Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
COMMD1	150684	broad.mit.edu	37	2	62132935	62132935	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr2:62132935C>A	ENST00000311832.5	+	1	154	c.122C>A	c.(121-123)cCa>cAa	p.P41Q	COMMD1_ENST00000472729.1_Intron|COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	41					copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			CAGCTATATCCAGAGGTGCCA	0.597000													3	49					1	1	1	1	0
AC008103.5	0	broad.mit.edu	37	22	18846029	18846029	+	RNA	SNP	C	C	T	rs148762447	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr22:18846029C>T	ENST00000412938.1	+	0	3387																											TTGAAGGCTGCCTTCAGTGCC	0.647000													5	52					0	0	1	0	0
HOXD12	3238	broad.mit.edu	37	2	176964720	176964720	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr2:176964720C>T	ENST00000406506.2	+	1	263	c.191C>T	c.(190-192)gCg>gTg	p.A64V	HOXD12_ENST00000404162.2_Missense_Mutation_p.A64V			P35452	HXD12_HUMAN	homeobox D12	64				QPA -> TC (in Ref. 1; AAF79044).		nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		GCGCAGCCTGCGGGCGCCACT	0.751000													2	1					0	0	1	0	0
NEIL3	55247	broad.mit.edu	37	4	178283471	178283471	+	Missense_Mutation	SNP	A	A	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr4:178283471A>G	ENST00000264596.3	+	10	1782	c.1664A>G	c.(1663-1665)aAc>aGc	p.N555S		NM_018248.2	NP_060718.2	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	555					base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		CCATTCTGCAACCATGGCAAG	0.388000								Base excision repair (BER), DNA glycosylases					15	73					0	0	1	0	0
CDK5RAP1	51654	broad.mit.edu	37	20	31981850	31981850	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr20:31981850G>A	ENST00000357886.4	-	4	584	c.431C>T	c.(430-432)aCa>aTa	p.T144I	CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000452723.3_Missense_Mutation_p.T54I|CDK5RAP1_ENST00000473997.1_5'UTR			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	144	CDK5 activation inhibition.|MTTase N-terminal.				brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						GATAGAGCATGTGACAAGGAG	0.403000													5	87					0	0	1	0	0
POLR1A	25885	broad.mit.edu	37	2	86297188	86297188	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr2:86297188C>T	ENST00000263857.6	-	13	2197	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K	POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	607					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGTAGGCCTCGGCCCGGCCC	0.572000													19	15					0	0	1	0	0
TP53BP1	7158	broad.mit.edu	37	15	43738684	43738684	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr15:43738684C>A	ENST00000263801.3	-	14	3178	c.2926G>T	c.(2926-2928)Ggg>Tgg	p.G976W	TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	976					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGGGCAGCCCCAGAATCCCCT	0.473000								Other conserved DNA damage response genes					84	87					1.02218e-41	1.27773e-41	1	1	0
PIDD	55367	broad.mit.edu	37	11	799816	799816	+	Splice_Site	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr11:799816G>A	ENST00000347755.5	-	15	2614	c.2474_splice	c.e15+1	p.R825_splice	PIDD_ENST00000411829.2_Splice_Site_p.R808_splice	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2	Q9HB75	PIDD_HUMAN	p53-induced death domain protein	825	Death.				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding										GAGCCTCACCGGAACTCGTGC	0.687000													2	0					0	0	1	0	0
PRPF40B	25766	broad.mit.edu	37	12	50027256	50027256	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr12:50027256G>A	ENST00000261897.1	+	7	973	c.422G>A	c.(421-423)gGc>gAc	p.G141D	PRPF40B_ENST00000548825.2_Missense_Mutation_p.G169D|PRPF40B_ENST00000380281.1_Missense_Mutation_p.G147D			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	147	WW 2.				mRNA processing|RNA splicing	nuclear speck				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						TCGGACACAGGCAAACCTTAT	0.552000													5	319					0	0	1	0	0
