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_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
SLC9A1	6548	broad.mit.edu	37	1	27480528	27480528	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:27480528G>A	uc001bnm.2	-	1	924	c.298C>T	c.(298-300)CGC>TGC	p.R100C	SLC9A1_uc010ofk.1_5'UTR|SLC9A1_uc001bnn.2_Missense_Mutation_p.R100C	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	100	Extracellular (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	AAGGGGGTGCGCACGTGTGTG	0.592													4	134	---	---	---	---	PASS
LOC728989	728989	broad.mit.edu	37	1	146494538	146494538	+	Missense_Mutation	SNP	G	A	A	rs141949470	by1000genomes	TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:146494538G>A	uc001epd.2	-	4	535	c.461C>T	c.(460-462)GCG>GTG	p.A154V		NR_024442				SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;												0						TGGCAGGGCCGCTCTCCAGAA	0.572													5	38	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158626393	158626393	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:158626393G>C	uc001fst.1	-	20	3058	c.2859C>G	c.(2857-2859)GAC>GAG	p.D953E		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	953	Spectrin 10.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CTTTCATACTGTCTCCAAATG	0.413													71	181	---	---	---	---	PASS
ASTN1	460	broad.mit.edu	37	1	177001717	177001717	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:177001717G>C	uc001glc.2	-	3	952	c.740C>G	c.(739-741)ACT>AGT	p.T247S	ASTN1_uc001glb.1_Missense_Mutation_p.T247S|ASTN1_uc001gld.1_Missense_Mutation_p.T247S|ASTN1_uc009wwx.1_Missense_Mutation_p.T247S|ASTN1_uc001gle.3_RNA	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	247					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						GCGCAGATCAGTGATGTCATA	0.622													18	106	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216371806	216371806	+	Missense_Mutation	SNP	G	A	A	rs79279902		TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:216371806G>A	uc001hku.1	-	18	4319	c.3932C>T	c.(3931-3933)TCG>TTG	p.S1311L	USH2A_uc001hkv.2_Missense_Mutation_p.S1311L	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1311	Fibronectin type-III 3.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTCATTGGCCGATTCTACAAA	0.413										HNSCC(13;0.011)			53	121	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371504	240371504	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:240371504C>T	uc010pyd.1	+	5	3617	c.3392C>T	c.(3391-3393)CCT>CTT	p.P1131L	FMN2_uc010pye.1_Missense_Mutation_p.P1135L	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1131	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGCATACCCCCTCCTCCCCCT	0.716													3	6	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371526	240371526	+	Silent	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:240371526G>A	uc010pyd.1	+	5	3639	c.3414G>A	c.(3412-3414)GCG>GCA	p.A1138A	FMN2_uc010pye.1_Silent_p.A1142A	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1138	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTCCCGGAGCGGGCATACCTC	0.716													3	8	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240371601	240371601	+	Silent	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:240371601C>T	uc010pyd.1	+	5	3714	c.3489C>T	c.(3487-3489)CCC>CCT	p.P1163P	FMN2_uc010pye.1_Silent_p.P1167P	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1163	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCACCTCCCC	0.692													2	1	---	---	---	---	PASS
TFB2M	64216	broad.mit.edu	37	1	246729332	246729332	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:246729332G>A	uc001ibn.2	-	1	234	c.109C>T	c.(109-111)CCG>TCG	p.P37S	CNST_uc001ibo.3_5'Flank|CNST_uc001ibp.2_5'Flank|TFB2M_uc010pys.1_RNA	NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	37					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			TTCCTCGCCGGCAAATGCTTT	0.627													4	101	---	---	---	---	PASS
