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
CAPN13	92291	broad.mit.edu	37	2	30987143	30987143	+	Missense_Mutation	SNP	T	T	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:30987143T>C	ENST00000295055.8	-	6	730	c.554A>G	c.(553-555)tAt>tGt	p.Y185C	CAPN13_ENST00000534090.2_Missense_Mutation_p.Y185C|CAPN13_ENST00000465960.2_5'UTR	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	185	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity	p.Y185C(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GAGGAAGCCATAGTGCAGATC	0.577													9	22	---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54753666	54753666	+	Silent	SNP	G	G	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:54753666G>A	ENST00000356805.4	+	2	392	c.111G>A	c.(109-111)gcG>gcA	p.A37A	AC092839.3_ENST00000433475.1_RNA	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	37	Actin-binding.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton	p.A37A(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACAGCTCTGCGCGGCTTTTTG	0.532													16	54	---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25778887	25778887	+	Missense_Mutation	SNP	T	T	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr3:25778887T>C	ENST00000428257.1	-	6	1048	c.941A>G	c.(940-942)aAt>aGt	p.N314S	NGLY1_ENST00000280700.5_Missense_Mutation_p.N314S|NGLY1_ENST00000417874.2_Missense_Mutation_p.N272S|NGLY1_ENST00000396649.3_Missense_Mutation_p.N314S|NGLY1_ENST00000422724.2_Missense_Mutation_p.I163V	NM_001145293.1	NP_001138765.1	Q96IV0	NGLY1_HUMAN	N-glycanase 1	314					glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding	p.N314S(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						TGTAAAACAATTGGCCCACTC	0.413													8	61	---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25678365	25678365	+	Silent	SNP	C	C	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr4:25678365C>T	ENST00000382051.3	+	13	2117	c.2067C>T	c.(2065-2067)gcC>gcT	p.A689A	SLC34A2_ENST00000503434.1_Silent_p.A688A|SLC34A2_ENST00000504570.1_Silent_p.A688A	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	689					cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity	p.A689A(1)	SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				AATGCACGGCCTTGTAGGGGA	0.562			T	ROS1	NSCLC								12	56	---	---	---	---
TMEM184C	55751	broad.mit.edu	37	4	148545026	148545026	+	Missense_Mutation	SNP	T	T	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr4:148545026T>G	ENST00000296582.3	+	2	739	c.165T>G	c.(163-165)ttT>ttG	p.F55L	TMEM184C_ENST00000508208.1_Missense_Mutation_p.F55L	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	55						integral to membrane		p.F55L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						CTGGAATCTTTTTGCTGTTGA	0.323													23	66	---	---	---	---
FZD6	8323	broad.mit.edu	37	8	104340556	104340556	+	Missense_Mutation	SNP	A	A	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr8:104340556A>G	ENST00000358755.4	+	5	1770	c.1453A>G	c.(1453-1455)Att>Gtt	p.I485V	FZD6_ENST00000522566.1_Missense_Mutation_p.I485V|FZD6_ENST00000523739.1_Missense_Mutation_p.I453V|FZD6_ENST00000540287.1_Missense_Mutation_p.I180V	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled family receptor 6	485					angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding	p.I485V(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			GATGACATTAATTGTTGGCAT	0.358													14	47	---	---	---	---
SLK	9748	broad.mit.edu	37	10	105761232	105761232	+	Missense_Mutation	SNP	C	C	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr10:105761232C>A	ENST00000369755.3	+	8	1440	c.895C>A	c.(895-897)Ccc>Acc	p.P299T	SLK_ENST00000335753.4_Missense_Mutation_p.P299T	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	299					apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity	p.P299T(1)		kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TTCCAACAAACCCATCCGAGA	0.388													7	32	---	---	---	---
KRTAP5-9	3846	broad.mit.edu	37	11	71259904	71259904	+	Silent	SNP	C	C	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr11:71259904C>T	ENST00000528743.2	+	1	439	c.201C>T	c.(199-201)ggC>ggT	p.G67G		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	67	8 X 4 AA repeats of C-C-X-P.				epidermis development	keratin filament		p.G67G(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CCTGTGGGGGCTCCAAGGGAG	0.627													8	159	---	---	---	---
