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Table 3 Prediction of pathogenicity of identified variants

From: Pattern of nucleotide variants of TP53 and their correlation with the expression of p53 and its downstream proteins in a Sri Lankan cohort of breast and colorectal cancer patients

NoHGVS NomenclatureLocationMutation typeNo. of carriers in the study cohortNovel or reported and the code reported in databases for reported variants*Pathogenicity prediction: In-silico or functionalConclusion
cDNAProteinBC patients (N = 30)CRC patients (N = 21)Healthy controls – Males (N = 11)Healthy controls - Females (N = 30)
1c.848_849delGCp.Arg283Hisfs*22E8F1000NovelIn-silicoPath
2c.851_855delCAGAGp.Thr284Argfs*20E8F1000NovelIn-silicoPath
3c.431_433delAGCp.Gln144delE5IF0100NovelIn-silicoPath
4c.637C > Tp.Arg213*E 6NS1100rs397516436In-silicoPath
5c.400 T > Gp.Phe134ValE5M1000COSM43941BothPath
6c.524G > Ap.Arg175HisE 5M0100rs28934578, COSM10648BothPath
7c.581 T > Gp.Leu194ArgE6M0100rs1057519998, COSM44571BothPath
8c.730G > Tp.Gly244CysE7M1000COSM11524BothPath
9c.733G > Ap.Gly245SerE7M0200rs28934575, COSM6932BothPath
10c.743G > Ap.Arg248GlnE7M3000rs11540652/ COSM10662BothPath
11c.840A > Tp.Arg280SerE8M1000COSM44171BothPath
12c.844C > Tp.Arg282TrpE 8M0100rs28934574, COSM10704BothPath
13c.626G > Ap.Arg209LysE6M1000COSM45995BothLP
14c.63C > Tp.Asp21AspE 2S2001rs1800369LB
15c.459C > Tp.Pro153ProE 5S0101rs72661116, COSM43964In-silicoLB
16c.903A > Gp.Pro301ProE8S1000rs72661120/ COSM44165In-silicoLB
17c.-140G > AE 13’UTR1200novelLB
18c.97-29C > AI 3I1203rs17883323In-silicoUS
19c.74 + 16G > CI 2I0100NovelLB
20c.74 + 38C > GI 2I2014624rs1642785LB
21c.96 + 41_96 + 56delACCTGGAGGGCTGGGGI 3I2861127rs59758982LB
22c.97-52G > AI3I0001rs540683791LB
23c.782 + 72C > TI 7I11979rs12947788LB
24c.782 + 92 T > GI 7I11979rs12951053LB
25c.75-42G > AI 2I0010NovelLB
26c.782 + 79C > TI 7I0010NovelLB
27c.673-36G > CI 6I0100rs17880604In-silicoB
  1. Path Pathogenic, LP Likely pathogenic, US variant with uncertain significance, LB Likely Benign, B Benign, FS Frameshift, IF In-frame, M Missense, NS Nonsense, S Silent, I Intron, E Exon, 3’UTR 3′ Untranslated Region
  2. *Details of in-silico and functional prediction are given in supplementary Table 2