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1 Table S5: List of gene mutations identified with Sanger sequencing/qPCR in tumor samples
2 Case ID hmGBC vs
non-hm
tumors
Site of primary disease Gene CCDS ID mutation
type
protein coding function exon Functional
Domain/Moti
f (HPRD
database)
COSMIC Predicted
functional
implication
(COSMIC)
3 CH014 non-hm Extrahepatic CTNNB1 2694.1 missense p.D164E c.492C>G missense 3 ARM    
4 CH014 non-hm Extrahepatic KRAS 8702.1 missense p.G12A c.35G>C missense 1 RAS COSM522 Pathogenic
5 CH040 non-hm Extrahepatic PIK3R1 3993.1 missense p.S429P c. 1285T>C missense 9      
6 CH045 non-hm Extrahepatic KRAS 8702.1 missense p.E63K c.187G>A missense 2 RAS COSM27159 Pathogenic
7 CH105 non-hm Extrahepatic PTEN 31238.1 missense p.V365I c.1093G>A missense 9   COSM5056 (rs758542021) Pathogenic
8 CH112 non-hm Extrahepatic CTNNB1 2694.1 missense p.V167M c. 499G>A missense 4 ARM    
9 CH112 non-hm Extrahepatic PIK3R1 3993.1 missense p.E485G c.1454A>G missense 11    
10 CH112 non-hm Extrahepatic PIK3R1 3993.1 missense p.L573P c. 1718T>C missense 12   COSM1069619 Pathogenic
11 CH112 non-hm Extrahepatic PTEN 31238.1 missense p.D236N c.706G>A missense 7    
12 CH112 non-hm Extrahepatic PTEN 31238.1 missense p.V351I c.1051G>A missense 9    
13 CH112 non-hm Extrahepatic PTEN 31238.1 missense p.R14T c.41G>C missense 1    
14 CH112 non-hm Extrahepatic PTEN 31238.1 missense p.V365I c.1093G>A missense 9   COSM5056 (rs758542021) Pathogenic
15 CH147 non-hm Extrahepatic CTNNB1 2694.1 missense p.A117T c.349G>A missense 3      
16 CH159 non-hm Extrahepatic CTNNB1 2694.1 missense p.V122D c.365T>A missense 3      
17 CH159 non-hm Extrahepatic PTEN 31238.1 nonsense p.R233* c.697C>T nonsense 7   COSM5154 Pathogenic
18 CH002 hmGBC Gallbladder PTEN 31238.1 missenseframeshift p.L23fs*1 c.del68T frameshift 1      
19 CH018 hmGBC Gallbladder PIK3CA 43171.1 missense p.E545K c.1633G>A missense 9 PI3KA COSM763 Pathogenic
20 CH120 hmGBC Gallbladder PIK3R1 3993.1 nonsense p.Q415* c.1243C>T nonsense 9   COSM4834480 Pathogenic
21 CH120 hmGBC Gallbladder PIK3R1 3993.1 missense p.S429F c.1286C>T missense 9   COSM5537072 Pathogenic
22 CH120 hmGBC Gallbladder PIK3R1 3993.1 missense p.R577G c.1729A>G missense 12      
23 CH005 non-hm Gallbladder PTEN 31238.1 missense p.H259Y c.775C>T missense 7    
24 CH010 non-hm Gallbladder PIK3CA 43171.1 missense p.E545K c.1633G>A missense 9 PI3KA COSM763 Pathogenic
25 CH010 non-hm Gallbladder PTEN 31238.1 missense p.A192T c.574G>A missense 6   COSM1492349 Pathogenic
26 CH010 non-hm Gallbladder PTEN 31238.1 missense p.P204L c.611C>T missense 6   COSM1577256 Pathogenic
27 CH010 non-hm Gallbladder PTEN 31238.1 missense p.M264I c.792G>A missense 7   COSM5351742 Pathogenic
