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
AHNAK2	113146	broad.mit.edu	37	14	105413382	105413382	+	Silent	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr14:105413382G>A	ENST00000333244.5	-	7	8525	c.8406C>T	c.(8404-8406)gcC>gcT	p.A2802A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2802						nucleus				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCCCTTGTCGGCCAGGGACA	0.617000													6	477					0	0	1	0	0
POTEF	728378	broad.mit.edu	37	2	130877845	130877845	+	Missense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:130877845C>T	ENST00000357462.5	-	1	337	c.244G>A	c.(244-246)Gct>Act	p.A82T	POTEF_ENST00000360967.5_Missense_Mutation_p.A82T|POTEF_ENST00000361163.4_Missense_Mutation_p.A82T|POTEF_ENST00000409914.2_Missense_Mutation_p.A82T			A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	82						cell cortex	ATP binding			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TCTCCAGAAGCGCCCACGTTG	0.602000													5	388					0	0	1	0	0
SMPD4	55627	broad.mit.edu	37	2	130930857	130930857	+	Silent	SNP	A	A	G	rs151328892	by1000genomes	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:130930857A>G	ENST00000409031.1	-	5	1605	c.457T>C	c.(457-459)Ttg>Ctg	p.L153L	SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000351288.6_Silent_p.L153L|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000339679.7_Intron|SMPD4_ENST00000443958.2_Intron|SMPD4_ENST00000431183.2_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000453750.1_Intron	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	114					sphingomyelin catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|trans-Golgi network	metal ion binding|protein binding|sphingomyelin phosphodiesterase activity|sphingomyelin phosphodiesterase D activity			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CTTACAGGCAAGTAGGAGACA	0.488000													4	116					0	0	1	0	0
IMMP1L	196294	broad.mit.edu	37	11	31477878	31477878	+	Silent	SNP	T	T	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr11:31477878T>G	ENST00000278200.1	-	5	445	c.250A>C	c.(250-252)Aga>Cga	p.R84R	IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000528161.1_5'UTR|IMMP1L_ENST00000532287.1_Silent_p.R84R|IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000526776.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	84					proteolysis	mitochondrial inner membrane	serine-type peptidase activity			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					CCAATTACTCTTTTACAAATA	0.318000													7	50					0	0	1	0	0
RPTN	126638	broad.mit.edu	37	1	152128186	152128186	+	Silent	SNP	A	A	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr1:152128186A>G	ENST00000316073.3	-	3	1453	c.1389T>C	c.(1387-1389)taT>taC	p.Y463Y		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	463	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CTGTCTGACCATAGTGGGAAC	0.512000													9	973					0	0	1	0	0
SDHAP3	0	broad.mit.edu	37	5	1593264	1593264	+	RNA	SNP	C	C	T	rs111700178	by1000genomes	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:1593264C>T	ENST00000436493.2	-	0	361																											AGGGCACATGCCTGACCAAAG	0.557000													5	46					0	0	1	0	0
WFDC9	259240	broad.mit.edu	37	20	44236772	44236772	+	Missense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:44236772G>A	ENST00000326000.1	-	5	464	c.247C>T	c.(247-249)Ctt>Ttt	p.L83F		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	83						extracellular region				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				ATTGATTTAAGGGGCTCTCTA	0.423000													4	185					0	0	1	0	0
FNDC3A	22862	broad.mit.edu	37	13	49765404	49765404	+	Missense_Mutation	SNP	A	A	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr13:49765404A>G	ENST00000492622.2	+	19	2415	c.2110A>G	c.(2110-2112)Ata>Gta	p.I704V	FNDC3A_ENST00000541916.1_Missense_Mutation_p.I704V|FNDC3A_ENST00000398316.3_Missense_Mutation_p.I648V	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	704	Fibronectin type-III 5.					Golgi membrane|integral to membrane				endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		AATGTCTCCTATAGAAAAAGA	0.413000													12	81					0	0	1	0	0
CD97	976	broad.mit.edu	37	19	14507920	14507920	+	Silent	SNP	G	G	A	rs148941728		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr19:14507920G>A	ENST00000242786.5	+	6	590	c.510G>A	c.(508-510)ccG>ccA	p.P170P	CD97_ENST00000358600.3_Intron|CD97_ENST00000357355.3_Intron|CD97_ENST00000587728.1_Intron	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	170	EGF-like 4; calcium-binding (Potential).				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GACAAAACCCGTGCCACAGCT	0.627000													4	108					0	0	1	0	0
ROS1	6098	broad.mit.edu	37	6	117662679	117662679	+	Missense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:117662679C>T	ENST00000368508.3	-	29	4984	c.4786G>A	c.(4786-4788)Gca>Aca	p.A1596T	ROS1_ENST00000368507.3_Missense_Mutation_p.A1590T|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS_HUMAN	c-ros oncogene 1 , receptor tyrosine kinase	1596	Fibronectin type-III 7.				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TGTGAGATTGCCAACTGATAA	0.438000			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								4	95					0	0	1	0	0
