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
CA6	765	broad.mit.edu	37	1	9027761	9027761	+	Silent	SNP	G	G	T	rs151137875		TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:9027761G>T	uc001apm.2	+	6	639	c.615G>T	c.(613-615)CTG>CTT	p.L205L	CA6_uc009vmn.2_Silent_p.L145L	NM_001215	NP_001206	P23280	CAH6_HUMAN	carbonic anhydrase VI precursor	205					one-carbon metabolic process	extracellular region	carbonate dehydratase activity|zinc ion binding			ovary(2)	2	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)		AGGACATGCTGCCCAGGAACC	0.557000												
SPTA1	6708	broad.mit.edu	37	1	158646014	158646014	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:158646014C>A	uc001fst.1	-	8	1228	c.1029G>T	c.(1027-1029)GAG>GAT	p.E343D		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	343	Spectrin 4.				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)					CTTCTTTCATCTCCTGGATCT	0.483000												
TADA1	117143	broad.mit.edu	37	1	166829516	166829516	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:166829516C>T	uc001gdw.2	-	6	783	c.599G>A	c.(598-600)CGA>CAA	p.R200Q	TADA1_uc001gdv.2_Missense_Mutation_p.R58Q	NM_053053	NP_444281	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1-like	200					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1						ATGACCATCTCGTAACCGATA	0.363000												
CACNA1E	777	broad.mit.edu	37	1	181695296	181695296	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:181695296C>T	uc001gow.2	+	18	2403	c.2238C>T	c.(2236-2238)ATC>ATT	p.I746I	CACNA1E_uc009wxs.2_Silent_p.I653I	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	746	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						TGCCTTCGATCGAGTGAGTCA	0.423000												
CACNA1E	777	broad.mit.edu	37	1	181724463	181724463	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:181724463G>A	uc001gow.2	+	28	4084	c.3919G>A	c.(3919-3921)GCA>ACA	p.A1307T	CACNA1E_uc009wxs.2_Missense_Mutation_p.A1195T|CACNA1E_uc001gox.1_Missense_Mutation_p.A533T|CACNA1E_uc009wxt.2_Missense_Mutation_p.A533T	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1307	III.|Helical; Name=S5 of repeat III.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						TGCTGTCATCGCAGTTCAGCT	0.468000												
LRRN2	10446	broad.mit.edu	37	1	204587180	204587180	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:204587180C>T	uc001hbe.1	-	3	2329	c.1941G>A	c.(1939-1941)GCG>GCA	p.A647A	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Silent_p.A647A|LRRN2_uc009xbf.1_Silent_p.A647A|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	647	Helical; (Potential).				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			CAAGGTGGGCCGCTAGCCCAG	0.662000												
OR6F1	343169	broad.mit.edu	37	1	247875662	247875662	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:247875662G>A	uc001idj.1	-	1	396	c.396C>T	c.(394-396)TAC>TAT	p.Y132Y		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	132	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TGATGGCTCCGTAGTGTAAAG	0.557000												
OR2T12	127064	broad.mit.edu	37	1	248457952	248457952	+	Missense_Mutation	SNP	T	T	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr1:248457952T>G	uc010pzj.1	-	1	929	c.929A>C	c.(928-930)AAA>ACA	p.K310T		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	310	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	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;0.0201)			TTGCTGGTGTTTTAGGTTTAC	0.433000												
OSBPL5	114879	broad.mit.edu	37	11	3114795	3114795	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr11:3114795C>T	uc001lxk.2	-	17	2066	c.1908G>A	c.(1906-1908)ACG>ACA	p.T636T	OSBPL5_uc010qxq.1_Silent_p.T547T|OSBPL5_uc009ydw.2_Silent_p.T568T|OSBPL5_uc001lxl.2_Silent_p.T568T|OSBPL5_uc009ydx.2_Silent_p.T660T|OSBPL5_uc001lxj.2_Silent_p.T90T	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	636					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CCAGCGGCACCGTGTGCTGCC	0.652000												