28 CH026 non-hm Gallbladder CTNNB1 2694.1 missense p.G235E c.704G>A missense 4 ARM    
29 CH026 non-hm Gallbladder PIK3R1 3993.1 missense p. E411K c.1231G>A missense 9 SH2    
30 CH028 non-hm Gallbladder CTNNB1 2694.1 missense p.R274C c.820C>T missense 5 ARM    
31 CH028 non-hm Gallbladder PIK3R1 3993.1 nonsense p.R544* c.1630A>T nonsense 12 Coiled Coil COSM1069604 Neutral
32 CH028 non-hm Gallbladder PTEN 31238.1 missense p.S364F c.1091C>T missense 9      
33 CH029 non-hm Gallbladder PIK3R1 3993.1 missense p.S412P c. 1234T>C missense 9 SH2    
34 CH030 non-hm Gallbladder PIK3R1 3993.1 nonsense p.L581* c.1742T>A nonsense 12      
35 CH032 non-hm Gallbladder PIK3CA 43171.1 missense p.E545K c.1633G>A missense 9 PI3KA COSM763 Pathogenic
36 CH035 non-hm Gallbladder CTNNB1 2694.1 missense p.H224Y c.670C>T missense 4 ARM    
37 CH035 non-hm Gallbladder PTEN 31238.1 missense p.S229P c.685C>T missense 7    
38 CH035 non-hm Gallbladder PTEN 31238.1 missense p.D52N c.154G>A missense 2 DSPC COSM5059 Pathogenic
39 CH035 non-hm Gallbladder PTEN 31238.1 nonsense p.E352* c.1054G>T nonsense 9   COSM5297 Pathogenic
40 CH037 non-hm Gallbladder CTNNB1 2694.1 missense p.D299N c.895G>A missense 5 ARM    
41 CH037 non-hm Gallbladder CTNNB1 2694.1 missense p.N161Y c.481A>T missense 3 ARM    
42 CH037 non-hm Gallbladder CTNNB1 2694.1 missense p.T201I c. 602C>T missense 4 ARM    
43 CH037 non-hm Gallbladder PIK3CA 43171.1 missense p.E545K c.1633G>A missense 9 PI3KA COSM763 Pathogenic
44 CH037 non-hm Gallbladder PIK3R1 3993.1 missenseframeshift p.P418fs*5 c. 1254delC frameshift 9      
45 CH037 non-hm Gallbladder PTEN 31238.1 missense p.G20E c.59G>A missense 1   COSM5094 Pathogenic
46 CH044 non-hm Gallbladder CTNNB1 2694.1 missense p.L229M c.685C>A missense 4 ARM    
47 CH044 non-hm Gallbladder CTNNB1 2694.1 missense p.M282I c. 846G>A missense 5 ARM    
48 CH044 non-hm Gallbladder CTNNB1 2694.1 missense p.P154T c. 461C>A missense 3 ARM    
49 CH044 non-hm Gallbladder PIK3CA 43171.1 missense p.E542K c.1624G>A missense 9 PI3KA COSM760 Pathogenic
50 CH044 non-hm Gallbladder PTEN 31238.1 missense p.D375N c.1123G>A missense 9   COSM5062 Pathogenic
51 CH044 non-hm Gallbladder PTEN 31238.1 missense p.S364F c.1091C>T missense 9      
52 CH046 non-hm Gallbladder CTNNB1 2694.1 missense p.K281E c.841A>G missense 5 ARM    
53 CH047 non-hm Gallbladder PIK3R1 3993.1 missense p.A553T c.1657G>A missense 12 Coiled Coil    
54 CH055 non-hm Gallbladder CTNNB1 2694.1 missense p.G268R c.802G>A missense 5 ARM    
55 CH055 non-hm Gallbladder CTNNB1 2694.1 missense p.V283I c.847G>A missense 5 ARM    
56 CH055 non-hm Gallbladder KRAS 8702.1 missense p.A59T c.175G>A missense 2 RAS COSM546 Pathogenic
57 CH055 non-hm Gallbladder PTEN 31238.1 missense p.G165R c.493G>A missense 6 DSPC COSM5091 Pathogenic
