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
NOTCH2	4853	broad.mit.edu	37	1	120539834	120539834	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr1:120539834A>T	ENST00000256646.2	-	4	756	c.537T>A	c.(535-537)tgT>tgA	p.C179*	NOTCH2_ENST00000602566.1_Nonsense_Mutation_p.C140*	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	179	EGF-like 4.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity	p.C179*(1)|p.C140*(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATCAGTCTCACATTTCTGCC	0.552			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				9	81	---	---	---	---
OR2T6	254879	broad.mit.edu	37	1	248551568	248551568	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr1:248551568G>T	ENST00000355728.2	+	1	659	c.659G>T	c.(658-660)aGg>aTg	p.R220M		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	220					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTACACCAGGATTCTCATC	0.517													7	106	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32824954	32824954	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr2:32824954A>C	ENST00000421745.2	+	70	14113	c.13979A>C	c.(13978-13980)tAt>tCt	p.Y4660S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4660	Ubiquitin-conjugating.				anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding	p.Y4660S(2)|p.Y4632S(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CCAAACCTTTATAATGATGGC	0.333													3	39	---	---	---	---
C2orf40	84417	broad.mit.edu	37	2	106690370	106690370	+	Silent	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr2:106690370C>A	ENST00000409944.1	+	4	279	c.48C>A	c.(46-48)gcC>gcA	p.A16A	C2orf40_ENST00000238044.3_Silent_p.A52A|C2orf40_ENST00000489174.1_3'UTR			Q9H1Z8	AUGN_HUMAN	chromosome 2 open reading frame 40	52						extracellular region|transport vesicle				lung(7)|urinary_tract(1)	8						CTAAAGTGGCCGTTGATGAGA	0.527													4	187	---	---	---	---
ZNF621	285268	broad.mit.edu	37	3	40573524	40573524	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr3:40573524G>A	ENST00000339296.5	+	5	715	c.263G>A	c.(262-264)gGt>gAt	p.G88D	ZNF621_ENST00000403205.2_Missense_Mutation_p.G88D|ZNF621_ENST00000310898.1_Missense_Mutation_p.G88D|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000431278.1_5'UTR	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	88					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.G88D(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		TGGTCAGGTGGTGAGTCCTGG	0.403													13	81	---	---	---	---
SEC61A1	29927	broad.mit.edu	37	3	127779441	127779441	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr3:127779441A>G	ENST00000243253.3	+	7	737	c.553A>G	c.(553-555)Act>Gct	p.T185A	SEC61A1_ENST00000464451.1_Missense_Mutation_p.T191A|SEC61A1_ENST00000424880.2_Missense_Mutation_p.T65A	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	185					protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding	p.T185A(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						CTTCATTGCAACTAACATCTG	0.478													29	45	---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140754115	140754115	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr5:140754115G>A	ENST00000517434.1	+	1	465	c.465G>A	c.(463-465)atG>atA	p.M155I	PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1												p.M155I(1)		breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCACTAATGGAGGTCTATG	0.448													3	49	---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16145318	16145318	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr6:16145318T>C	ENST00000349606.4	+	5	979	c.475T>C	c.(475-477)Tca>Cca	p.S159P	MYLIP_ENST00000356840.3_Missense_Mutation_p.S340P			Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	340	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding	p.S340P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			GGACCTCGTTTCAAGAAACAA	0.517													10	123	---	---	---	---
MOCS1	4337	broad.mit.edu	37	6	39880665	39880665	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr6:39880665C>A	ENST00000373186.4	-	6	978	c.841G>T	c.(841-843)Gtg>Ttg	p.V281L	MOCS1_ENST00000425303.2_Missense_Mutation_p.V281L|MOCS1_ENST00000340692.5_Missense_Mutation_p.V281L|MOCS1_ENST00000308559.7_Missense_Mutation_p.V281L|MOCS1_ENST00000373195.3_Missense_Mutation_p.V194L|MOCS1_ENST00000373188.2_Missense_Mutation_p.V281L|MOCS1_ENST00000373175.4_Missense_Mutation_p.V252L|MOCS1_ENST00000432280.2_Missense_Mutation_p.V252L	NM_005943.5	NP_005934.2	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	281	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding	p.V281L(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCCTCTGGCACCTTCTCCAGC	0.577													136	185	---	---	---	---
