

List of variants reported as pathogenic for Lynch syndrome by All of Us Research Program, National Institutes of Health

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ClinVar version:
Total variants: 136
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HGVS dbSNP gnomAD frequency
NM_000251.3(MSH2):c.942+3A>T rs193922376 0.00072
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_000535.7(PMS2):c.1A>G (p.Met1Val) rs587779333 0.00004
NM_000251.3(MSH2):c.1906G>C (p.Ala636Pro) rs63750875 0.00003
NM_000179.3(MSH6):c.10C>T (p.Gln4Ter) rs786201042 0.00002
NM_000179.3(MSH6):c.1168del (p.Asp390fs) rs753796271 0.00002
NM_000179.3(MSH6):c.3202C>T (p.Arg1068Ter) rs63749843 0.00002
NM_000179.3(MSH6):c.1346T>C (p.Leu449Pro) rs63750741 0.00001
NM_000179.3(MSH6):c.1444C>T (p.Arg482Ter) rs63750909 0.00001
NM_000179.3(MSH6):c.2731C>T (p.Arg911Ter) rs63751017 0.00001
NM_000179.3(MSH6):c.3103C>T (p.Arg1035Ter) rs63749999 0.00001
NM_000179.3(MSH6):c.3487G>T (p.Glu1163Ter) rs587779267 0.00001
NM_000179.3(MSH6):c.3514dup (p.Arg1172fs) rs63751327 0.00001
NM_000179.3(MSH6):c.3939_3957dup (p.Ala1320delinsSerLysGlyThrTer) rs63750767 0.00001
NM_000179.3(MSH6):c.742del (p.Arg248fs) rs587781691 0.00001
NM_000249.4(MLH1):c.244A>G (p.Thr82Ala) rs587778998 0.00001
NM_000249.4(MLH1):c.306G>A (p.Glu102=) rs63751665 0.00001
NM_000251.3(MSH2):c.2131C>T (p.Arg711Ter) rs63750636 0.00001
NM_000535.7(PMS2):c.1927C>T (p.Gln643Ter) rs63751422 0.00001
NM_000535.7(PMS2):c.248T>G (p.Leu83Ter) rs1064794083 0.00001
NM_000535.7(PMS2):c.251-2A>T rs587779340 0.00001
NM_000535.7(PMS2):c.400C>T (p.Arg134Ter) rs63750871 0.00001
NM_000535.7(PMS2):c.709C>T (p.Gln237Ter) rs1458321358 0.00001
NM_000535.7(PMS2):c.825A>G (p.Gln275=) rs876659736 0.00001
NM_000535.7(PMS2):c.943C>T (p.Arg315Ter) rs200640585 0.00001
NM_000179.3(MSH6):c.1108_1109del (p.Leu370fs) rs786204252
NM_000179.3(MSH6):c.1168_1170delinsAA (p.Asp390fs) rs863225398
NM_000179.3(MSH6):c.1243C>T (p.Gln415Ter) rs1114167756
NM_000179.3(MSH6):c.1249_1252dup (p.Ser418Ter)
NM_000179.3(MSH6):c.1483C>T (p.Arg495Ter) rs587779212
NM_000179.3(MSH6):c.1571dup (p.Tyr524Ter) rs1553412966
NM_000179.3(MSH6):c.1610_1613del (p.Lys537fs) rs863224829
NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs) rs267608064
NM_000179.3(MSH6):c.1634_1637del (p.Lys545fs) rs63749874
NM_000179.3(MSH6):c.1637_1638del (p.Glu546fs) rs267608076
NM_000179.3(MSH6):c.1705_1706del (p.Phe569fs) rs587783056
NM_000179.3(MSH6):c.1901T>A (p.Leu634Ter) rs63751097
NM_000179.3(MSH6):c.1969C>T (p.Gln657Ter) rs1114167709
NM_000179.3(MSH6):c.2062_2063del (p.Val688fs) rs63750075
