Skip to main content
. 2019 Sep 26;20:324–336. doi: 10.1016/j.isci.2019.09.030

Table 2.

Details of Unconventional Alterations Found by NGS Targeted Sequencing

Case Gene Mutation VAF (%) Status dbSNP ID MAF COSMIC ID α HGMD ID β ClinVar Prediction γ MutTaster Prediction δ Notes
88 KRAS c.389C > T; p.A130V 44.9 Germ line rs730880473 <0.01 COSM4169153 α Uncertain significance γ Simultaneous RET M918T (s);
reported as “neutral” (Wang et al., 2019)
41 RET c.2774A > C; p.D925A 46.7 Somatic Novel Novel Disease causing δ Occurring in -cis with RET M918T (s)
242 RET c.890G > A; p.R297H 11.8 Somatic Novel Novel Polymorphism δ Simultaneous RET M918T (s)
196 RET c.2497C > T; p.R833C 25 Somatic rs377767422 <0.01 CM068590 β Likely pathogenic γ Simultaneous RET M918T (s)
20,169,196251,253 MET c.3029C > T; p.T1010I Various Somatic; germ line rs56391007 <0.01 COSM707 α
CM118113 β
Conflicting results δ
176 NRAS c.53C > T; p.A18V 7.5 Somatic Novel Novel Disease causing δ Simultaneous RET C634W (s)
91 RET c.644G > T; R215L 49.9 Germ line rs748128929 <0.01 Polymorphism δ Simultaneous RET C634Y (s)
201 PPM1D c.1405A > G; p.K469E 37.5 Germ line rs61756416 <0.01 Disease causing δ Simultaneous RET E898_E901del (s); reported as “benign” in breast and ovarian cancer (Ruark et al., 2013)
132 RET c.2710T > C; p.S904P 30.8 Somatic Novel Novel Disease causing δ Occurring in -cis with RET E898_E901del (s)
128 RET c.1908_1909insTGCCG
CACG; p.T636_V637delinsCRT
35.4 Somatic rs377767437 CI983210 β Likely pathogenic γ Described germ-line in MEN2A (Höppner et al., 1998)
122 RET c.1886_1891delTGTGCG; p.L629_D631delinsH 38.4 Somatic NA COSM27040 α Likely driver
302 RET c.1894_1902delGAGCT
GTGC; p.E632_C634del
42.9 Somatic Novel Novel Likely driver
252 RET c.3071C > T; p.S1024F 17.6 Somatic Novel Novel Disease causing δ Likely driver
3 TP53 c.847C > T; p.R283C 48.1 n.v. rs149633775 <0.01 COSM10911 α/CM041458 β Conflicting results δ Simultaneous RET C618G (s)
52 TSHR c.1888A > C; p.I630L 31 Somatic COSM26432 α/CM100952 β Disease causing δ Simultaneous TP53 R158C (g)
52 TP53 c.472C > T; p.R158C 52.8 Germinal rs587780068 <0.01 COSM43848 α/CM121763 β Pathogenic γ Simultaneous TSHR I630L (s)
196 EIF1AX c.404G > C; G135A 41.4 n.v. Novel Novel Disease causing δ
198 CHK2 c.341G > A; W114* 10.1 n.v. in blood Novel Novel Disease causing δ

n.v., not detectable by direct sequencing.