EIF4H	7458	broad.mit.edu	37	7	73604629	73604629	+	Silent	SNP	C	C	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr7:73604629C>T	ENST00000265753.8	+	5	601	c.462C>T	c.(460-462)ttC>ttT	p.F154F	EIF4H_ENST00000495187.1_3'UTR|EIF4H_ENST00000353999.6_Intron	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	154	HHV-1 Vhs binding site.				interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity	p.F154F(1)		endometrium(1)|lung(2)|prostate(1)	4						GGGATGACTTCAATTCTGGTA	0.453													14	26	---	---	---	---
NKX3-1	4824	broad.mit.edu	37	8	23539041	23539041	+	Missense_Mutation	SNP	T	T	G			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr8:23539041T>G	ENST00000380871.4	-	2	435	c.398A>C	c.(397-399)cAc>cCc	p.H133P	NKX3-1_ENST00000523261.1_Missense_Mutation_p.H58P	NM_006167.3	NP_006158.2	Q99801	NKX31_HUMAN	NK3 homeobox 1	133					negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding	p.H133P(1)		large_intestine(3)|lung(4)|prostate(5)|skin(2)	14		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		CACCTGAGTGTGGGAGAAGGC	0.587													90	33	---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55049839	55049839	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr8:55049839A>C	ENST00000260102.4	+	3	349	c.275A>C	c.(274-276)cAg>cCg	p.Q92P		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	92					translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome	p.Q92P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			TTCAGACGCCAGTATAAGCCT	0.398													55	39	---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71844114	71844114	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr9:71844114G>C	ENST00000377245.4	+	10	1676	c.1468G>C	c.(1468-1470)Gca>Cca	p.A490P	TJP2_ENST00000453658.2_Missense_Mutation_p.A467P|TJP2_ENST00000539225.1_Missense_Mutation_p.A521P|TJP2_ENST00000535702.1_Missense_Mutation_p.A494P|TJP2_ENST00000348208.4_Missense_Mutation_p.A490P|TJP2_ENST00000265384.7_Missense_Mutation_p.A490P	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	490					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding	p.A490P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						TCAACCAAAAGCAGCCCCGAG	0.388													7	141	---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127765792	127765792	+	Missense_Mutation	SNP	C	C	G			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr9:127765792C>G	ENST00000336505.6	-	10	977	c.919G>C	c.(919-921)Gag>Cag	p.E307Q	SCAI_ENST00000487795.1_5'UTR|SCAI_ENST00000373549.4_Missense_Mutation_p.E330Q	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity	p.E330Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TTCATTGGCTCCCTTTCCAGA	0.413													20	56	---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7780658	7780658	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr10:7780658A>G	ENST00000358415.4	+	16	2198	c.2032A>G	c.(2032-2034)Atc>Gtc	p.I678V	ITIH2_ENST00000379587.4_Missense_Mutation_p.I667V	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	678					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity	p.I678V(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						AACGCCCGTGATCTCCATGCT	0.552													9	75	---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24884077	24884077	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr10:24884077G>C	ENST00000396432.2	-	20	4241	c.3755C>G	c.(3754-3756)cCt>cGt	p.P1252R	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.P1039R	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1251	Rho-GAP.				signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding	p.P1251R(1)|p.P1251fs*2(1)|p.P1252R(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						ACGATCTAGAGGATCTTCTTT	0.299													4	25	---	---	---	---
TPH1	7166	broad.mit.edu	37	11	18062244	18062244	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr11:18062244A>C	ENST00000250018.2	-	1	628	c.66T>G	c.(64-66)ttT>ttG	p.F22L	TPH1_ENST00000341556.2_Missense_Mutation_p.F22L	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	22	ACT.				aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity	p.F22L(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	TCTTTAAGGAAAAAATGAGAC	0.328													5	38	---	---	---	---
CD82	3732	broad.mit.edu	37	11	44626916	44626916	+	Silent	SNP	C	C	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr11:44626916C>T	ENST00000227155.4	+	6	521	c.273C>T	c.(271-273)ttC>ttT	p.F91F	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Intron	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	91						integral to plasma membrane	protein binding	p.F91F(1)		large_intestine(1)|ovary(1)	2						ACTTTGCTTTCCTGCTCCTGA	0.617													27	32	---	---	---	---