CAD	790	broad.mit.edu	37	2	27457443	27457443	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr2:27457443G>A	uc002rji.2	+	23	3838	c.3676G>A	c.(3676-3678)GTT>ATT	p.V1226I	CAD_uc010eyw.2_Missense_Mutation_p.V1163I	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1226	CPSase B.|ATP-grasp 2.|CPSase (Carbamoyl-phosphate synthase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	CTTCCCCTTCGTTTCCAAGAC	0.507													48	99	---	---	---	---	PASS
UQCRC1	7384	broad.mit.edu	37	3	48638151	48638151	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr3:48638151C>T	uc003cub.1	-	9	1134	c.1089G>A	c.(1087-1089)ATG>ATA	p.M363I	UQCRC1_uc003cua.1_Missense_Mutation_p.M248I|UQCRC1_uc003cuc.1_Missense_Mutation_p.M364I|UQCRC1_uc003cud.1_Missense_Mutation_p.M362I	NM_003365	NP_003356	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	363					aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Atovaquone(DB01117)	CATCGATTTTCATTCGGTCAC	0.542													14	92	---	---	---	---	PASS
GZMA	3001	broad.mit.edu	37	5	54405924	54405924	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr5:54405924G>A	uc003jpm.2	+	5	740	c.703G>A	c.(703-705)GGA>AGA	p.G235R		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	235	Peptidase S1.				cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity	p.G235A(1)		ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AAATAAATGCGGAGACCCTCG	0.468													35	106	---	---	---	---	PASS
PPARGC1B	133522	broad.mit.edu	37	5	149212486	149212486	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr5:149212486A>T	uc003lrc.2	+	5	892	c.850A>T	c.(850-852)ATG>TTG	p.M284L	PPARGC1B_uc003lrb.1_Missense_Mutation_p.M284L|PPARGC1B_uc003lrd.2_Missense_Mutation_p.M245L|PPARGC1B_uc003lrf.2_Missense_Mutation_p.M263L|PPARGC1B_uc003lre.1_Missense_Mutation_p.M263L	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	284					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCAGGAAGACATGCAGGCGAT	0.672													31	87	---	---	---	---	PASS
SLC26A2	1836	broad.mit.edu	37	5	149360521	149360521	+	Silent	SNP	T	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr5:149360521T>A	uc003lrh.2	+	3	1633	c.1365T>A	c.(1363-1365)CTT>CTA	p.L455L		NM_000112	NP_000103	P50443	S26A2_HUMAN	solute carrier family 26 member 2	455	Helical; (Potential).					integral to plasma membrane|membrane fraction	secondary active sulfate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			ATACTCAGCTTTCTGGTGTGG	0.418													39	92	---	---	---	---	PASS
NKAPL	222698	broad.mit.edu	37	6	28227527	28227527	+	Silent	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr6:28227527G>A	uc003nkt.2	+	1	430	c.378G>A	c.(376-378)GAG>GAA	p.E126E	ZKSCAN4_uc011dlb.1_5'Flank	NM_001007531	NP_001007532	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	126										upper_aerodigestive_tract(1)|ovary(1)	2						AGGAGAGAGAGAGGATTGGGG	0.542													38	73	---	---	---	---	PASS
MAS1L	116511	broad.mit.edu	37	6	29454710	29454710	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr6:29454710T>C	uc011dlq.1	-	1	970	c.970A>G	c.(970-972)AGG>GGG	p.R324G		NM_052967	NP_443199	P35410	MAS1L_HUMAN	MAS1 oncogene-like	324	Cytoplasmic (Potential).					cytoplasm|integral to membrane|nucleus|plasma membrane	G-protein coupled receptor activity			ovary(7)|lung(2)	9						TCCTTCAGCCTTTTCTTTCTG	0.463													5	220	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112486397	112486397	+	Missense_Mutation	SNP	G	A	A	rs138153075	byFrequency	TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr6:112486397G>A	uc003pvu.2	-	13	1942	c.1633C>T	c.(1633-1635)CGT>TGT	p.R545C	LAMA4_uc003pvv.2_Missense_Mutation_p.R538C|LAMA4_uc003pvt.2_Missense_Mutation_p.R538C	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	545	Domain II and I.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AGAGTTAGACGAGGTGTTGTC	0.448													35	83	---	---	---	---	PASS
WNT2	7472	broad.mit.edu	37	7	116937778	116937778	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr7:116937778G>C	uc003viz.2	-	4	1041	c.741C>G	c.(739-741)AAC>AAG	p.N247K	WNT2_uc003vja.2_Missense_Mutation_p.N151K	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	247					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TGCCATCCTGGTTCATGACCA	0.498													61	120	---	---	---	---	PASS