AFF1	4299	broad.mit.edu	37	4	88055713	88055713	+	Missense_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr4:88055713T>G	ENST00000307808.6	+	19	3798	c.3378T>G	c.(3376-3378)agT>agG	p.S1126R	AFF1_ENST00000544085.1_Missense_Mutation_p.S765R|AFF1_ENST00000395146.4_Missense_Mutation_p.S1134R	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1126						nucleus	sequence-specific DNA binding transcription factor activity			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TGGGGAGCAGTGGGGTGGCTG	0.567000													10	179					0	0	1	0	0
AC004466.1	0	broad.mit.edu	37	12	48179336	48179336	+	Silent	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr12:48179336C>T	ENST00000599515.1	+	1	631	c.420C>T	c.(418-420)ttC>ttT	p.F140F	HDAC7_ENST00000354334.3_Intron|HDAC7_ENST00000552960.1_Intron|HDAC7_ENST00000427332.2_Intron|HDAC7_ENST00000380610.4_Intron|HDAC7_ENST00000080059.7_Intron																							CCCCAGCCTTCTAGCCACAAG	0.577000													7	12					0	0	1	0	0
SEZ6L	23544	broad.mit.edu	37	22	26743742	26743742	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr22:26743742C>A	ENST00000529632.2	+	11	2466	c.2270C>A	c.(2269-2271)aCc>aAc	p.T757N	SEZ6L_ENST00000404234.3_Missense_Mutation_p.T757N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T757N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T757N|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T530N|SEZ6L_ENST00000411842.2_5'UTR|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T530N|SEZ6L_ENST00000248933.6_Missense_Mutation_p.T757N	NM_001184774.1|NM_001184775.1|NM_001184777.1	NP_001171703.1|NP_001171704.1|NP_001171706.1	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	757	Sushi 3.					endoplasmic reticulum membrane|integral to membrane				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGCTGGAAAACCACTTCTCAC	0.532000													5	66					0.0293803	0.0303131	1	1	0
NEIL3	55247	broad.mit.edu	37	4	178283471	178283471	+	Missense_Mutation	SNP	A	A	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr4:178283471A>G	ENST00000264596.3	+	10	1782	c.1664A>G	c.(1663-1665)aAc>aGc	p.N555S		NM_018248.2	NP_060718.2	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	555					base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		CCATTCTGCAACCATGGCAAG	0.388000								Base excision repair (BER), DNA glycosylases					15	73					0	0	1	0	0
CDK5RAP1	51654	broad.mit.edu	37	20	31981850	31981850	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr20:31981850G>A	ENST00000357886.4	-	4	584	c.431C>T	c.(430-432)aCa>aTa	p.T144I	CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000473997.1_5'UTR|CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000452723.3_Missense_Mutation_p.T54I			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	144	CDK5 activation inhibition.|MTTase N-terminal.				brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						GATAGAGCATGTGACAAGGAG	0.403000													5	87					0	0	1	0	0
LINC00969	0	broad.mit.edu	37	3	195410627	195410627	+	RNA	SNP	A	A	G	rs6583272	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr3:195410627A>G	ENST00000445430.1	+	0	1824																											CCTCAGGTGCAGATTGATGAG	0.473000													3	13					0	0	1	0	0
ANKRD32	84250	broad.mit.edu	37	5	94014548	94014548	+	Silent	SNP	A	A	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr5:94014548A>G	ENST00000265140.5	+	15	2282	c.1863A>G	c.(1861-1863)ggA>ggG	p.G621G		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	621								p.G621G(4)		NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		TATTGGCTGGAATTCTTGGAG	0.308000													34	34					0	0	1	0	0
