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. 2016 Sep 30;16(2):195–203. doi: 10.1007/s10689-016-9934-0

Table 2.

Classification of missense variants with a MAF < 1 % among 91 index patients

Clinical group: patient number Gene Position (GRCh37/hg19)/dbSNP (rs) Genotype Consequence ExAc All# SIFT& PolyPhen-2¤ C-score+ Classification^
III:61 APC Chr5:112170806 NM_000038:c.1902T > G Exon 14 skipping Not present Deleterious Probably damaging 20.9 5
III:61 APC Chr5:112175763 NM_000038:c.4472T > A p.Phe1491Tyr Not present Deleterious Probably damaging 22.8 3
V:89 APC Chr5:112176431/rs148275069 NM_000038:c.5140G > A p.Asp1714Asn 0.020 % Deleterious Benign 13.5 3
I:1 APC Chr5:112177415 NM_000038:c.6124T > C p.Cys2042Arg Not present Deleterious Probably damaging 15.7 3
I:38 APC Chr5:112176196/rs137988845 NM_000038:c.4905G > A p.Gly1635Gly 0.038 % Not ava na 3.2 3
I:50 APC Chr5:112178693 NM_000038:c.7402T > C p.Ser2468Pro 0.002 % Tolerated Possibly damaging 23.5 3
I:11 AXIN2 Chr17:63532528/rs138287857 NM_004655:c.2051C > T p.Ala684Val 0.19 % Deleterious Possibly damaging 22.6 3
II:58 BMPR1A Chr10:88683199/rs199476089 NM_004329:c.1409T > C p.Met470Thr Not present Deleterious Probably damaging 21.6 4
V:90 CDH1 Chr16:68855966/rs35187787 NM_004360:c.1774G > A p.Ala592Pro 0.32 % Deleterious Benign 15.3 3
V:87 CHEK2 Chr22:29130520/rs141568342 NM_007194:c.190G > A p.Glu64Lys 0.016 % Tolerated Possibly damaging 18.2 3
V:87 CHEK2 Chr22:29121087/rs17879961 NM_007194:c.470T > C p.Ile157Thr 0.41 % Deleterious Probably damaging 21.1 4
III:27 CTNNB1 Chr3:41275730 NM_001904:c.1625G > A p.Arg542His 0.00082 % Deleterious Benign 18 3
I:1 MET Chr7:116340039/rs201687037 NM_001127500:c.901A > G p.Thr301Ala 0.022 % Tolerated Probably damaging 11.3 3
I:57, IV:79 MLH1 Chr3:37089130/rs35001569 NM_000249:c.1852A > G p.Lys618Glu 0.34 % Deleterious Probably damaging 27.8 3in
IV:85 MLH1 Chr3:37090050/rs63750109 NM_000249:c.1939G > A p.Val647Met 0.015 % Deleterious Benign 18 3in
I:41 MLH1 Chr3:g.37053590/rs63751711 NM_000249:c.677G > A ex 8 skipping Not present Deleterious Probably damaging 34 5in
I:8, I:10, I:47 MLH3 Chr:75514489/rs28756986 NM_001040108:c.1870G > C p.Glu624Gln 0.73 % Tolerated Probably damaging 17 3
I:4, I:33 MLH3 Chr14:75509146/rs28757008 NM_001040108:c.3315C > A p.Asp1105Glu 0.29 % Tolerated Possible damaging 17.7 3
II:24 MLH3 Chr14:75506718/rs184741686 NM_001040108:c.3466G > A p.Val1156Ile 0.011 % Tolerated Benign 16.8 3
IV:81 MLH3 Chr14:75483796/rs28939071 NM_001040108:c.4351G > A p.Glu1451Lys 0.074 % Tolerated Probably damaging 14. 3
I:12, I:37 MSH3 Chr5:80109479/rs41545019 NM_002439:c.2732T > G p.Leu911Trp 0.24 % Deleterious Probably damaging 17.4 3
I:55 MSH2 Chr2:g.47657079/rs63751650 NM_000251.2:c.1275A > G p.Glu425Glu 0.01 % na na 13.6 3in
I:92 MSH2 Chr2:g.47703513/rs587779127 NM_000251.2:c.2013T > A p.Asn671Lys Not present Deleterious Probably damaging 28.2 3in
IV:79 MSH6 Chr2:48027790 NM_000179:c.2668G > T p.Val890Phe Not present Deleterious Possibly damaging 12.9 3
I:56 MSH6 Chr2:g.48030612 NM_000179:c.3226C > T p.Arg1076Cys 0.0091 % Deleterious Probably damaging 32 3in
III:71 MUTYH Chr1:45798475/rs34612342 NM_001128425:c.536A > G p.Tyr179Cys 0.16 % Deleterious Probably damaging 19 5ho
I:42 MUTYH Chr1:g.45797228/rs36053993 NM_001128425:c.1187G > A p.Gly396Asp 0.28 % Deleterious Probably damaging 29.4 5ho
I:51 MUTYH Chr1:g.45797846/rs138089183 NM_001128425:c.925C > T p.Arg309Cys 0.044 % Tolerated Benign 13.9 3ho
I:33 PMS1 Chr2:190660640 NM_000534:c.278G > A p.Arg93His 0.0025 % Deleterious Probably damaging 36 3
IV:31 PMS1 Chr2:190708701/rs143010673 NM_000534:c.594G > T p.Trp198Cys 0.015 % Deleterious Probably damaging 20.8 3
I:51 PMS1 Chr2:g.190660536/rs143323454 NM_000534:c.174G > T p.Gly58Gly 0.33 % na na 9.3 3
I:48 STK11 Chr19:g.1226474/rs199973552 NM_000455:c.1130C > T p.Ala377Val 0.01 % Tolerated Benign 13.7 3

#URL: http://exac.broadinstitute.org; and [20]; ¤ [3]; ho, pathogenic in homozygote state; ^, manual classification unless indicated with in, when marked with in classified according to InSiGHT [46], na, not available