Table 3.
Prediction of pathogenicity of identified variants
| No | HGVS Nomenclature | Location | Mutation type | No. of carriers in the study cohort | Novel or reported and the code reported in databases for reported variants | *Pathogenicity prediction: In-silico or functional | Conclusion | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| cDNA | Protein | BC patients (N = 30) | CRC patients (N = 21) | Healthy controls – Males (N = 11) | Healthy controls - Females (N = 30) | ||||||
| 1 | c.848_849delGC | p.Arg283Hisfs*22 | E8 | F | 1 | 0 | 0 | 0 | Novel | In-silico | Path |
| 2 | c.851_855delCAGAG | p.Thr284Argfs*20 | E8 | F | 1 | 0 | 0 | 0 | Novel | In-silico | Path |
| 3 | c.431_433delAGC | p.Gln144del | E5 | IF | 0 | 1 | 0 | 0 | Novel | In-silico | Path |
| 4 | c.637C > T | p.Arg213* | E 6 | NS | 1 | 1 | 0 | 0 | rs397516436 | In-silico | Path |
| 5 | c.400 T > G | p.Phe134Val | E5 | M | 1 | 0 | 0 | 0 | COSM43941 | Both | Path |
| 6 | c.524G > A | p.Arg175His | E 5 | M | 0 | 1 | 0 | 0 | rs28934578, COSM10648 | Both | Path |
| 7 | c.581 T > G | p.Leu194Arg | E6 | M | 0 | 1 | 0 | 0 | rs1057519998, COSM44571 | Both | Path |
| 8 | c.730G > T | p.Gly244Cys | E7 | M | 1 | 0 | 0 | 0 | COSM11524 | Both | Path |
| 9 | c.733G > A | p.Gly245Ser | E7 | M | 0 | 2 | 0 | 0 | rs28934575, COSM6932 | Both | Path |
| 10 | c.743G > A | p.Arg248Gln | E7 | M | 3 | 0 | 0 | 0 | rs11540652/ COSM10662 | Both | Path |
| 11 | c.840A > T | p.Arg280Ser | E8 | M | 1 | 0 | 0 | 0 | COSM44171 | Both | Path |
| 12 | c.844C > T | p.Arg282Trp | E 8 | M | 0 | 1 | 0 | 0 | rs28934574, COSM10704 | Both | Path |
| 13 | c.626G > A | p.Arg209Lys | E6 | M | 1 | 0 | 0 | 0 | COSM45995 | Both | LP |
| 14 | c.63C > T | p.Asp21Asp | E 2 | S | 2 | 0 | 0 | 1 | rs1800369 | – | LB |
| 15 | c.459C > T | p.Pro153Pro | E 5 | S | 0 | 1 | 0 | 1 | rs72661116, COSM43964 | In-silico | LB |
| 16 | c.903A > G | p.Pro301Pro | E8 | S | 1 | 0 | 0 | 0 | rs72661120/ COSM44165 | In-silico | LB |
| 17 | c.-140G > A | – | E 1 | 3’UTR | 1 | 2 | 0 | 0 | novel | – | LB |
| 18 | c.97-29C > A | – | I 3 | I | 1 | 2 | 0 | 3 | rs17883323 | In-silico | US |
| 19 | c.74 + 16G > C | – | I 2 | I | 0 | 1 | 0 | 0 | Novel | – | LB |
| 20 | c.74 + 38C > G | – | I 2 | I | 20 | 14 | 6 | 24 | rs1642785 | – | LB |
| 21 | c.96 + 41_96 + 56delACCTGGAGGGCTGGGG | – | I 3 | I | 28 | 6 | 11 | 27 | rs59758982 | – | LB |
| 22 | c.97-52G > A | – | I3 | I | 0 | 0 | 0 | 1 | rs540683791 | – | LB |
| 23 | c.782 + 72C > T | – | I 7 | I | 11 | 9 | 7 | 9 | rs12947788 | – | LB |
| 24 | c.782 + 92 T > G | – | I 7 | I | 11 | 9 | 7 | 9 | rs12951053 | – | LB |
| 25 | c.75-42G > A | – | I 2 | I | 0 | 0 | 1 | 0 | Novel | – | LB |
| 26 | c.782 + 79C > T | – | I 7 | I | 0 | 0 | 1 | 0 | Novel | – | LB |
| 27 | c.673-36G > C | – | I 6 | I | 0 | 1 | 0 | 0 | rs17880604 | In-silico | B |
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
*Details of in-silico and functional prediction are given in supplementary Table 2