Table 2.
Sequence variants in cancer-related genes identified by whole-exome sequencing.
| Gene Symbol: Mutation | Case 1 | Case 2 | Case 3 | Case 4 | Gene Name | KEGG Pathway/Function |
|---|---|---|---|---|---|---|
| ACAP2 :c.C976T:p.R326X | ✓ | ArfGAP with coiled-coil, ankyrin repeat, and PH domains 2 | Endocytosis/Arf6 signaling events | |||
| ACTL6A: c.T673A:p.S225T | ✓ | Actin like 6A | Chromatin organization/DNA Double-Strand Break Repair | |||
| BUB1B :c.T2609C:p.V870A | ✓ | Budding uninhibited by benzimidazoles 1 homolog beta | Cell cycle/Mitotic function (TS) | |||
| DDX11: c.G814A:p.V272M | ✓ | DEAD/H-box helicase 11 | NA/(TS) | |||
| EPB41::c.G1264A:p.E422K | ✓ | Erythrocyte membrane protein band 4.1 | Tight junction/Sertoli–Sertoli Cell Junction dynamics | |||
| MEN1 : c.G301A:p.V101I | ✓ | Menin 1 | Transcriptional misregulation in cancer/Putative TS associated with a syndrome known as multiple endocrine neoplasia type 1 | |||
| ACACA :c.C1948T:p.R650W | ✓ | Acetyl-Coenzyme A carboxylase alpha | Fatty acid biosynthesis, pyruvate metabolism, propanoate metabolism, and insulin signaling pathway | |||
| AMIGO3 : c.C669A:p.C223X | ✓ | Adhesion molecule with Ig like domain 3 | NA | |||
| AVL9: c.37_38del:p.R13fs | ✓ | AVL9 cell migration associated | NA/Late secretory pathway protein AVL9 homolog | |||
| CTBP2: c.C2149T:p.R717C | ✓ | C-terminal binding protein 2 | Wnt signaling, notch signaling, and pathways in cancer | |||
| CTSZ:c.G358A:p.V120M | ✓ | Cathepsin Z | Lysosome/Apoptosis (candidate O) | |||
| DEPTOR : c.A631T:p.R211X | ✓ | DEP domain containing MTOR-interacting protein | mTOR signaling pathway/ | |||
| ENO3 : c.C642G:p.Y214X | ✓ | Enolase 3 | Glycolysis, gluconeogenesis, and RNA degradation/possible TS in lung cancer (17p13.3) | |||
| GRM1:c.C2185A:p.P729T | ✓ | Glutamate receptor, metabotropic 1 | Calcium signaling pathway, neuroactive ligand–receptor interaction, and gap junction | |||
| MYO10: c.C5690T:p.S1897F | ✓ | Myosin X | Fc gamma R-mediated phagocytosis/Epithelial adherens junctions, innate immune system, and RhoGDI (Putative O) | |||
| PFKP:c.G311A:p.R104Q | ✓ | Phosphofructokinase, platelet | Glycolysis, gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and galactose metabolism | |||
| PSCA :c.G326A:p.W109X | ✓ | Prostate stem cell antigen | NA/Overexpressed in prostate cancer | |||
| ROCK1:c.C727T:p.P243S | ✓ | Rho-associated, coiled-coil containing protein kinase 1 | Chemokine signaling pathway, vascular smooth muscle contraction, Wnt signaling pathway, TGF-beta signaling pathway, axon guidance, focal adhesion, leukocyte transendothelial migration, and regulation of actin cytoskeleton/cytoskeleton remodeling | |||
| WWTR1 :c.1199_1200insTTTA:p.L400_X401delinsLX | ✓ | WW domain containing transcription regulator 1 | Hippo signaling pathway/Gene Expression (TS) | |||