PIDD	55367	broad.mit.edu	37	11	799816	799816	+	Splice_Site	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr11:799816G>A	ENST00000347755.5	-	15	2614	c.2474_splice	c.e15+1	p.R825_splice	PIDD_ENST00000411829.2_Splice_Site_p.R808_splice	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2	Q9HB75	PIDD_HUMAN	p53-induced death domain protein	825	Death.				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding										GAGCCTCACCGGAACTCGTGC	0.687000													2	0					0	0	1	0	0
MXRA5	25878	broad.mit.edu	37	X	3228358	3228358	+	Missense_Mutation	SNP	A	A	C			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chrX:3228358A>C	ENST00000217939.6	-	7	8040	c.7886T>G	c.(7885-7887)gTc>gGc	p.V2629G		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2629	Ig-like C2-type 10.					extracellular region				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTTCAGGGAGACCAGCCTCTC	0.612000													6	30					0	0	1	0	0
COMMD1	150684	broad.mit.edu	37	2	62132935	62132935	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:62132935C>A	ENST00000311832.5	+	1	154	c.122C>A	c.(121-123)cCa>cAa	p.P41Q	COMMD1_ENST00000472729.1_Intron|COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	41					copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			CAGCTATATCCAGAGGTGCCA	0.597000													3	49					1	1	1	1	0
POLR2B	5431	broad.mit.edu	37	4	57876368	57876368	+	Splice_Site	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr4:57876368T>G	ENST00000510355.1	+	1	28		c.e1+2		POLR2B_ENST00000381227.1_Intron|POLR2B_ENST00000441246.2_Intron|POLR2B_ENST00000431623.2_Intron|POLR2B_ENST00000314595.5_Intron			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					AAGTGGCAGGTAAGTTAAAGT	0.353000													5	9					0	0	1	0	0
EPG5	57724	broad.mit.edu	37	18	43487997	43487997	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr18:43487997C>T	ENST00000282041.5	-	24	4289	c.4255G>A	c.(4255-4257)Gga>Aga	p.G1419R	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1419					autophagy					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TAGGTATCTCCTTTTTGAAAA	0.313000													9	89					0	0	1	0	0
SCMH1	22955	broad.mit.edu	37	1	41514523	41514523	+	Missense_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:41514523T>G	ENST00000402904.2	-	11	1483	c.1115A>C	c.(1114-1116)cAc>cCc	p.H372P	SCMH1_ENST00000361191.5_Missense_Mutation_p.H311P|SCMH1_ENST00000361705.3_Missense_Mutation_p.H325P|SCMH1_ENST00000337495.5_Missense_Mutation_p.H382P|SCMH1_ENST00000326197.7_Missense_Mutation_p.H372P|SCMH1_ENST00000456518.2_Missense_Mutation_p.H214P|SCMH1_ENST00000397171.2_Missense_Mutation_p.H311P|SCMH1_ENST00000397174.2_Missense_Mutation_p.H352P|SCMH1_ENST00000372595.1_Missense_Mutation_p.H311P|SCMH1_ENST00000372596.1_Missense_Mutation_p.H311P|SCMH1_ENST00000372597.1_Missense_Mutation_p.H325P	NM_001031694.2	NP_001026864.1	Q96GD3	SCMH1_HUMAN	sex comb on midleg homolog 1 (Drosophila)	372					anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CTTATCTAAGTGGGGGCCTGT	0.498000													9	102					0	0	1	0	0
TP53BP1	7158	broad.mit.edu	37	15	43738684	43738684	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr15:43738684C>A	ENST00000263801.3	-	14	3178	c.2926G>T	c.(2926-2928)Ggg>Tgg	p.G976W	TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	976					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGGGCAGCCCCAGAATCCCCT	0.473000								Other conserved DNA damage response genes					84	87					1.02218e-41	1.30278e-41	1	1	0
PRPF40B	25766	broad.mit.edu	37	12	50027256	50027256	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr12:50027256G>A	ENST00000261897.1	+	7	973	c.422G>A	c.(421-423)gGc>gAc	p.G141D	PRPF40B_ENST00000548825.2_Missense_Mutation_p.G169D|PRPF40B_ENST00000380281.1_Missense_Mutation_p.G147D			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	147	WW 2.				mRNA processing|RNA splicing	nuclear speck				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						TCGGACACAGGCAAACCTTAT	0.552000													5	319					0	0	1	0	0