SOX6	55553	broad.mit.edu	37	11	16340111	16340111	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr11:16340111C>T	uc001mme.2	-	3	398	c.365G>A	c.(364-366)CGT>CAT	p.R122H	SOX6_uc001mmd.2_Missense_Mutation_p.R112H|SOX6_uc001mmf.2_Missense_Mutation_p.R109H|SOX6_uc001mmg.2_Missense_Mutation_p.R109H|SOX6_uc001mmh.1_RNA|SOX6_uc009ygs.2_RNA|SOX6_uc001mmi.3_Missense_Mutation_p.R109H|SOX6_uc001mmj.2_Missense_Mutation_p.R109H	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	109					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						CATTATCTCACGGTCCCGACT	0.453000												
OR5R1	219479	broad.mit.edu	37	11	56184928	56184928	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr11:56184928G>T	uc010rji.1	-	1	781	c.781C>A	c.(781-783)CAG>AAG	p.Q261K		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					GATTTGGGCTGTAGGTACATA	0.448000												
EHBP1L1	254102	broad.mit.edu	37	11	65350742	65350742	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr11:65350742C>T	uc001oeo.3	+	9	2864	c.2599C>T	c.(2599-2601)CGT>TGT	p.R867C	EHBP1L1_uc001oep.1_Intron	NM_001099409	NP_001092879	Q8N3D4	EH1L1_HUMAN	tangerin	867	Glu-rich.									central_nervous_system(1)	1						ACTGATGACCCGTAAGACAGA	0.557000												
ACSM4	341392	broad.mit.edu	37	12	7475048	7475048	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr12:7475048G>A	uc001qsx.1	+	7	1036	c.1036G>A	c.(1036-1038)GGA>AGA	p.G346R		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	346					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						CTGCTTGACCGGAGGGGAGCC	0.498000												
ADAMTS20	80070	broad.mit.edu	37	12	43833818	43833818	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr12:43833818G>A	uc010skx.1	-	17	2345	c.2345C>T	c.(2344-2346)ACG>ATG	p.T782M	ADAMTS20_uc001rno.1_5'Flank|ADAMTS20_uc001rnp.1_5'Flank	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	782	Spacer.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTTTTTTGACGTACTTAGAAG	0.313000												
ANO6	196527	broad.mit.edu	37	12	45795715	45795715	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr12:45795715G>A	uc001roo.2	+	13	1859	c.1524G>A	c.(1522-1524)ACG>ACA	p.T508T	ANO6_uc010sld.1_Silent_p.T508T|ANO6_uc010sle.1_Silent_p.T508T|ANO6_uc010slf.1_Silent_p.T529T|ANO6_uc010slg.1_Silent_p.T490T	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	508	Extracellular (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						AGACAGCCACGTCCATCACGG	0.403000												
FRY	10129	broad.mit.edu	37	13	32745282	32745282	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr13:32745282G>A	uc001utx.2	+	18	2522	c.2026G>A	c.(2026-2028)GAT>AAT	p.D676N	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	676					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GGAAGTAAATGATATGCATCA	0.438000												
WDHD1	11169	broad.mit.edu	37	14	55474071	55474071	+	Missense_Mutation	SNP	A	A	C			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr14:55474071A>C	uc001xbm.1	-	7	605	c.527T>G	c.(526-528)CTG>CGG	p.L176R	WDHD1_uc001xbn.1_Missense_Mutation_p.L53R	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	176						cytoplasm|nucleoplasm	DNA binding			skin(1)	1						TTTTTGTAGCAGTGGCCAACT	0.318000												
OTX2	5015	broad.mit.edu	37	14	57268588	57268588	+	Silent	SNP	A	A	C			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr14:57268588A>C	uc001xcp.2	-	3	906	c.735T>G	c.(733-735)GCT>GCG	p.A245A	OTX2_uc010aou.2_Silent_p.A245A|OTX2_uc001xcq.2_Silent_p.A253A	NM_172337	NP_758840	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform b	245					axon guidance|forebrain development|midbrain development|positive regulation of embryonic development|positive regulation of gastrulation|primitive streak formation|protein complex assembly|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway	growth cone|nucleus|protein complex	eukaryotic initiation factor 4E binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CCAAGCTTGAAGCTCCATATC	0.493000												