TRYX3	136541	broad.mit.edu	37	7	141955370	141955370	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr7:141955370G>A	uc003vxb.2	-	2	484	c.164C>T	c.(163-165)GCA>GTA	p.A55V	TRYX3_uc003vxc.3_Missense_Mutation_p.A55V	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3 precursor	55	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)					ATTGCAGTGTGCAGCTGTGAT	0.522													33	78	---	---	---	---	PASS
C10orf71	118461	broad.mit.edu	37	10	50531524	50531524	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr10:50531524C>A	uc010qgp.1	+	3	1273	c.934C>A	c.(934-936)CTA>ATA	p.L312I		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	312											0						CACGACCTTGCTAAGAGAACC	0.577													3	65	---	---	---	---	PASS
TACC2	10579	broad.mit.edu	37	10	123954657	123954657	+	Silent	SNP	C	T	T	rs138045107	byFrequency	TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr10:123954657C>T	uc001lfv.2	+	8	6297	c.5937C>T	c.(5935-5937)CCC>CCT	p.P1979P	TACC2_uc001lfw.2_Silent_p.P125P|TACC2_uc009xzx.2_Silent_p.P1934P|TACC2_uc010qtv.1_Silent_p.P1983P|TACC2_uc001lfx.2_5'UTR|TACC2_uc001lfy.2_5'UTR|TACC2_uc001lfz.2_Silent_p.P57P|TACC2_uc001lga.2_Silent_p.P57P|TACC2_uc009xzy.2_Silent_p.P57P|TACC2_uc010qtw.1_Silent_p.P74P	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1979	Pro-rich.					microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCCCAGAACCCGAGGTCAGCA	0.622													26	53	---	---	---	---	PASS
DMBT1	1755	broad.mit.edu	37	10	124358388	124358388	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr10:124358388G>A	uc001lgk.1	+	26	3161	c.3055G>A	c.(3055-3057)GAT>AAT	p.D1019N	DMBT1_uc001lgl.1_Missense_Mutation_p.D1009N|DMBT1_uc001lgm.1_Missense_Mutation_p.D520N|DMBT1_uc009xzz.1_Missense_Mutation_p.D1019N|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_5'UTR	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1019	SRCR 8.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CACCGTGTGCGATGACAGCTG	0.602													219	349	---	---	---	---	PASS
OR4C13	283092	broad.mit.edu	37	11	49974537	49974537	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr11:49974537C>T	uc010rhz.1	+	1	563	c.563C>T	c.(562-564)ACT>ATT	p.T188I		NM_001001955	NP_001001955	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C,	188	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4						CTTGCCTGCACTAATACCCAC	0.438													73	202	---	---	---	---	PASS
MYO7A	4647	broad.mit.edu	37	11	76868351	76868351	+	Silent	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr11:76868351G>A	uc001oyb.2	+	8	1034	c.762G>A	c.(760-762)GTG>GTA	p.V254V	MYO7A_uc010rsl.1_Silent_p.V254V|MYO7A_uc010rsm.1_Silent_p.V243V|MYO7A_uc001oyc.2_Silent_p.V254V	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1	254	Myosin head-like.				actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						ACTACCACGTGTTCTACTGCA	0.582													11	14	---	---	---	---	PASS
CACNA2D4	93589	broad.mit.edu	37	12	1988135	1988135	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr12:1988135G>A	uc001qjp.2	-	15	1862	c.1631C>T	c.(1630-1632)GCG>GTG	p.A544V	CACNA2D4_uc009zds.1_RNA|CACNA2D4_uc009zdt.1_Missense_Mutation_p.A432V	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	544	Cache.|Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GTACCGGGGCGCCAGCTTCAT	0.622													8	24	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6172165	6172165	+	Silent	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr12:6172165C>T	uc001qnn.1	-	13	1738	c.1488G>A	c.(1486-1488)GAG>GAA	p.E496E	VWF_uc010set.1_Silent_p.E496E	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	496	VWFD 2.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	TCTGCAGGTCCTCCCCGTAGC	0.657											OREG0021618	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	21	---	---	---	---	PASS