GPR160	26996	broad.mit.edu	37	3	169802316	169802316	+	Missense_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr3:169802316T>G	ENST00000355897.5	+	4	1164	c.556T>G	c.(556-558)Tca>Gca	p.S186A		NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	186						integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TTACTGGCTGTCATTTTTCAT	0.398000													9	45					0	0	1	0	0
PURG	29942	broad.mit.edu	37	8	30889322	30889322	+	Missense_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr8:30889322T>G	ENST00000475541.1	-	1	1909	c.977A>C	c.(976-978)aAc>aCc	p.N326T	PURG_ENST00000339382.2_Intron	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	326						nucleus	DNA binding			endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		TTTATGGCTGTTGCAAATTTT	0.388000													3	1					0	0	1	0	0
MTHFR	4524	broad.mit.edu	37	1	11856448	11856448	+	Missense_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:11856448T>G	ENST00000376592.1	-	4	723	c.595A>C	c.(595-597)Aaa>Caa	p.K199Q	MTHFR_ENST00000376590.3_Missense_Mutation_p.K199Q|MTHFR_ENST00000376583.3_Missense_Mutation_p.K240Q|MTHFR_ENST00000376585.1_Missense_Mutation_p.K240Q			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	199					blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	GGGTGGCCTTTGGGGTAACCT	0.562000													7	96					0	0	1	0	0
HOXD12	3238	broad.mit.edu	37	2	176964720	176964720	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:176964720C>T	ENST00000406506.2	+	1	263	c.191C>T	c.(190-192)gCg>gTg	p.A64V	HOXD12_ENST00000404162.2_Missense_Mutation_p.A64V			P35452	HXD12_HUMAN	homeobox D12	64				QPA -> TC (in Ref. 1; AAF79044).		nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		GCGCAGCCTGCGGGCGCCACT	0.751000													2	1					0	0	1	0	0
FCRL1	115350	broad.mit.edu	37	1	157772382	157772382	+	Missense_Mutation	SNP	A	A	C			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:157772382A>C	ENST00000358292.3	-	4	443	c.392T>G	c.(391-393)gTc>gGc	p.V131G	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000368176.3_Missense_Mutation_p.V131G|FCRL1_ENST00000491942.1_Missense_Mutation_p.V131G	NM_001159397.1	NP_001152869.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	131	Ig-like C2-type 2.					integral to membrane|plasma membrane	receptor activity			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GCAGATGAGGACCAGCCTGTC	0.542000													5	23					0	0	1	0	0
POLR1A	25885	broad.mit.edu	37	2	86297188	86297188	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:86297188C>T	ENST00000263857.6	-	13	2197	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K	POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	607					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGTAGGCCTCGGCCCGGCCC	0.572000													19	15					0	0	1	0	0
C1orf172	126695	broad.mit.edu	37	1	27276560	27276560	+	Nonstop_Mutation	SNP	T	T	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:27276560T>G	ENST00000320567.5	-	4	1285	c.1197A>C	c.(1195-1197)taA>taC	p.*399Y		NM_152365.2	NP_689578.2	Q8NAX2	CA172_HUMAN	chromosome 1 open reading frame 172	0										NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CTGGCAGGGGTTAGCAGTACA	0.602000													5	45					0	0	1	0	0
PADI2	11240	broad.mit.edu	37	1	17411155	17411155	+	Frame_Shift_Del	DEL	G	G	-	rs149752241	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr1:17411155delG	ENST00000375486.4	-	8	940	c.877delC	c.(877-879)ggfs	p.R293fs	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	293					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGAGCAATCCGGAATATCACG	0.577													2	4	---	---	---	---					
RP11-453E17.1	0	broad.mit.edu	37	4	68632404	68632404	+	RNA	DEL	C	C	-			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr4:68632404delC	ENST00000500538.2	+	0	1905				RP11-453E17.1_ENST00000502758.1_RNA																							cacacacacacacacacacac	0.443													2	4	---	---	---	---					