SIX6	4990	broad.mit.edu	37	14	60976532	60976532	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr14:60976532C>T	uc001xfa.3	+	1	595	c.416C>T	c.(415-417)ACG>ATG	p.T139M		NM_007374	NP_031400	O95475	SIX6_HUMAN	SIX homeobox 6	139	Homeobox.				organ morphogenesis|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.088)		AAGGAGCGCACGCGGCACCTG	0.607000												
FLRT2	23768	broad.mit.edu	37	14	86088177	86088177	+	Missense_Mutation	SNP	C	C	A	rs117507441	byFrequency	TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr14:86088177C>A	uc001xvr.2	+	2	1086	c.319C>A	c.(319-321)CTT>ATT	p.L107I	FLRT2_uc010atd.2_Missense_Mutation_p.L107I	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	107	Extracellular (Potential).|LRR 2.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CCCCATGAACCTTCCCAAGAA	0.473000												
ATP10A	57194	broad.mit.edu	37	15	25972389	25972389	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr15:25972389G>A	uc010ayu.2	-	4	871	c.765C>T	c.(763-765)GCC>GCT	p.A255A		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	255	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TATACAGCCCGGCCTTTTTCC	0.572000												
CIB2	10518	broad.mit.edu	37	15	78398116	78398116	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr15:78398116G>A	uc002bdb.1	-	5	828	c.507C>T	c.(505-507)TTC>TTT	p.F169F	CIB2_uc002bdc.1_Silent_p.F126F|CIB2_uc010ums.1_Silent_p.F169F	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic	169	EF-hand 3.						calcium ion binding				0						TCATGTCCTCGAAGTCAGCAA	0.617000												
BNC1	646	broad.mit.edu	37	15	83933367	83933367	+	Missense_Mutation	SNP	A	A	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr15:83933367A>T	uc002bjt.1	-	4	724	c.636T>A	c.(634-636)AGT>AGA	p.S212R	BNC1_uc010uos.1_Missense_Mutation_p.S200R	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	212					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						AACTCCTGTGACTGCAGCTCT	0.463000												
OR1E1	8387	broad.mit.edu	37	17	3301695	3301695	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr17:3301695G>T	uc002fvj.1	-	1	10	c.10C>A	c.(10-12)CAA>AAA	p.Q4K		NM_003553	NP_003544	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E,	4	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GTTTGATTTTGTCCCATCATG	0.433000												
TP53	7157	broad.mit.edu	37	17	7578370	7578370	+	Splice_Site	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr17:7578370C>T	uc002gim.2	-	5	753	c.559_splice	c.e5+1	p.G187_splice	TP53_uc002gig.1_Splice_Site_p.G187_splice|TP53_uc002gih.2_Splice_Site_p.G187_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Intron|TP53_uc010cng.1_Intron|TP53_uc002gii.1_Intron|TP53_uc010cnh.1_Splice_Site_p.G187_splice|TP53_uc010cni.1_Splice_Site_p.G187_splice|TP53_uc002gij.2_Splice_Site_p.G187_splice|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Splice_Site_p.G94_splice|TP53_uc002gio.2_Splice_Site_p.G55_splice|TP53_uc010vug.1_Splice_Site_p.G148_splice	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.?(24)|p.0?(7)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CAGCTGCTCACCATCGCTATC	0.632000		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)		
MYH2	4620	broad.mit.edu	37	17	10428137	10428137	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr17:10428137G>A	uc010coi.2	-	34	5036	c.4908C>T	c.(4906-4908)AAC>AAT	p.N1636N	uc002gml.1_Intron|MYH2_uc002gmp.3_Silent_p.N1636N|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1636	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GGTTGGCATGGTTCAGCTGGA	0.512000												