NAA25	80018	broad.mit.edu	37	12	112516059	112516059	+	Silent	SNP	A	G	G			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr12:112516059A>G	uc001ttm.2	-	7	617	c.597T>C	c.(595-597)TAT>TAC	p.Y199Y	NAA25_uc001ttn.3_RNA|NAA25_uc009zvz.1_Silent_p.Y171Y|NAA25_uc009zwa.1_Silent_p.Y199Y	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	199						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GGATCATATAATAAAGTTCAA	0.299													7	163	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	29600584	29600584	+	Silent	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr13:29600584G>A	uc001usl.3	+	1	1837	c.1779G>A	c.(1777-1779)ACG>ACA	p.T593T		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	583						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						TGTTGAACACGTCCCCCAAAG	0.552													22	68	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107095199	107095199	+	RNA	SNP	G	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr14:107095199G>T	uc010tyt.1	-	101		c.4888C>A								Parts of antibodies, mostly variable regions.												0						GTTCTTGGACGTGTCTACTGA	0.552													4	129	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20644830	20644830	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr15:20644830T>C	uc001ytg.2	-	21	3137	c.2428A>G	c.(2428-2430)ATG>GTG	p.M810V	uc010tyx.1_RNA|uc001yth.3_Missense_Mutation_p.M810V|uc010tyy.1_Missense_Mutation_p.M810V					RecName: Full=Putative HERC2-like protein 3;																		AGCTTCTCCATGAGGCATTTC	0.498													3	72	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48736776	48736776	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr15:48736776C>A	uc001zwx.1	-	49	6327	c.5999G>T	c.(5998-6000)TGC>TTC	p.C2000F	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	2000	EGF-like 34; calcium-binding.				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			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCCAGGTGGGCAAATGCATCT	0.433													58	118	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51855614	51855614	+	Nonsense_Mutation	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr15:51855614C>T	uc002abf.2	-	6	756	c.531G>A	c.(529-531)TGG>TGA	p.W177*	DMXL2_uc010ufy.1_Nonsense_Mutation_p.W177*|DMXL2_uc010bfa.2_Nonsense_Mutation_p.W177*	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	177	WD 2.					cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		CATCAGGAGACCATTCCATCA	0.308													3	72	---	---	---	---	PASS
RUNDC2A	84127	broad.mit.edu	37	16	12136839	12136839	+	Silent	SNP	C	T	T			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr16:12136839C>T	uc002dbw.1	+	5	395	c.333C>T	c.(331-333)GAC>GAT	p.D111D		NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A	111	RUN.									ovary(1)	1						TCGCCTCAGACGTGGGCCGGG	0.652			T	CIITA	PMBL|Hodgkin Lymphona|								3	34	---	---	---	---	PASS
RUNDC2C	440352	broad.mit.edu	37	16	29376056	29376056	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr16:29376056T>A	uc002dsj.1	+	5	795	c.398T>A	c.(397-399)ATC>AAC	p.I133N	uc010vct.1_Intron|RUNDC2C_uc010bys.1_RNA|RUNDC2C_uc010vdo.1_Missense_Mutation_p.I114N	NM_001012391	NP_001012391			RecName: Full=RUN domain-containing protein 2A;												0						ACCAACATTATCTCATTTGAT	0.393													5	85	---	---	---	---	PASS
USP22	23326	broad.mit.edu	37	17	20910262	20910262	+	Silent	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr17:20910262G>A	uc002gym.3	-	10	1473	c.1269C>T	c.(1267-1269)ACC>ACT	p.T423T	USP22_uc002gyn.3_Silent_p.T411T|USP22_uc002gyl.3_Silent_p.T318T	NM_015276	NP_056091	Q9UPT9	UBP22_HUMAN	ubiquitin thiolesterase 22	423					cell cycle|embryo development|histone deubiquitination|histone H4 acetylation|histone ubiquitination|positive regulation of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1						ACACATACGTGGTGATCTTCC	0.547													4	25	---	---	---	---	PASS