RP11-551L14.1	0	broad.mit.edu	37	12	31269189	31269190	+	RNA	INS	-	-	ATCAT	rs35880498		TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr12:31269189_31269190insATCAT	ENST00000542490.1	-	0	165																				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(25)|prostate(3)|stomach(3)|urinary_tract(1)	41						CATGAGAACTCATTACCATGAT	0.351													6	8	---	---	---	---					
PADI2	11240	broad.mit.edu	37	1	17411155	17411155	+	Frame_Shift_Del	DEL	G	G	-	rs149752241	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:17411155delG	ENST00000375486.4	-	8	940	c.877delC	c.(877-879)ggfs	p.R293fs	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	293					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGAGCAATCCGGAATATCACG	0.577													2	4	---	---	---	---					
C2orf78	388960	broad.mit.edu	37	2	74043341	74043342	+	Frame_Shift_Ins	INS	-	-	C	rs74479148	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:74043341_74043342insC	ENST00000409561.1	+	3	2112_2113	c.1991_1992insC	c.(1990-1992)acgfs	p.T664fs		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	664										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						AACACCCAAAACCGCCAGCCAT	0.495													13	48	---	---	---	---					
AC073321.4	0	broad.mit.edu	37	2	217475031	217475032	+	RNA	INS	-	-	AA	rs71401156		TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:217475031_217475032insAA	ENST00000441803.1	+	0	195																											AATTTTATTTCAAAAAAAAAAA	0.376													3	5	---	---	---	---					
RP11-453E17.1	0	broad.mit.edu	37	4	68632404	68632404	+	RNA	DEL	C	C	-			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr4:68632404delC	ENST00000500538.2	+	0	1905				RP11-453E17.1_ENST00000502758.1_RNA																							cacacacacacacacacacac	0.443													2	4	---	---	---	---					
PCLO	27445	broad.mit.edu	37	7	82595145	82595146	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr7:82595145_82595146insG	ENST00000423517.2	-	4	4295_4296	c.3958_3959insC	c.(3958-3960)gccfs	p.A1320fs	PCLO_ENST00000333891.8_Frame_Shift_Ins_p.A1320fs	NM_014510.2	NP_055325.2	Q9Y6V0	PCLO_HUMAN	piccolo presynaptic cytomatrix protein	1259					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGCTGTGGCTGTTCTTTTATT	0.406													9	150	---	---	---	---					
ZAN	7455	broad.mit.edu	37	7	100352835	100352836	+	RNA	INS	-	-	G	rs145118358	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr7:100352835_100352836insG	ENST00000542585.1	+	0	3272				ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000538115.1_RNA	NM_003386.1	NP_003377.1	Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TGACAGAGGCTGTTTTCCCCTT	0.545													16	199	---	---	---	---					
PNPLA8	50640	broad.mit.edu	37	7	108155503	108155504	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr7:108155503_108155504insC	ENST00000426128.2	-	2	557_558	c.432_433insG	c.(430-435)tgtaaafs	p.CK144fs	PNPLA8_ENST00000453144.1_Frame_Shift_Ins_p.CK44fs|PNPLA8_ENST00000436062.1_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000388728.5_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000422087.1_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000257694.8_Frame_Shift_Ins_p.CK144fs|PNPLA8_ENST00000483879.1_Intron	NM_001256009.1	NP_001242938.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	144					fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TTCTGTTTTAACCAGCCACTAT	0.327													8	92	---	---	---	---					
PODXL	5420	broad.mit.edu	37	7	131195806	131195807	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr7:131195806_131195807insG	ENST00000541194.1	-	2	749_750	c.492_493insC	c.(490-495)aggccafs	p.RP164fs	PODXL_ENST00000322985.9_Frame_Shift_Ins_p.RP162fs|PODXL_ENST00000378555.3_Frame_Shift_Ins_p.RP162fs|PODXL_ENST00000537928.1_Frame_Shift_Ins_p.RP162fs	NM_001018111.2	NP_001018121.1	O00592	PODXL_HUMAN	podocalyxin-like	162	Thr-rich.				cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					ACACTGTGGCTGCTTTTCCCCC	0.535													7	329	---	---	---	---					