NM_000179.3(MSH6):c.2219T>G (p.Leu740Ter) rs745483465
NM_000179.3(MSH6):c.2230dup (p.Glu744fs) rs786201050
NM_000179.3(MSH6):c.2238dup (p.Leu747fs) rs1553413599
NM_000179.3(MSH6):c.246dup (p.Ala83fs) rs1668136752
NM_000179.3(MSH6):c.2535dup (p.Glu846Ter) rs587779241
NM_000179.3(MSH6):c.2550C>G (p.Tyr850Ter) rs374230313
NM_000179.3(MSH6):c.2569_2572del (p.Asp857fs) rs587779243
NM_000179.3(MSH6):c.2665C>T (p.Gln889Ter) rs1558666177
NM_000179.3(MSH6):c.2831_2832del (p.Ile944fs)
NM_000179.3(MSH6):c.2872C>T (p.Gln958Ter) rs1553414236
NM_000179.3(MSH6):c.2906_2907del (p.Tyr969fs) rs786203924
NM_000179.3(MSH6):c.2931C>G (p.Tyr977Ter) rs63750111
NM_000179.3(MSH6):c.3013C>T (p.Arg1005Ter) rs63750563
NM_000179.3(MSH6):c.3155_3156del (p.Glu1052fs) rs63750833
NM_000179.3(MSH6):c.3188T>G (p.Leu1063Arg) rs1060502901
NM_000179.3(MSH6):c.3261del (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.3311_3312del (p.Phe1104fs) rs267608092
NM_000179.3(MSH6):c.3356_3358delinsGAT (p.Glu1119_Glu1120delinsGlyTer) rs1114167695
NM_000179.3(MSH6):c.3439-2A>G rs267608098
NM_000179.3(MSH6):c.3491dup (p.Cys1165fs) rs876661073
NM_000179.3(MSH6):c.3516_3517del (p.Arg1172fs) rs398123232
NM_000179.3(MSH6):c.3573dup (p.Val1192fs) rs1057517764
NM_000179.3(MSH6):c.3633dup (p.Val1212fs) rs587776706
NM_000179.3(MSH6):c.3654_3657del (p.Thr1219fs)
NM_000179.3(MSH6):c.3699_3702del (p.Lys1233fs) rs193922343
NM_000179.3(MSH6):c.3716_3717del (p.Ile1239fs) rs1064794384
NM_000179.3(MSH6):c.3724_3726del (p.Arg1242del) rs63749942
NM_000179.3(MSH6):c.3725G>A (p.Arg1242His) rs63750119
NM_000179.3(MSH6):c.3743_3744insT (p.Tyr1249fs) rs786201084
NM_000179.3(MSH6):c.3768T>G (p.Tyr1256Ter) rs63751058
NM_000179.3(MSH6):c.3847_3850dup (p.Thr1284fs) rs267608128
NM_000179.3(MSH6):c.3860_3882dup (p.Pro1295fs)
NM_000179.3(MSH6):c.3861T>G (p.Tyr1287Ter) rs1060504739
NM_000179.3(MSH6):c.3920_3923dup (p.Pro1309fs) rs1572747278
NM_000179.3(MSH6):c.3939_3940dup (p.Gln1314fs) rs730881830
NM_000179.3(MSH6):c.3959_3962del (p.Ala1320fs) rs267608120
NM_000179.3(MSH6):c.3991C>T (p.Arg1331Ter) rs267608094
NM_000179.3(MSH6):c.4001G>A (p.Arg1334Gln) rs267608122
NM_000179.3(MSH6):c.741del (p.Lys247fs) rs267608041
NM_000179.3(MSH6):c.742C>T (p.Arg248Ter) rs63749980
NM_000179.3(MSH6):c.752_756del (p.Ile251fs)
NM_000249.4(MLH1):c.1219C>T (p.Gln407Ter) rs1057517541
NM_000249.4(MLH1):c.1279C>T (p.Gln427Ter) rs1559553501
NM_000249.4(MLH1):c.1380_1381del (p.Lys461fs) rs587778909
NM_000249.4(MLH1):c.1459C>T (p.Arg487Ter) rs63749795
NM_000249.4(MLH1):c.1489dup (p.Arg497fs) rs63750855
NM_000249.4(MLH1):c.1559-1G>T rs267607837