58 CH055 non-hm Gallbladder PTEN 31238.1 missense p.S227F c.680C>T missense 7   COSM5095 Pathogenic
59 CH056 non-hm Gallbladder CTNNB1 2694.1 nonsense p.Q309* c. 925C>T nonsense 5 ARM    
60 CH056 non-hm Gallbladder PIK3R1 3993.1 missense p.M582I c.1746G>A missense 13      
61 CH059 non-hm Gallbladder CTNNB1 2694.1 missense p.V199I c.595G>A missense 4 ARM COSM1044591 Pathogenic
62 CH059 non-hm Gallbladder CTNNB1 2694.1 missense p.V283I c.847G>A missense 5 ARM    
63 CH059 non-hm Gallbladder PTEN 31238.1 missense p.R172L c.515G>A missense 6 DSPC    
64 CH061 non-hm Gallbladder CTNNB1 2694.1 missense p.T120I c.359C>T missense 3      
65 CH062 non-hm Gallbladder CTNNB1 2694.1 missense p.E226K c.676G>A missense 4 ARM    
66 CH062 non-hm Gallbladder CTNNB1 2694.1 missense p.G216E c.647G>A missense 4 ARM    
67 CH062 non-hm Gallbladder PTEN 31238.1 Nonstop extension p.*404L (p.*404LIFFYQEG*) c.1211G>T Nonstop extension 9   COSM5333 Pathogenic
68 CH101 non-hm Gallbladder CTNNB1 2694.1 missense p.V175I c.523G>A missense 4 ARM    
69 CH102 non-hm Gallbladder CTNNB1 2694.1 missense p.H134Y c.400C>T missense 3      
70 CH114 non-hm Gallbladder KRAS 8702.1 missense p.G12D c.35G>A missense 1 RAS COSM521 Pathogenic
71 CH114 non-hm Gallbladder PTEN 31238.1 missense p.R41G c.121A>G missense 2 DSPC    
72 CH130 non-hm Gallbladder CTNNB1 2694.1 missenseframeshift p.A295fs*10 c.883delG frameshift 5 ARM    
73 CH130 non-hm Gallbladder CTNNB1 2694.1 missense p.L244F c.730C>T missense 4 ARM    
74 CH130 non-hm Gallbladder PIK3R1 3993.1 missense p.R577K c.1730G>A missense 12   COSM1069630 Pathogenic
75 CH132 non-hm Gallbladder CTNNB1 2694.1 missense p.P100L c.299C>T missense 3      
76 CH132 non-hm Gallbladder PIK3R1 3993.1 missense p.S412F c. 1235C>T missense 9 SH2    
77 CH132 non-hm Gallbladder PTEN 31238.1 missense p.V222M c.664G>A missense 7    
78 CH132 non-hm Gallbladder PTEN 31238.1 missense p.P244S c.730C>T missense 7   COSM5119 Pathogenic
79 CH133 non-hm Gallbladder KRAS 8702.1 missense p.G13D c.38G>A missense 1 RAS COSM532 Pathogenic
80 CH136 non-hm Gallbladder CTNNB1 2694.1 missense p.A116V c.347C>T missense 3      
81 CH136 non-hm Gallbladder CTNNB1 2694.1 missense p.A284T c.850G>A missense 5 ARM    
82 CH136 non-hm Gallbladder CTNNB1 2694.1 missense p.A2T c.4G>A missense 1      
83 CH136 non-hm Gallbladder PIK3CA 43171.1 missense p.E542K c.1624G>A missense 9 PI3KA COSM760 Pathogenic
84 CH136 non-hm Gallbladder PTEN 31238.1 missense p.A192V c.575C>T missense 6      
85 CH142 non-hm Gallbladder PTEN 31238.1 missense p.P190L c.569C>T missense 6   COSM249903 none
86 CH155 non-hm Gallbladder CTNNB1 2694.1 missense p.M88I c.264G>A missense 3      