ADAM28	10863	broad.mit.edu	37	8	24207413	24207414	+	Frame_Shift_Ins	INS	-	-	G	rs139883608	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr8:24207413_24207414insG	ENST00000265769.4	+	19	2137_2138	c.2027_2028insG	c.(2026-2028)ggtfs	p.G676fs	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Frame_Shift_Ins_p.S425fs|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	676					proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding	p.A676V(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TTCCCAATGGCGGTCATTTTTG	0.505													8	140	---	---	---	---					
FBN1	2200	broad.mit.edu	37	15	48704823	48704824	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr15:48704823_48704824insT	ENST00000316623.5	-	65	8623_8624	c.8168_8169insA	c.(8167-8169)tccfs	p.S2723fs	FBN1_ENST00000561429.1_5'UTR	NM_000138.4	NP_000129.3	P35555	FBN1_HUMAN	fibrillin 1	2723					heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CCCGTTTGGGGTAGCCATTGAT	0.515													9	230	---	---	---	---					
CNOT1	23019	broad.mit.edu	37	16	58633164	58633165	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr16:58633164_58633165insC	ENST00000317147.5	-	2	409_410	c.77_78insG	c.(76-78)cgcfs	p.R26fs	CNOT1_ENST00000441024.2_Frame_Shift_Ins_p.R26fs|CNOT1_ENST00000569240.1_Frame_Shift_Ins_p.R26fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	26					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GCTGGCTGGCTCGGTAATTTTT	0.455													7	72	---	---	---	---					
SYNRG	11276	broad.mit.edu	37	17	35914100	35914101	+	Frame_Shift_Ins	INS	-	-	G	rs147693241	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr17:35914100_35914101insG	ENST00000339208.6	-	14	1864_1865	c.1724_1725insC	c.(1723-1725)agcfs	p.S575fs	SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000591288.1_Frame_Shift_Ins_p.S414fs|SYNRG_ENST00000585472.1_Frame_Shift_Ins_p.S496fs|SYNRG_ENST00000502449.2_Frame_Shift_Ins_p.S497fs|SYNRG_ENST00000345615.4_Frame_Shift_Ins_p.S497fs|SYNRG_ENST00000346661.4_Frame_Shift_Ins_p.S575fs|SYNRG_ENST00000394378.2_Frame_Shift_Ins_p.S497fs	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	575	Interaction with A1P1G1 and A1P1G2.				endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CACTATCGGCTGTTTTAAAATC	0.401													40	156	---	---	---	---					
RNF43	54894	broad.mit.edu	37	17	56435501	56435502	+	Frame_Shift_Ins	INS	-	-	G	rs144487242	by1000genomes	TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr17:56435501_56435502insG	ENST00000584437.1	-	8	3590_3591	c.1635_1636insC	c.(1633-1638)tcgccafs	p.P546fs	RNF43_ENST00000583753.1_Frame_Shift_Ins_p.P505fs|RNF43_ENST00000577625.1_Frame_Shift_Ins_p.P419fs|RNF43_ENST00000407977.2_Frame_Shift_Ins_p.P546fs|RNF43_ENST00000500597.2_Frame_Shift_Ins_p.P505fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Frame_Shift_Ins_p.P546fs|RNF43_ENST00000581868.1_Frame_Shift_Ins_p.P419fs			Q68DV7	RNF43_HUMAN	ring finger protein 43	546						endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGGACATGGCTGGAAACCTGGG	0.624													11	152	---	---	---	---					
SIX5	147912	broad.mit.edu	37	19	46269225	46269226	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr19:46269225_46269226insG	ENST00000317578.6	-	3	2134_2135	c.1753_1754insC	c.(1753-1755)gccfs	p.A585fs	AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR	NM_175875.4	NP_787071.2	Q8N196	SIX5_HUMAN	SIX homeobox 5	585						cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		CTTCAGTGGCAGGGCCAGGCCG	0.698													4	8	---	---	---	---					
RSPH6A	81492	broad.mit.edu	37	19	46299147	46299149	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr19:46299147_46299149delCCT	ENST00000221538.3	-	6	2274_2276	c.2132_2134delAGG	c.(2131-2136)ggc>g	p.EG711del	RSPH6A_ENST00000597055.1_3'UTR|RSPH6A_ENST00000600188.1_In_Frame_Del_p.EG447del	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	711	Glu-rich.					intracellular				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GTctcctcgccctcctcctcctc	0.557													7	186	---	---	---	---					