MKS1	54903	broad.mit.edu	37	17	56293543	56293543	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr17:56293543C>T	uc002ivr.1	-	4	398	c.323G>A	c.(322-324)CGT>CAT	p.R108H	MKS1_uc010wnq.1_5'UTR|MKS1_uc002ivs.1_Missense_Mutation_p.R108H	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	108					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1						GATCTCCTGACGGTACTGATA	0.423000												
MPO	4353	broad.mit.edu	37	17	56350133	56350133	+	Missense_Mutation	SNP	G	G	A	rs142082076		TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr17:56350133G>A	uc002ivu.1	-	10	1945	c.1768C>T	c.(1768-1770)CGC>TGC	p.R590C		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	590					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)	TCCCTGCTGCGCTGCATGTTC	0.607000												
CEP192	55125	broad.mit.edu	37	18	13049261	13049261	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr18:13049261C>T	uc010xac.1	+	16	2551	c.2471C>T	c.(2470-2472)CCG>CTG	p.P824L	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Missense_Mutation_p.P349L|CEP192_uc002kru.2_RNA|CEP192_uc002krs.1_Missense_Mutation_p.P565L	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	824										ovary(4)|pancreas(1)	5						GACATTCATCCGGTGGACTTA	0.393000												
C19orf21	126353	broad.mit.edu	37	19	757262	757262	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:757262C>T	uc002lpo.2	+	2	399	c.316C>T	c.(316-318)CGT>TGT	p.R106C		NM_173481	NP_775752	Q8IVT2	CS021_HUMAN	hypothetical protein LOC126353	106										upper_aerodigestive_tract(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000145)|all_lung(49;0.000236)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACCAGGGACGTCCAACATG	0.662000												
RFX2	5990	broad.mit.edu	37	19	6026240	6026240	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:6026240C>T	uc002meb.2	-	6	800	c.531G>A	c.(529-531)ATG>ATA	p.M177I	RFX2_uc002mec.2_Intron	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a	177					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6						TTTCAATCGCCATTTCAAGCT	0.358000												
FBN3	84467	broad.mit.edu	37	19	8176646	8176646	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:8176646C>A	uc002mjf.2	-	31	3991	c.3970G>T	c.(3970-3972)GAA>TAA	p.E1324*		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1324	EGF-like 20; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GAGACGCATTCATCCAGGTCT	0.632000												
ZNF43	7594	broad.mit.edu	37	19	21991815	21991815	+	Missense_Mutation	SNP	A	A	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:21991815A>G	uc002nqj.2	-	4	1154	c.1024T>C	c.(1024-1026)TAC>CAC	p.Y342H	ZNF43_uc010ecv.2_Missense_Mutation_p.Y336H|ZNF43_uc002nql.2_Missense_Mutation_p.Y336H|ZNF43_uc002nqm.2_Missense_Mutation_p.Y336H|ZNF43_uc002nqk.2_Missense_Mutation_p.Y272H	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43	342	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TCACATGTGTAGGGTTTCTCT	0.383000												
PSG8	440533	broad.mit.edu	37	19	43258502	43258502	+	Missense_Mutation	SNP	A	A	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:43258502A>T	uc002ouo.2	-	5	1324	c.1226T>A	c.(1225-1227)ATG>AAG	p.M409K	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_RNA|PSG8_uc002oui.2_Missense_Mutation_p.M248K|PSG8_uc002ouh.2_Missense_Mutation_p.M409K|PSG8_uc010ein.2_Missense_Mutation_p.M287K|PSG8_uc002ouj.3_Missense_Mutation_p.M191K|PSG8_uc002ouk.3_Missense_Mutation_p.M248K|PSG8_uc002oul.3_Missense_Mutation_p.M409K|PSG8_uc002oum.3_Missense_Mutation_p.M316K|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Missense_Mutation_p.M316K	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	409	Ig-like C2-type 3.					extracellular region					0		Prostate(69;0.00899)				TTTTACTGTCATGGATTTGGA	0.458000												