BBS10	79738	broad.mit.edu	37	12	76740951	76740951	+	Missense_Mutation	SNP	C	C	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr12:76740951C>T	ENST00000393262.3	-	2	897	c.814G>A	c.(814-816)Gga>Aga	p.G272R		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	272					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding	p.G272R(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						AACTCTGATCCAGAAGTGGAA	0.373									Bardet-Biedl syndrome				12	26	---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91360831	91360831	+	Missense_Mutation	SNP	T	T	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr14:91360831T>G	ENST00000261991.3	-	13	1743	c.1570A>C	c.(1570-1572)Atc>Ctc	p.I524L	RPS6KA5_ENST00000418736.2_Missense_Mutation_p.I524L|RPS6KA5_ENST00000536315.2_Missense_Mutation_p.I445L	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	524	Protein kinase 2.				axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|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	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	p.I524L(2)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		TTCCTCATGATGTAGCTGGCT	0.448													25	54	---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83346500	83346500	+	Missense_Mutation	SNP	C	C	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:83346500C>A	ENST00000261722.3	-	12	1508	c.1301G>T	c.(1300-1302)gGa>gTa	p.G434V	AP3B2_ENST00000535348.1_Missense_Mutation_p.G402V|AP3B2_ENST00000535359.1_Missense_Mutation_p.G434V|RP11-752G15.3_ENST00000560650.1_RNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	434					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity	p.G433V(1)|p.G434V(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			TGCACAGCGTCCAATGGCCTG	0.537													4	14	---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	91027480	91027480	+	Missense_Mutation	SNP	C	C	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:91027480C>G	ENST00000268182.5	+	30	3941	c.3817C>G	c.(3817-3819)Cca>Gca	p.P1273A	IQGAP1_ENST00000560738.1_Missense_Mutation_p.P701A	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1273	C1.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity	p.P1273A(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTGTGATGTCCCAGAGCTTCA	0.423													33	121	---	---	---	---
DNM1P46	196968	broad.mit.edu	37	15	100331077	100331077	+	RNA	SNP	C	C	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:100331077C>A	ENST00000341853.1	-	0	3114					NR_003260.1																						GCGGCCCCTCCCCTCAGAGTA	0.517													4	91	---	---	---	---
TMEM105	284186	broad.mit.edu	37	17	79287646	79287646	+	Missense_Mutation	SNP	C	C	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:79287646C>A	ENST00000332900.1	-	3	744	c.195G>T	c.(193-195)tgG>tgT	p.W65C		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	65						integral to membrane				NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CACAGTCCCCCCAAGGAGACC	0.642													4	112	---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3236652	3236652	+	Splice_Site	SNP	C	C	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:3236652C>G	ENST00000252032.9	-	34	3328	c.3261G>C	c.(3259-3261)caG>caC	p.Q1087H	C20orf194_ENST00000453730.2_3'UTR	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	1087								p.Q1087H(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						TGGAAACCACCTGCTTAGCTG	0.597													8	27	---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40735499	40735499	+	Missense_Mutation	SNP	T	T	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:40735499T>G	ENST00000373198.4	-	25	3609	c.3374A>C	c.(3373-3375)aAt>aCt	p.N1125T	PTPRT_ENST00000373184.1_Missense_Mutation_p.N1116T|PTPRT_ENST00000373201.1_Missense_Mutation_p.N1096T|PTPRT_ENST00000373190.1_Missense_Mutation_p.N1105T|PTPRT_ENST00000356100.2_Missense_Mutation_p.N1115T|PTPRT_ENST00000373193.3_Missense_Mutation_p.N1109T|PTPRT_ENST00000373187.1_Missense_Mutation_p.N1106T	NM_133170.3	NP_573400.3	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T		Tyrosine-protein phosphatase 1.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity	p.N1128T(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CACCCCTTCATTCTCGGCCAT	0.562													4	103	---	---	---	---