PFDN5	5204	broad.mit.edu	37	12	53689395	53689395	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr12:53689395T>C	ENST00000551018.1	+	1	321	c.44T>C	c.(43-45)cTa>cCa	p.L15P	PFDN5_ENST00000334478.4_Missense_Mutation_p.L15P|PFDN5_ENST00000351500.3_Missense_Mutation_p.L15P|PFDN5_ENST00000550846.1_Missense_Mutation_p.L15P	NM_002624.3	NP_002615.2	Q99471	PFD5_HUMAN	prefoldin subunit 5	15					'de novo' posttranslational protein folding|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent	nucleus|prefoldin complex	transcription corepressor activity|unfolded protein binding	p.L15P(1)		kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)	8						CTGCCGCAGCTAGAAATGCTC	0.592													3	93	---	---	---	---
LHFP	10186	broad.mit.edu	37	13	40175053	40175053	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr13:40175053G>A	ENST00000379589.3	-	2	763	c.301C>T	c.(301-303)Ctc>Ttc	p.L101F		NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	101						integral to membrane	DNA binding	p.L101F(1)	HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGGGCAGTGAGCGCCACCAGG	0.587			T	HMGA2	lipoma								12	136	---	---	---	---
BBS4	585	broad.mit.edu	37	15	73015166	73015166	+	Missense_Mutation	SNP	T	T	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr15:73015166T>A	ENST00000268057.4	+	7	478	c.437T>A	c.(436-438)aTa>aAa	p.I146K	BBS4_ENST00000395205.2_Missense_Mutation_p.I154K|BBS4_ENST00000564239.1_3'UTR|BBS4_ENST00000539603.1_Missense_Mutation_p.I134K|BBS4_ENST00000542334.1_5'UTR	NM_033028.4	NP_149017.2	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	146	Interaction with PCM1.				adult behavior|brain morphogenesis|cell cycle cytokinesis|centrosome organization|cerebral cortex development|convergent extension involved in gastrulation|dendrite development|fat cell differentiation|heart looping|hippocampus development|intracellular transport|maintenance of protein location in nucleus|melanosome transport|microtubule anchoring at centrosome|neural tube closure|nonmotile primary cilium assembly|photoreceptor cell maintenance|pigment granule aggregation in cell center|positive regulation of flagellum assembly|regulation of cilium beat frequency involved in ciliary motility|regulation of cytokinesis|regulation of lipid metabolic process|retina homeostasis|retinal rod cell development|sensory perception of smell|sensory processing|spermatid development|striatum development	BBSome|centriolar satellite|centriole|cilium membrane|microtubule basal body|motile cilium|nonmotile primary cilium|nucleus|pericentriolar material	alpha-tubulin binding|beta-tubulin binding|dynactin binding|microtubule motor activity	p.I146K(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(1)	19						GTTTGCTACATATACCTGAAG	0.373									Bardet-Biedl syndrome				18	46	---	---	---	---
NAA60	79903	broad.mit.edu	37	16	3529476	3529476	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr16:3529476C>A	ENST00000407558.4	+	4	419	c.116C>A	c.(115-117)cCa>cAa	p.P39Q	NAA60_ENST00000360862.5_5'UTR|NAA60_ENST00000610180.1_Missense_Mutation_p.P39Q|NAA60_ENST00000576916.1_Missense_Mutation_p.P39Q|NAA60_ENST00000570819.1_Missense_Mutation_p.P39Q|NAA60_ENST00000421765.3_Missense_Mutation_p.P39Q|NAA60_ENST00000414063.2_Missense_Mutation_p.P39Q|NAA60_ENST00000424546.2_Missense_Mutation_p.P46Q|NAA60_ENST00000575076.1_Missense_Mutation_p.P39Q|NAA60_ENST00000570551.1_Intron|NAA60_ENST00000577013.1_Missense_Mutation_p.P39Q|NAA60_ENST00000608722.1_Missense_Mutation_p.P39Q|LA16c-306E5.3_ENST00000574423.2_RNA|NAA60_ENST00000608993.1_5'UTR|NAA60_ENST00000573580.1_5'UTR|NAA60_ENST00000572584.1_Missense_Mutation_p.P39Q|NAA60_ENST00000572942.1_Missense_Mutation_p.P39Q			Q9H7X0	NAT15_HUMAN	N(alpha)-acetyltransferase 60, NatF catalytic subunit	39	N-acetyltransferase.						N-acetyltransferase activity			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)	7						CTCAGGTACCCAGACTCATGG	0.478													3	32	---	---	---	---
TAOK2	9344	broad.mit.edu	37	16	29996717	29996717	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr16:29996717G>T	ENST00000308893.4	+	14	2649	c.1606G>T	c.(1606-1608)Ggg>Tgg	p.G536W	TAOK2_ENST00000543033.1_Missense_Mutation_p.G536W|TAOK2_ENST00000416441.2_Missense_Mutation_p.G363W|TAOK2_ENST00000279394.3_Missense_Mutation_p.G536W	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	536					actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity	p.G536W(3)		breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						GGCTGGCTTTGGGGCAGAGGC	0.672													8	10	---	---	---	---