CACNG6	59285	broad.mit.edu	37	19	54502911	54502911	+	Missense_Mutation	SNP	A	A	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr19:54502911A>G	uc002qct.2	+	3	1020	c.430A>G	c.(430-432)ATA>GTA	p.I144V	CACNG6_uc002qcu.2_Intron|CACNG6_uc002qcv.2_Intron	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN	voltage-dependent calcium channel gamma-6	144	Helical; (Potential).					voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(2)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		AGCTGCGGTGATAGCAGTGCT	0.557000												
ALLC	55821	broad.mit.edu	37	2	3749215	3749215	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:3749215C>T	uc010ewt.2	+	11	1125	c.964C>T	c.(964-966)CCA>TCA	p.P322S	ALLC_uc002qyf.2_Missense_Mutation_p.P93S	NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	341							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		ACCACTGCTTCCAGTGACCAA	0.488000										HNSCC(21;0.051)		
FAM179A	165186	broad.mit.edu	37	2	29268228	29268228	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:29268228C>T	uc010ezl.2	+	19	3025	c.2674C>T	c.(2674-2676)CGT>TGT	p.R892C	FAM179A_uc010ymm.1_Missense_Mutation_p.R837C|FAM179A_uc002rmr.3_Missense_Mutation_p.R419C|FAM179A_uc002rms.1_Missense_Mutation_p.R190C	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	892							binding			ovary(3)|skin(1)	4						TGGGCGAGTGCGTTTCCTGAG	0.612000												
POLR1A	25885	broad.mit.edu	37	2	86308050	86308050	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:86308050C>T	uc002sqs.2	-	9	1354	c.975G>A	c.(973-975)ACG>ACA	p.T325T	POLR1A_uc002sqv.2_Silent_p.T325T	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	325					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						GCAAGTTCACCGTCTGGCCAT	0.493000												
UGGT1	56886	broad.mit.edu	37	2	128922385	128922385	+	Missense_Mutation	SNP	T	T	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:128922385T>G	uc002tps.2	+	26	3085	c.2907T>G	c.(2905-2907)TTT>TTG	p.F969L	UGGT1_uc010fme.1_Missense_Mutation_p.F844L|UGGT1_uc002tpr.2_Missense_Mutation_p.F945L	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	969					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						ACCAGTTTTTTGAAGACAGAC	0.388000												
TTN	7273	broad.mit.edu	37	2	179424587	179424587	+	Missense_Mutation	SNP	T	T	C			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:179424587T>C	uc010zfg.1	-	275	78792	c.78568A>G	c.(78568-78570)AGT>GGT	p.S26190G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.S19885G|TTN_uc010zfi.1_Missense_Mutation_p.S19818G|TTN_uc010zfj.1_Missense_Mutation_p.S19693G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27117							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCATTTCACTGTCAATATCA	0.443000												
DIDO1	11083	broad.mit.edu	37	20	61513050	61513050	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr20:61513050C>T	uc002ydr.1	-	16	4522	c.4258G>A	c.(4258-4260)GAG>AAG	p.E1420K	DIDO1_uc002yds.1_Missense_Mutation_p.E1420K	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1420					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					TCTTCCCGCTCGGCTGCAGCT	0.612000												
UFD1L	7353	broad.mit.edu	37	22	19445627	19445627	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr22:19445627G>A	uc002zpm.2	-	7	661	c.531C>T	c.(529-531)GAC>GAT	p.D177D	UFD1L_uc002zpo.2_Silent_p.D177D|UFD1L_uc011agy.1_Silent_p.D177D|UFD1L_uc002zpp.2_Silent_p.D130D	NM_005659	NP_005650	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1-like isoform A	177					skeletal system development|ubiquitin-dependent protein catabolic process	cytosol|nucleus	protein binding|ubiquitin-specific protease activity				0	Colorectal(54;0.0993)					ACACTGCCTTGTCGGGTTTGG	0.547000												