87 CH155 non-hm Gallbladder PIK3R1 3993.1 missense p.M582I c.1746G>A missense 13      
88 CH155 non-hm Gallbladder PTEN 31238.1 missense p.D381N c.1141G>A missense 9      
89 CH156 non-hm Gallbladder CTNNB1 2694.1 missense p.M131T c.392C>T missense 3      
90 CH156 non-hm Gallbladder PTEN 31238.1 missense p.C105Y c.314G>A missense 5 DSPC COSM5113 Pathogenic
91 CH158 non-hm Gallbladder PIK3R1 3993.1 missense p.D569N c.1705A>G missense 12      
92 CH158 non-hm Gallbladder PTEN 31238.1 missense p.V175E c.524T>A missense 6 DSPC    
93 CH177 non-hm Gallbladder KRAS 8702.1 missense p.G12A c.35G>C missense 1 RAS COSM522 Pathogenic
94 CH177 non-hm Gallbladder PIK3R1 3993.1 nonsense p. W597* c. 1791G>A nonsense 13      
95 CH184 non-hm Gallbladder PIK3R1 3993.1 missense p.M582V c.1744A>G missense 12      
96 CH184 non-hm Gallbladder PIK3R1 3993.1 missense p.R577S c.1731A>G missense 12      
97 CH185 non-hm Gallbladder CTNNB1 2694.1 missense p.M107I c.321G>A missense 3      
98 CH185 non-hm Gallbladder CTNNB1 2694.1 missense p.V166M c. 496G>A missense 4 ARM    
99 CH185 non-hm Gallbladder PTEN 31238.1 missense p.H185Y c.553C>T missense 6      
100 CH008 non-hm Intrahepatic CTNNB1 2694.1 missense p.A269V c.806C>T missense 5 ARM    
101 CH008 non-hm Intrahepatic KRAS 8702.1 missense p.G12V c.35G>T missense 1 RAS COSM520 Pathogenic
102 CH008 non-hm Intrahepatic PTEN 31238.1 nonsense p.Q214* c.640C>T nonsense 7   COSM5150 (rs121909227) Pathogenic
103 CH008 non-hm Intrahepatic PTEN 31238.1 missense p.P367L c.1100C>T missense 9      
104 CH163 non-hm Intrahepatic CTNNB1 2694.1 missense p.V122I c.364G>A missense 4      
105 CH163 non-hm Intrahepatic KRAS 8702.1 missense p.G12A c.35G>C missense 1 RAS COSM522 Pathogenic
106 CH166 non-hm Intrahepatic CTNNB1 2694.1 missense p.K288R c.863A>G missense 5 ARM    
107 CH166 non-hm Intrahepatic PTEN 31238.1 missense p.P204L c.611C>T missense 6   COSM1577256 Pathogenic
108 CH168 non-hm Intrahepatic PIK3R1 3993.1 missense p.A360T c.1078G>A missense 8 SH2    
109 CH168 non-hm Intrahepatic PIK3R1 3993.1 missense p.M582I c.1746G>A missense 13      
110 CH176 non-hm Intrahepatic CTNNB1 2694.1 missense p.G277D c.830G>A missense 5 ARM COSM1044594 Pathogenic
111 CH176 non-hm Intrahepatic PIK3CA 43171.1 missense p.A1046T c.3136G>A missense 20 PI3KC COSM27273 Pathogenic
112 CH176 non-hm Intrahepatic PIK3CA 43171.1 missense p.S1003P c.3007T>C missense 20 PI3KC COSM328020 Pathogenic
113 CH176 non-hm Intrahepatic PIK3R1 3993.1 nonsense p.L424* c.1271T>A nonsense 9    
114 CH176 non-hm Intrahepatic PIK3R1 3993.1 missense p.R503Q c.1508G>A missense 11   Pathogenic
115 CH176 non-hm Intrahepatic PTEN 31238.1 missense p.R41G c.121A>G missense 2 DSPC    
116 CH180 non-hm Intrahepatic PIK3R1 3993.1 missense p. K382E c.1144A>G missense 9 SH2