NM_000249.4(MLH1):c.1667+2_1667+8delinsATTT rs587778938
NM_000249.4(MLH1):c.1773dup (p.Ser592Ter)
NM_000249.4(MLH1):c.177del (p.Gln60fs)
NM_000249.4(MLH1):c.1846AAG[2] (p.Lys618del) rs63751247
NM_000249.4(MLH1):c.1896G>A (p.Glu632=) rs63751632
NM_000249.4(MLH1):c.1989G>T (p.Glu663Asp) rs63751662
NM_000249.4(MLH1):c.2070_2071insTT (p.Ile691fs) rs876659681
NM_000249.4(MLH1):c.2135G>A (p.Trp712Ter) rs63750561
NM_000249.4(MLH1):c.22del (p.Ile8fs) rs2125693612
NM_000249.4(MLH1):c.230G>A (p.Cys77Tyr) rs63750437
NM_000249.4(MLH1):c.350C>T (p.Thr117Met) rs63750781
NM_000249.4(MLH1):c.380+2T>A rs267607742
NM_000249.4(MLH1):c.676C>T (p.Arg226Ter) rs63751615
NM_000249.4(MLH1):c.677+3A>G rs267607780
NM_000249.4(MLH1):c.982C>T (p.Gln328Ter) rs587779058
NM_000251.3(MSH2):c.1165C>T (p.Arg389Ter) rs587779075
NM_000251.3(MSH2):c.1226_1227del (p.Gln409fs) rs63750086
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) rs63749831
NM_000251.3(MSH2):c.1915C>T (p.His639Tyr) rs28929484
NM_000251.3(MSH2):c.204del (p.Pro69fs) rs63750199
NM_000251.3(MSH2):c.2089T>C (p.Cys697Arg) rs63750961
NM_000251.3(MSH2):c.2246_2250del (p.Glu749fs) rs1553369665
NM_000251.3(MSH2):c.943-1G>T rs12476364
NM_000535.7(PMS2):c.1196dup (p.Gln400fs) rs1554298056
NM_000535.7(PMS2):c.1239dup (p.Asp414fs) rs267608159
NM_000535.7(PMS2):c.1275_1279del (p.Leu426fs) rs1554297962
NM_000535.7(PMS2):c.1472_1485del (p.Glu491fs) rs1562632035
NM_000535.7(PMS2):c.1488_1489insTGCC (p.Gly497fs)
NM_000535.7(PMS2):c.164-1G>C rs763308607
NM_000535.7(PMS2):c.1687C>T (p.Arg563Ter) rs587778618
NM_000535.7(PMS2):c.1738A>T (p.Lys580Ter) rs267608169
NM_000535.7(PMS2):c.1778del (p.Lys593fs) rs766389591
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000535.7(PMS2):c.1939A>T (p.Lys647Ter) rs201451115
NM_000535.7(PMS2):c.1957del (p.Cys653fs)
NM_000535.7(PMS2):c.247_250dup (p.Thr84fs) rs1554304940
NM_000535.7(PMS2):c.325dup (p.Glu109fs) rs587781716
NM_000535.7(PMS2):c.354-2A>G rs786202098
NM_000535.7(PMS2):c.433C>T (p.Gln145Ter)
NM_000535.7(PMS2):c.691_694del (p.Phe231fs) rs1784787989
NM_000535.7(PMS2):c.736_741delinsTGTGTGTGAAG (p.Pro246_Pro247delinsCysValTer) rs267608150
NM_000535.7(PMS2):c.765C>A (p.Tyr255Ter) rs573125799
NM_000535.7(PMS2):c.780del (p.Asp261fs) rs587779344
NM_000535.7(PMS2):c.802dup (p.Tyr268fs) rs267608149
NM_000535.7(PMS2):c.823C>T (p.Gln275Ter) rs587780062
NM_000535.7(PMS2):c.829dup (p.Thr277fs)
NM_000535.7(PMS2):c.861_864del (p.Arg287fs) rs267608154
NM_000535.7(PMS2):c.862_863del (p.Gln288fs) rs63750246
NM_000535.7(PMS2):c.989-1G>T rs587780064

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