PISD	23761	broad.mit.edu	37	22	32017095	32017095	+	Missense_Mutation	SNP	A	A	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr22:32017095A>G	uc003alm.3	-	6	738	c.731T>C	c.(730-732)GTC>GCC	p.V244A	PISD_uc003alk.2_Missense_Mutation_p.V210A|PISD_uc003all.2_Missense_Mutation_p.V209A|PISD_uc011alr.1_Missense_Mutation_p.V209A|PISD_uc003aln.3_Missense_Mutation_p.V244A	NM_014338	NP_055153	Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	244					phospholipid biosynthetic process	mitochondrion	phosphatidylserine decarboxylase activity			central_nervous_system(2)|ovary(1)	3					Phosphatidylserine(DB00144)	TTCCCGGGTGACCAGCTGGTT	0.627000											OREG0003530	type=REGULATORY REGION|Gene=PISD|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay
SREBF2	6721	broad.mit.edu	37	22	42271622	42271622	+	Missense_Mutation	SNP	A	A	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr22:42271622A>G	uc003bbi.2	+	7	1449	c.1280A>G	c.(1279-1281)AAT>AGT	p.N427S	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_RNA	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	427	Interaction with LMNA (By similarity).|Cytoplasmic (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4						TTTAATCAGAATGTCCTTCTG	0.532000												
RARB	5915	broad.mit.edu	37	3	25637920	25637920	+	Missense_Mutation	SNP	G	G	C			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:25637920G>C	uc011awl.1	+	8	1247	c.1181G>C	c.(1180-1182)CGT>CCT	p.R394P	RARB_uc003cdi.1_Missense_Mutation_p.R275P|RARB_uc003cdh.2_Missense_Mutation_p.R387P	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2	394	Ligand-binding.				embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GGTGCAGAGCGTGTAATTACC	0.378000												
TRAK1	22906	broad.mit.edu	37	3	42264466	42264466	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:42264466G>A	uc003cky.2	+	16	2315	c.2099G>A	c.(2098-2100)AGC>AAC	p.S700N	TRAK1_uc011azi.1_Missense_Mutation_p.S679N	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein	700					endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						GCTTGTGGCAGCACCAGCCAC	0.557000												
COL7A1	1294	broad.mit.edu	37	3	48629354	48629354	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:48629354C>T	uc003ctz.2	-	10	1335	c.1334G>A	c.(1333-1335)CGG>CAG	p.R445Q		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	445	Nonhelical region (NC1).|Fibronectin type-III 3.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCATTCCAACCGGTAGCCACG	0.632000												
LAMB2	3913	broad.mit.edu	37	3	49159423	49159423	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:49159423C>T	uc003cwe.2	-	29	5176	c.4877G>A	c.(4876-4878)CGG>CAG	p.R1626Q	USP19_uc003cvz.3_5'Flank|USP19_uc011bcg.1_5'Flank|USP19_uc003cwb.2_5'Flank|USP19_uc003cwd.1_5'Flank|USP19_uc011bch.1_5'Flank|USP19_uc011bci.1_5'Flank	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1626	Potential.|Domain I.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity	p.R1626P(1)		ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACTGCCCCCCGGATGGCACC	0.602000												
ITIH1	3697	broad.mit.edu	37	3	52824909	52824909	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:52824909G>A	uc003dfs.2	+	20	2490	c.2466G>A	c.(2464-2466)CGG>CGA	p.R822R	ITIH1_uc010hmn.1_RNA|ITIH1_uc003dft.2_Silent_p.R423R|ITIH1_uc010hmo.1_Silent_p.R376R|ITIH1_uc003dfu.2_Silent_p.R188R	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1	822	Hyaluronan-binding.				hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ACAGTCATCGGATGTCAGCCC	0.632000												