GPCPD1	56261	broad.mit.edu	37	20	5559094	5559094	+	Missense_Mutation	SNP	G	G	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:5559094G>T	ENST00000379019.4	-	8	849	c.637C>A	c.(637-639)Cgt>Agt	p.R213S	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	213					glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						TCTGTCCAACGATCAGGCTGC	0.443000													4	75					0.000602214	0.000602214	1	1	0
RYR3	6263	broad.mit.edu	37	15	34115225	34115225	+	Missense_Mutation	SNP	A	A	G			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr15:34115225A>G	ENST00000389232.4	+	81	11094	c.11024A>G	c.(11023-11025)aAg>aGg	p.K3675R	RYR3_ENST00000415757.3_Missense_Mutation_p.K3670R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3675					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAGGAGAAAAAGGATGCTGGA	0.418000													3	52					0	0	1	0	0
CPS1	1373	broad.mit.edu	37	2	211473267	211473267	+	Missense_Mutation	SNP	T	T	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr2:211473267T>C	ENST00000233072.5	+	19	2571	c.2375T>C	c.(2374-2376)aTg>aCg	p.M792T	CPS1_ENST00000430249.2_Missense_Mutation_p.M798T|CPS1_ENST00000451903.2_Missense_Mutation_p.M341T	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	792					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		GGTAGCTCTATGAAAAGTGTA	0.418000													4	117					0	0	1	0	0
CDH6	1004	broad.mit.edu	37	5	31299603	31299603	+	Nonsense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:31299603C>T	ENST00000265071.2	+	5	941	c.676C>T	c.(676-678)Cga>Tga	p.R226*	CDH6_ENST00000514738.1_Nonsense_Mutation_p.R171*	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	226	Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CAACATGGATCGAGAAAACAG	0.438000													4	82					0	0	1	0	0
UVSSA	57654	broad.mit.edu	37	4	1343499	1343499	+	Missense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:1343499G>A	ENST00000389851.4	+	3	733	c.286G>A	c.(286-288)Gca>Aca	p.A96T	UVSSA_ENST00000511216.1_Missense_Mutation_p.A96T|UVSSA_ENST00000507531.1_Missense_Mutation_p.A96T	NM_020894.2	NP_065945.2	Q2YD98	K1530_HUMAN	UV-stimulated scaffold protein A	96																	CACAGACCCCGCACAGCCTCT	0.627000													3	47					0	0	1	0	0
PCDHB5	0	broad.mit.edu	37	5	140517245	140517245	+	Silent	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:140517245C>T	ENST00000231134.5	+	1	2446	c.2229C>T	c.(2227-2229)acC>acT	p.T743T		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN		743					calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCACCGGGACCCTATCCCAGA	0.642000													26	236					0	0	1	0	0
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537000													3	34					0	0	1	0	0
LL22NC03-80A10.6	0	broad.mit.edu	37	22	22661276	22661276	+	RNA	SNP	T	T	C	rs2329972		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr22:22661276T>C	ENST00000426066.1	+	0	360					NR_027293.1																						GATGTACGTCTGCGTTGAGAT	0.488000													5	42					0	0	1	0	0
HRG	3273	broad.mit.edu	37	3	186395480	186395480	+	Silent	SNP	T	T	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr3:186395480T>C	ENST00000232003.4	+	7	1466	c.1386T>C	c.(1384-1386)ccT>ccC	p.P462P		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	462	His/Pro-rich (HRR).				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		ACCGACTCCCTCCTCTAAGAA	0.552000													37	30					0	0	1	0	0
DNM1P47	0	broad.mit.edu	37	15	102304884	102304884	+	RNA	SNP	G	G	C	rs143982735	by1000genomes	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr15:102304884G>C	ENST00000561463.1	+	0	12930																											GCGTGGGAACGAGAAGACACT	0.562000													3	17					0	0	1	0	0
CRB2	286204	broad.mit.edu	37	9	126133381	126133381	+	Missense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr9:126133381G>A	ENST00000373631.3	+	8	1961	c.1960G>A	c.(1960-1962)Gcc>Acc	p.A654T	CRB2_ENST00000359999.3_Missense_Mutation_p.A654T|CRB2_ENST00000373629.2_Missense_Mutation_p.A322T	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 (Drosophila)	654	Laminin G-like 2.					extracellular region|integral to membrane|plasma membrane	calcium ion binding			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CTTGGGAGGCGCCCCAAGCTC	0.617000													4	138					0	0	1	0	0
ANGPTL2	23452	broad.mit.edu	37	9	129870241	129870241	+	Missense_Mutation	SNP	G	G	C			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr9:129870241G>C	ENST00000373425.3	-	2	1387	c.770C>G	c.(769-771)aCt>aGt	p.T257S	RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000491991.1_5'UTR|RALGPS1_ENST00000373436.1_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000259351.5_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	257					multicellular organismal development|signal transduction	extracellular space	receptor binding			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						AGTGGGCATAGTGGGCAGAGG	0.577000													26	52					0	0	1	0	0