| CARS :c.G775A:p.G259S | ✓ | ✓ | Cysteinyl-tRNA synthetase | Aminoacyl-tRNA biosynthesis/Localized in an important tumor-suppressor gene region (11p15.5) | ||
| ANGPTL4 :c.637delC:p.P213fs | ✓ | Angiopoietin-Like 4 | PPAR signaling pathway. Also known as peroxisome proliferator-activated receptor (PPAR). PPAR activates gene expression. | |||
| CUX1: c.2413dupC:p.G804fs | ✓ | Cut like homeobox 1 | NA/FGFR1 mutant receptor activation (TS) | |||
| EPHB6: c.840delC:p.S280fs | ✓ | EPH receptor B6 | Axon guidance/(TS) | |||
| FBN2 :c.G3883A:p.D1295N | ✓ | Fibrillin 2 | NA/ ERK Signaling, and degradation of the extracellular matrix (TS) | |||
| GANAB: c.C583T:p.R195C | ✓ | Glucosidase II alpha subunit | N-Glycan biosynthesis/Metabolism (TS) | |||
| KDM4C:c.3110delG:p.S1037fs | ✓ | Lysine demethylase 4C | NA/Involved in signal transduction, signaling by Rho GTPases, and chromatin organization (Putative O) | |||
| MMP14 :c.C609A:p.Y203X | ✓ | Matrix metallopeptidase 14 | GnRH signaling pathway/Cell adhesion_ECM remodeling | |||
| PTPN23:c.G4189T:p.G1397C | ✓ | Protein tyrosine phosphatase non-receptor type 23 | Involved in the regulation of small nuclear ribonucleoprotein assembly and pre-mRNA splicing (within a putative tumor suppressor region) | |||
| RNASEL : c.G793T:p.E265X | ✓ | Ribonuclease L | Immune system/Mutations in this gene have been associated with predisposition to prostate cancer | |||
| TP73 :c.G749T:p.G250V | ✓ | Tumor protein p73 | p53 signaling pathway, neurotrophin signaling pathway/cell cycle (TS) | |||
| ESRRA: c.C1162T:p.L388F | ✓ | ✓ | Estrogen-related receptor alpha | NA/Nuclear receptor transcription pathway (O) | ||
| ESRRA: c.C1165T:p.R389C | ✓ | ✓ | Estrogen-related receptor alpha | NA/Nuclear receptor transcription pathway (O) | ||
| ABHD5:c.G341T:p.R114L | ✓ | Abhydrolase domain containing 5 | Regulation of lipolysis in adipocytes/Metabolism of lipids and lipoproteins | |||
| ACAD9:c.G976A:p.A326T | ✓ | Acyl-CoA dehydrogenase family member 9 | Mitochondrial biogenesis/Respiratory electron transport | |||
| EPHA7: c.A2009C:p.Q670P | ✓ | EPH receptor A7 | Axon guidance | |||
| EPN3:c.879delA:p.L293fs | ✓ | Epsin 3 | Endocytosis/Promoting senescence (O) | |||
| FAM188A:c.1107delT:p.F369fs | ✓ | Family with sequence similarity 188 member A | NA (Novel TS in NSCLC) | |||
| IQGAP2 :c.G1135C:p.E379Q | ✓ | IQ motif containing GTPase activating protein 2 | Regulation of actin cytoskeleton | |||
| ITIH5: c.1063delG:p.D355fs | ✓ | Inter-alpha-trypsin inhibitor heavy chain family member 5 | NA/RHO GTPase effectors (TS) | |||
| PSAT1:c.G511C:p.A171P | ✓ | Phosphoserine aminotransferase 1 | Glycine, serine, and threonine metabolism, vitamin B6 metabolism/metabolism of amino acids and derivatives | |||
| URI1 :c.G1303T:p.E435X | ✓ | URI1, prefoldin like chaperone | NA/Scaffolding protein with roles in ubiquitination and transcription (Putative TS) |
In bold: mutations associated with an effect at RNA level. NA, not applicable.