ST6GALNAC2	10610	broad.mit.edu	37	17	74562331	74562331	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr17:74562331G>A	uc002jsg.3	-	9	1235	c.980C>T	c.(979-981)ACA>ATA	p.T327I		NM_006456	NP_006447	Q9UJ37	SIA7B_HUMAN	sialyltransferase 7B	327	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity				0						GTAGTTGCTTGTGATGAATCC	0.448													78	155	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14513675	14513675	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr18:14513675T>C	uc010dln.2	-	10	1973	c.1519A>G	c.(1519-1521)AAA>GAA	p.K507E	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	507	Potential.									skin(3)	3						GAATTCATTTTCTTTTCAGCC	0.284													3	110	---	---	---	---	PASS
MYO1F	4542	broad.mit.edu	37	19	8604860	8604860	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr19:8604860G>A	uc002mkg.2	-	16	1777	c.1663C>T	c.(1663-1665)CGC>TGC	p.R555C		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	555	Myosin head-like.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3						GTGCTGGGGCGCCCCTTCTTG	0.637													20	46	---	---	---	---	PASS
ZNF285	26974	broad.mit.edu	37	19	44891202	44891202	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr19:44891202C>G	uc002ozd.3	-	4	1292	c.1205G>C	c.(1204-1206)TGC>TCC	p.C402S	ZFP112_uc010xwz.1_Intron|ZNF285_uc010xxa.1_Missense_Mutation_p.C409S	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	402	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(2)	4						ACACTCACTGCATTTGTAGGG	0.478													3	93	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42524924	42524924	+	Silent	SNP	A	G	G	rs111606937	by1000genomes	TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr22:42524924A>G	uc003bce.2	-	4	618	c.528T>C	c.(526-528)GGT>GGC	p.G176G	uc003bcd.1_Intron|CYP2D6_uc010gyu.2_5'UTR|CYP2D6_uc003bcf.2_Silent_p.G125G	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	176							electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						TGTCCAAGAGACCGTTGGGGC	0.667													3	9	---	---	---	---	PASS
STS	412	broad.mit.edu	37	X	7223203	7223203	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chrX:7223203G>A	uc004cry.3	+	7	1320	c.1075G>A	c.(1075-1077)GGA>AGA	p.G359R		NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor	359	Lumenal.				female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	AATTCATGGCGGAAGTAATGG	0.458									Ichthyosis				3	70	---	---	---	---	PASS
PUM1	9698	broad.mit.edu	37	1	31406163	31406163	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:31406163delA	uc001bsi.1	-	22	3569	c.3456delT	c.(3454-3456)CGTfs	p.R1152fs	PUM1_uc001bsf.1_Frame_Shift_Del_p.R820fs|PUM1_uc001bsg.1_Frame_Shift_Del_p.R886fs|PUM1_uc001bsh.1_Frame_Shift_Del_p.R1154fs|PUM1_uc001bsj.1_Frame_Shift_Del_p.R1128fs|PUM1_uc010oga.1_Frame_Shift_Del_p.R1010fs|PUM1_uc001bsk.1_Frame_Shift_Del_p.R1190fs|PUM1_uc010ogb.1_Frame_Shift_Del_p.R1093fs	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	1152	PUM-HD.				cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		AGGTGTACTTACGAAGAGTTG	0.532													165	68	---	---	---	---	
FLG2	388698	broad.mit.edu	37	1	152329411	152329415	+	Frame_Shift_Del	DEL	TTGCT	-	-			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr1:152329411_152329415delTTGCT	uc001ezw.3	-	3	920_924	c.847_851delAGCAA	c.(847-852)AGCAATfs	p.S283fs	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	283_284	Ser-rich.|Filaggrin 1.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCACTTGAATTGCTATAACCACAT	0.429													272	78	---	---	---	---	
MIR620	693205	broad.mit.edu	37	12	116586415	116586418	+	RNA	DEL	TATA	-	-	rs10549054		TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr12:116586415_116586418delTATA	hsa-mir-620|MI0003634	-			c.42_45delTATA			MED13L_uc001tvw.2_Intron																	0						tggagatatctatatatatatata	0.196													4	3	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16612678	16612678	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EJ-5532-01A-01D-1576-08	TCGA-EJ-5532-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	64b492d0-73c0-4de0-bad1-5ef62275b035	d441d979-16c2-4638-a963-550f1bffd4e8	g.chr17:16612678delT	uc002gqk.1	+	5	1383	c.1307delT	c.(1306-1308)GTTfs	p.V436fs	CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_5'Flank	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	436											0						CCAGAAGTGGTTATGGTTGAA	0.353													47	27	---	---	---	---	
