Table 2.
Four genes with disease-related mutations were determined to be significant: SLC39A7, GPR19, ZNF717, and TP53 by using the Cancer-Related Analysis of Variants Toolkit (CRAVAT) for genomic variant interpretation.
| HUGO symbol | SLC39A7 | GPR19 | ZNF717 | TP53 |
|---|---|---|---|---|
| Chrom | chr6 | chr12 | chr3 | chr17 |
| Position | 33171585 | 12815066 | 75790516 | 7577539 |
| Strand | + | + | + | + |
| Ref. base(s) | G | G | T | G |
| Alt. base(s) | C | C | A | A |
| Sample ID | P1 | P2 | P3 | P3 |
| Sequence ontology | MS | MS | MS | MS |
| Protein sequence change | E469Q | S106C | H63L | R248W |
| CHASM cancer driver p-value (missense) | 0.0064 | 0.0193 | 0.0247 | 0.0016 |
| CHASM cancer driver FDR (missense) | 0.2 | 0.4 | 0.4 | 0.1 |
| VEST pathogenicity p-value (non-silent) | 0.01875577 | 0.00651641 | 0.025987 | 0.00672533 |
| VEST pathogenicity FDR (non-silent) | 0.25 | 0.2 | 0.3 | 0.2 |
| dbSNP | rs201105907 | rs121912651 | ||
| 1000 Genomes allele frequency | 0 | 0 | 0 | 0 |
| COSMIC ID | COSM4852625 | COSM4594535 | COSM10656 |
And the P-values of CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) and VEST (Variant Effect Scoring Tool) were both set at < 0.05.