Table 2. Somatic variants in HCC samples.
| Region/gene | Position | Replacement | Reported | AA change | Inter-species conservation# |
|---|---|---|---|---|---|
| Control region | 71 | G-A | Yes | ||
| 72 | T-C | Yes | |||
| 74 | T-G | Yes | |||
| 94 | G-A | Yes | |||
| 157 | T-C | No | |||
| 294-341 | Del | No | |||
| 302 | A-AC | Yes | |||
| 353 | C-CC | Yes | |||
| 394 | C-A | No | |||
| 528 | T-C | No | |||
| 540 | A-C | No | |||
| 573 | C-CCCCC | Yes | |||
| 16368 | T-C | Yes | |||
| 16540 | C-T | Yes | |||
| MT-TF | 617 | G-A | No | ||
| 12S rRNA | 988 | G-A | Yes | ||
| 1472 | G-A | Yes | |||
| 16S rRNA | 2623 | A-G | Yes | ||
| MT-ND1 | 3710 | C-T | Yes | Ala-Val | 16/17 |
| 3877 | T-C | No | Ala-Pro | 17/17 | |
| MT-ND2 | 4963 | G-A | No | Gly-Asp | 17/17 |
| 5112 | G-A | Yes | Ala-Thr | 5/17 | |
| MT-TN | 5705 | A-G | Yes | ||
| MT-CO1 | 6582 | G-A | No | Asp-Asn | 17/17 |
| 7347 | G-A | Yes | Val-Ile | 16/17 | |
| MT-ATP8 | 8369 | C-G | Yes | Pro - Ser | 17/17 |
| MT-ATP6 | *8628 | C-CC | No | frameshift (stop) | 12/17 |
| MT-CO3 | *9253 | G-A | Yes | Trp-stop | 17/17 |
| 9670 | A-G | Yes | Asn - Ser | 13/17 | |
| MT-ND3 | 10365 | G-A | Yes | Ala-Thr | 13/17 |
| MT-ND4L | 10689 | G-A | Yes | Gly-Ser | 16/17 |
| MT-ND4 | 11226 | G-A | No | Gly-Asp | 17/17 |
| 11929 | T-C | Yes | Syn | ||
| MT-TS2 | 12209 | G-A | Yes | ||
| MT-ND5 | 12634 | A-G | Yes | Ile-Val | 14/17 |
| 12711 | A-G | Yes | Syn | 17/17 | |
| 12954 | T-C | Yes | Syn | 17/17 | |
| 13063 | G-A | Yes | Val-Ile | 17/17 | |
| 13267 | G-T | No | Gly-Trp | 17/17 | |
| *13475 | T-Del | No | frameshift (stop) | 17/17 | |
| 13603 | A-G | No | Ser - Gly | 17/17 | |
| 13676 | A-G | Yes | Asn - Ser | 15/17 | |
| 13718 | G-A | Yes | Ser-Asn | 17/17 | |
| MT-CYB | *14984 | C-CA | No | frameshift (stop) | 15/17 |
| 15860 | A-G | Yes | Ile - Val | 12/17 | |
| MT-TP | 16017 | T-C | Yes |
*, four truncating mutations in the protein-coding region.
#, 17 species: Bos taurus, Pan troglodytes, Cebus albifrons, Gorilla gorilla, Homo sapiens, Hylobates lar, Lemur catta, Macaca mulatta, Macaca sylvanus, Mus musculus, Nycticebus coucang, Pan paniscus, Pongo Pygmaeus, Tarsius bancanus, and Xenopus laevis.
Conservation was calculated by comparing the human nucleotide variants with those of other 16 vertebrates, and defined as the percentage of species from the list of 17 different vertebrates that had the wild-type nucleotide at that position.