ZNRD1-AS1	0	broad.mit.edu	37	6	29977327	29977327	+	RNA	SNP	T	T	C	rs143365191	by1000genomes	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:29977327T>C	ENST00000376797.3	-	0	731				HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA																							GACAGCTGCCTTGTGTGGGAC	0.438000													4	94					0	0	1	0	0
DHX29	54505	broad.mit.edu	37	5	54579230	54579230	+	Missense_Mutation	SNP	C	C	T			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:54579230C>T	ENST00000251636.5	-	11	1914	c.1766G>A	c.(1765-1767)cGg>cAg	p.R589Q	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	589	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|translation initiation factor activity			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AACCACTACCCGATGCCTTTT	0.398000													5	202					0	0	1	0	0
PSMA7	5688	broad.mit.edu	37	20	60715937	60715937	+	Nonsense_Mutation	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr20:60715937G>A	ENST00000370873.4	-	2	286	c.160C>T	c.(160-162)Cag>Tag	p.Q54*	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370861.1_5'UTR|PSMA7_ENST00000370858.3_Nonsense_Mutation_p.Q54*	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	54					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			CTTTCATCCTGCAGTTTGGCC	0.468000													60	94					0	0	1	0	0
ZNRD1-AS1	0	broad.mit.edu	37	6	29977342	29977342	+	RNA	SNP	A	A	T	rs116382006	by1000genomes	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr6:29977342A>T	ENST00000376797.3	-	0	731				HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA																							TGGGACTGAGAGGCAAGATTT	0.438000													5	86					0	0	1	0	0
RET	5979	broad.mit.edu	37	10	43617416	43617416	+	Missense_Mutation	SNP	T	T	C	rs74799832		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr10:43617416T>C	ENST00000355710.3	+	16	2985	c.2753T>C	c.(2752-2754)aTg>aCg	p.M918T	RET_ENST00000340058.5_Missense_Mutation_p.M918T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	918	Protein kinase.		M -> T (in RADYS, MEN2B and MTC; sporadic form; somatic mutation).		homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development	integral to membrane	ATP binding|calcium ion binding|transmembrane receptor protein tyrosine kinase activity	p.M918T(247)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Sunitinib(DB01268)	GTTAAATGGATGGCAATTGAA	0.443000		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				53	131					0	0	1	0	0
GC	2638	broad.mit.edu	37	4	72629626	72629626	+	Silent	SNP	G	G	A	rs149884974	byFrequency	TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:72629626G>A	ENST00000273951.8	-	5	844	c.501C>T	c.(499-501)taC>taT	p.Y167Y	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Silent_p.Y186Y|GC_ENST00000513476.1_Silent_p.Y167Y	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	167	Albumin 1.				hormone biosynthetic process|vitamin D metabolic process	cytosol|lysosomal lumen	actin binding|vitamin D binding|vitamin transporter activity	p.Y167Y(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Cholecalciferol(DB00169)	GAGCTTGTCCGTAATTAGTGG	0.363000													9	83					0	0	1	0	0
FOS	2353	broad.mit.edu	37	14	75746642	75746642	+	Silent	SNP	G	G	A			TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr14:75746642G>A	ENST00000303562.4	+	2	413	c.204G>A	c.(202-204)tcG>tcA	p.S68S	FOS_ENST00000555686.1_5'UTR|FOS_ENST00000555242.1_Silent_p.S68S|FOS_ENST00000554617.1_Silent_p.S68S|FOS_ENST00000535987.1_Silent_p.S68S	NM_005252.3	NP_005243.1	P01100	FOS_HUMAN	FBJ murine osteosarcoma viral oncogene homolog	68					cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway		protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)		CTGCCATCTCGACCAGTCCGG	0.642000													4	80					0	0	1	0	0
OTOP1	133060	broad.mit.edu	37	4	4228274	4228282	+	In_Frame_Del	DEL	CCACAGCAG	CCACAGCAG	-	rs111245977		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr4:4228274_4228282delCCACAGCAG	ENST00000296358.4	-	1	334_342	c.310_318delCTGCTGTGG	c.(310-318)del	p.LLW104del		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	104					biomineral tissue development	extracellular space|integral to membrane		p.L104_W106delLLW(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACCACAGCATCCACAGCAGCTGCAGCAGC	0.727													9	27	---	---	---	---					
RP11-1252I4.2	0	broad.mit.edu	37	5	177398373	177398396	+	RNA	DEL	AGGACGAAGAGCTGGAGAGCGCCA	AGGACGAAGAGCTGGAGAGCGCCA	-	rs70994948		TCGA-QT-A5XK-01A-11D-A35D-08	TCGA-QT-A5XK-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f0127fef-9769-4e69-8d9a-f63deb34af70	26681123-af85-48c8-a76f-8d200d1ea3cc	g.chr5:177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA	ENST00000511650.1	+	0	145																											GTCCCCGGGGAGGACGAAGAGCTGGAGAGCGCCAAGGACGACGA	0.683													3	3	---	---	---	---					
