Table 3 Pathogenic/likely pathogenic variants detected by next-generation sequencing.
From: Clinicopathological and genomic features in patients with head and neck neuroendocrine carcinoma
Patient ID | Gene | VAF | 1000 Genomes Browser | Nucleotide change | Type of mutation | Amino acid change | COSMIC recurrence | ClinVar | SIFT | PolyPhen2 | Fusion gene | TMB (mut/Mb) | MSI quantitative score | Clinical stage | OS (days) | OS status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2 | HIST3H3 | 0.49 | c.203_204delTCinsAA | Nonsense | p.F68* | NA | NA | NA | NA | 10.3 | 0.000 | Locally advanced | 3405 | Alive | ||
CDKN2A, RP11-145E5.5 | 0.22 | c.374_384delATGTCGCACGG | Frameshift | p.D125fs | NA | NA | NA | |||||||||
ANKRD26 | 0.16 | c.2084 C > G | Nonsense | p.S695* | NA | NA | NA | NA | ||||||||
3 | TP53 | 0.90 | rs11540652 | c.743 G > A | Missense | p.Arg248Gln | 1205 | Pathogenic | Damaging | Probably damaging | 3.9 | 0.042 | Locally advanced | 329 | Dead | |
RB1 | 0.77 | c.713_714delCA | Frameshift | p.P238fs | NA | NA | NA | NA | ||||||||
4 | RB1 | 0.57 | rs1131690858 | c.2520 + 3_2520 + 6del | Splice donor site | 2 | Pathogenic | NA | NA | SEC11C-MYC | 6.3 | 0.000 | Metastatic | 581 | Dead | |
6 | None | 7.1 | 0.030 | Locally advanced | 411 | Dead | ||||||||||
8 | TP53 | 0.85 | c.1027 G > T | Nonsense | p.E343* | 25 | NA | NA | NA | 5.5 | 0.022 | Metastatic | 124 | Dead | ||
11 | SMARCA4 | 0.37 | c.3031delA | Frameshift | p.M1011fs | NA | NA | NA | NA | 7.1 | 0.041 | Locally advanced | 3491 | Alive | ||
13 | RB1 | 0.46 | rs398123331 | c.1399 C > T | Nonsense | p.Arg467Ter | 14 | Pathogenic | NA | NA | 5.5 | 0.030 | Locally advanced | 2295 | Alive | |
TP53 | 0.88 | rs876660726 | c.902delC | Frameshift | p.Pro301Glnfs | NA | Pathogenic | NA | NA | |||||||
14 | None | FGFR3-TACC3 | 4.7 | 0.050 | Metastatic | 502 | Dead | |||||||||
15 | TP53 | 0.41 | rs397516436 | c.637 C > T | Nonsense | p.Arg213Ter | 636 | Pathogenic | NA | NA | 4.7 | 0.046 | Locally advanced | 205 | Dead | |
18 | None | 11.0 | 0.030 | Locally advanced | 1055 | Dead | ||||||||||
19 | NOTCH1 | 0.20 | NA | c.4222 G > T | Nonsense | p.Glu1408Ter | 1 | Pathogenic | NA | NA | 7.1 | 0.010 | Locally advanced | 1552 | Alive | |
20 | PREX2 | 0.11 | c.3271 G > T | Nonsense | p.G1091* | NA | NA | NA | NA | 17.2 | 0.010 | Locally advanced | 1433 | Alive | ||
NOTCH1 | 0.53 | c.1417 G > T | Nonsense | p.E473* | NA | NA | NA | NA | ||||||||
22 | PIK3CA | 0.34 | rs1057519941 | c.1031 T > G | Missense | p.Val344Gly | 33 | Likely pathogenic | Damaging | Probably damaging | 7.1 | 0.058 | Locally advanced | 238 | Dead | |
PTEN | 0.55 | rs121909224 | c.388 C > T | Nonsense | p.Arg130Ter | 145 | Pathogenic | NA | NA | |||||||
TP53 | 0.81 | c.406 C > T | Nonsense | p.Q136* | 75 | NA | NA | NA | ||||||||
24 | FAT1 | 0.62 | c.7259 C > G | Nonsense | p.S2420* | NA | NA | NA | NA | 7.1 | 0.056 | Locally advanced | 454 | Alive | ||
TP53 | 0.50 | rs876659802 | c.833 C > T | Missense | p.Pro278Leu | 119 | Pathogenic | Damaging | Probably damaging | |||||||
