Table 4: Coding mutations in the HPV-negative tumor.

ChrPositionReference alleleTumor alleleZygositydbSNP IDRegionTypeGeneTranscript nameExonCDS positionProtein changeStansky*Agrawal**

273679256CGHomoExonicNonsynonymousALMS1NM_0151208c.C5599Gp.L1867VYes
1037451586GAHeterors12766884ExonicNonsynonymousANKRD30ANM_05299716c.G1742Ap.G581EYes
933385733CTHeteroExonicNonsynonymousAQP7NM_0011707c.G657Ap.M219I
1742271663GCHomoExonicNonsynonymousATXN7L3NM_00109883312c.C1012Gp.P338A
6136599913ATHeteroExonicNonsynonymousBCLAF1NM_0010774414c.T106Ap.S36T
126646726AGHeterors1071849ExonicNonsynonymousCD52NM_0018032c.A119Gp.N40S
126646730AGHomors17645ExonicNonsynonymousCD52NM_0018032c.A123Gp.I41M
1942213948CGHeteroExonicNonsynonymousCEACAM5NM_0043632c.C414Gp.F138L
1231242362AGHeterors3950588ExonicNonsynonymousDDX11NM_0306538c.A818Gp.K273RYes
1583657820GCHeteroExonicStoplossFAM103A1NM_0314523c.G50Cp.X17S
676023130TGHomoExonicNonsynonymousFILIP1NM_0156875c.A2418Cp.Q806H, Yes
1152191709CGHeterors6662450ExonicNonsynonymousHRNRNM_0010099313c.G2396Cp.S799TYes
921202136AGHeterors145794215ExonicNonsynonymousIFNA7NM_0210571c.T29Cp.V10A
7100635103ACHeteroExonicNonsynonymousMUC12NM_0011644622c.A1259Cp.E420A
1710404435TGHeteroExonicNonsynonymousMYH1NM_00596327c.A3730Cp.K1244QYesYes
1847364086CTHeteroExonicNonsynonymousMYO5BNM_00108046737c.G4939Ap.D1647NYes
1257106659CGHeteroExonicNonsynonymousNACANM_00111320310c.G2674Cp.E892QYes
121795333CGHeteroExonicNonsynonymousNBPF3NM_0322643c.C286Gp.Q96EYesYes
10115370274TCHomors10749138ExonicNonsynonymousNRAPNM_00617530c.A3442Gp.I1148VYesYes
1148346916GCHomors77069283ExonicNonsynonymousOR4C3NM_0010047021c.G424Cp.V142LYes
114608046TAHeteroExonicNonsynonymousOR52I2NM_0010051701c.T4Ap.C2S
1156128081AGHeterors10896290ExonicNonsynonymousOR8J1NM_0010052051c.A359Gp.Y120CYes
1156143823GAHomors77614949ExonicNonsynonymousOR8U1, OR8U8NM_0010052041c.G724Ap.G242S
X82764042GCHeterors5921979ExonicNonsynonymousPOU3F4NM_0003071c.G710Cp.G237AYes
1943709656CGHomors11883278ExonicNonsynonymousPSG4NM_2136331c.G33Cp.Q11HYes
1421511497CTHomors1243469ExonicNonsynonymousRNASE7NM_0325722c.C346Tp.H116Y
1153004853CTHomors3795382ExonicNonsynonymousSPRR1BNM_0031252c.C32Tp.T11I
633410273TAHomoSplicingNASYNGAP1NM_00677214c.2336+2T>A
1211174327CTHeterors72475481ExonicNonsynonymousTAS2R19NM_1768881c.G844Ap.G282R
1211183676CTHeterors73049072ExonicNonsynonymousTAS2R31NM_1768851c.G259Ap.V87I
735244086ATHeteroExonicNonsynonymousTBX20NM_0010776537c.T999Ap.N333K
2110910347AGHeterors150482ExonicNonsynonymousTPTENM_19926122c.T1409Cp.L470P
799669149CTHeteroExonicNonsynonymousZNF3NM_0329246c.G958Ap.A320T
1957839150AGHomors8100491ExonicNonsynonymousZNF543NM_2135984c.A320Gp.Q107RYes
12124497119TAHeteroExonicNonsynonymousZNF664NM_0012042985c.T428Ap.F143Y
1912501852CTHeteroExonicNonsynonymousZNF799NM_0010808214c.G1360Ap.G454RYes

Chr: chromosome, *mutations present in Stransky et al., Science 2011 [7], **mutations present in Agrawal et al., Science 2011 [6], Homo: homozygous, Hetero: heterozygous.