LOC101927060	101927060	broad.mit.edu	37	17	45127331	45127331	+	RNA	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr17:45127331C>A	ENST00000575173.1	-	0	418																											AACTCGCTCCCGCATGACCCA	0.418													55	339	---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56385061	56385061	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr17:56385061C>A	ENST00000355701.3	-	24	5764	c.4894G>T	c.(4894-4896)Gct>Tct	p.A1632S	BZRAP1_ENST00000268893.6_Missense_Mutation_p.A1572S|BZRAP1_ENST00000343736.4_Missense_Mutation_p.A1632S	NM_001261835.1|NM_004758.3	NP_001248764.1|NP_004749.2	O95153	RIMB1_HUMAN	benzodiazapine receptor (peripheral) associated protein 1	1632	SH3 2.					mitochondrion	benzodiazepine receptor binding	p.A1632S(3)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCAAACAGAGCCACAAAGATC	0.567													7	64	---	---	---	---
SIRT7	51547	broad.mit.edu	37	17	79873382	79873382	+	Silent	SNP	G	G	A	rs146448282	byFrequency	TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr17:79873382G>A	ENST00000328666.6	-	5	476	c.414C>T	c.(412-414)gcC>gcT	p.A138A		NM_016538.2	NP_057622.1	Q9NRC8	SIRT7_HUMAN	sirtuin 7	138	Deacetylase sirtuin-type.				chromatin silencing|positive regulation of transcription on exit from mitosis|protein deacetylation|rRNA transcription	cytoplasm|nucleolus organizer region	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ binding|protein binding|zinc ion binding	p.A138A(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CGCTCAGGTCGGCAGCACTGC	0.652													3	28	---	---	---	---
HNRNPL	3191	broad.mit.edu	37	19	39334540	39334540	+	Silent	SNP	A	A	G			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr19:39334540A>G	ENST00000221419.5	-	6	1188	c.822T>C	c.(820-822)aaT>aaC	p.N274N	HNRNPL_ENST00000600873.1_Silent_p.N141N	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	274					nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding	p.N274N(1)|p.N141N(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TCTTGAACACATTCAAGCGTG	0.507													31	60	---	---	---	---
PSG2	5670	broad.mit.edu	37	19	43585093	43585093	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr19:43585093T>C	ENST00000406487.1	-	2	468	c.370A>G	c.(370-372)Atc>Gtc	p.I124V		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	124	Ig-like V-type.				cell migration|female pregnancy	extracellular region		p.I124V(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CGCTTTATGATGTGTAAGGTG	0.493													16	160	---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51870363	51870363	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr20:51870363G>A	ENST00000371497.5	+	2	1253	c.366G>A	c.(364-366)atG>atA	p.M122I	TSHZ2_ENST00000603338.2_Missense_Mutation_p.M119I|TSHZ2_ENST00000329613.6_Missense_Mutation_p.M119I	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	122					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.M122I(2)		NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			ACAATTGCATGGATAAAATGA	0.522													24	32	---	---	---	---
CCT8L2	150160	broad.mit.edu	37	22	17072407	17072407	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr22:17072407C>T	ENST00000359963.3	-	1	1293	c.1034G>A	c.(1033-1035)gGc>gAc	p.G345D		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	345					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity	p.G345A(1)|p.G345D(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTGGCACTTGCCTGGCCTCTG	0.547													4	137	---	---	---	---
SLC7A4	6545	broad.mit.edu	37	22	21384286	21384286	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr22:21384286C>T	ENST00000382932.2	-	3	1404	c.1337G>A	c.(1336-1338)gGc>gAc	p.G446D	SLC7A4_ENST00000403586.1_Missense_Mutation_p.G446D	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	446					cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity	p.G446D(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GTGTACAGTGCCCACCAGCTG	0.657													6	19	---	---	---	---
IGLV2-8	28817	broad.mit.edu	37	22	23165714	23165714	+	RNA	SNP	C	C	A			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr22:23165714C>A	ENST00000390317.2	+	0	447																											CCTCCCTGACCGTCTCTGGGC	0.522													5	245	---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40118655	40118656	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CH-5767-01A-11D-1786-08	TCGA-CH-5767-11B-01D-1786-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f07b8ebf-6f30-4011-b595-5571f05c364b	1ff17ff8-6ebe-4775-bc2a-07db1eadb340	g.chr20:40118655_40118656insT	ENST00000373233.3	-	12	1619_1620	c.1442_1443insA	c.(1441-1443)aacfs	p.N481fs	CHD6_ENST00000309279.7_Frame_Shift_Ins_p.N481fs	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	481	Helicase ATP-binding.				chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCAAAATACAGTTTTTTCTGCA	0.376													73	126	---	---	---	---