TP63	8626	broad.mit.edu	37	3	189612028	189612028	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr3:189612028C>T	uc003fry.2	+	14	1869	c.1780C>T	c.(1780-1782)CGA>TGA	p.R594*	TP63_uc003frz.2_3'UTR|TP63_uc010hzc.1_3'UTR|TP63_uc003fsc.2_Nonsense_Mutation_p.R500*|TP63_uc003fsd.2_3'UTR|TP63_uc010hzd.1_Nonsense_Mutation_p.R415*	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	594	SAM.				anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		TGAGCAATTTCGACATGCGAT	0.532000									Hay-Wells_syndrome	HNSCC(45;0.13)		
PCDHB7	56129	broad.mit.edu	37	5	140553745	140553745	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr5:140553745C>T	uc003lit.2	+	1	1503	c.1329C>T	c.(1327-1329)GAC>GAT	p.D443D		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	443	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGTCTCCGACGTCAATGACA	0.577000												
STK10	6793	broad.mit.edu	37	5	171520875	171520875	+	Silent	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr5:171520875C>T	uc003mbo.1	-	9	1395	c.1095G>A	c.(1093-1095)CCG>CCA	p.P365P		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	365							ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGGTGCCAGCGGGGTGGAAG	0.592000												
RAET1E	135250	broad.mit.edu	37	6	150211239	150211239	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr6:150211239G>A	uc003qnl.1	-	2	188	c.128C>T	c.(127-129)TCC>TTC	p.S43F	uc003qni.1_Intron|RAET1E_uc003qnj.2_Missense_Mutation_p.S43F|RAET1E_uc003qnk.1_Intron|RAET1E_uc010kih.1_RNA	NM_139165	NP_631904	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E precursor	43	MHC class I alpha-1 like.|Extracellular (Potential).				antigen processing and presentation|immune response|regulation of immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		TCCAGGTCTGGACAATGATTT	0.478000												
CRHR2	1395	broad.mit.edu	37	7	30695259	30695259	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr7:30695259G>A	uc003tbn.2	-	10	1234	c.990C>T	c.(988-990)CCC>CCT	p.P330P	CRHR2_uc010kvw.1_Silent_p.P330P|CRHR2_uc010kvx.1_Silent_p.P329P|CRHR2_uc010kvy.1_Silent_p.P166P|CRHR2_uc003tbo.2_Silent_p.P316P|CRHR2_uc003tbp.2_Silent_p.P357P	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	330	Helical; Name=6; (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4						CGTCCTCCCCGGGATTGACGA	0.602000												
LRRC4	64101	broad.mit.edu	37	7	127670639	127670639	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr7:127670639G>A	uc003vmk.2	-	2	192	c.55C>T	c.(55-57)CTC>TTC	p.L19F	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	19						cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)		ACGAACGGGAGCAGGATGGCA	0.602000												
ATP6V0A4	50617	broad.mit.edu	37	7	138447716	138447716	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr7:138447716C>T	uc003vuf.2	-	5	584	c.346G>A	c.(346-348)GCC>ACC	p.A116T	ATP6V0A4_uc003vug.2_Missense_Mutation_p.A116T|ATP6V0A4_uc003vuh.2_Missense_Mutation_p.A116T	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	116	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						TGTTTCAAGGCCTGCTGGTTC	0.443000												
RANBP6	26953	broad.mit.edu	37	9	6015394	6015394	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr9:6015394C>T	uc003zjr.2	-	1	225	c.214G>A	c.(214-216)GCA>ACA	p.A72T	RANBP6_uc011lmf.1_Intron|RANBP6_uc003zjs.2_Intron	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	72					protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CGTAGCAGTGCGGCAGCCATT	0.458000												
MXRA5	25878	broad.mit.edu	37	X	3229245	3229245	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:3229245G>A	uc004crg.3	-	7	7156	c.6999C>T	c.(6997-6999)GAC>GAT	p.D2333D		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2333	Ig-like C2-type 7.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTCTCATCTCGTCCTTCCCGA	0.532000												
SH3KBP1	30011	broad.mit.edu	37	X	19725084	19725084	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:19725084C>T	uc004czm.2	-	4	621	c.305G>A	c.(304-306)CGG>CAG	p.R102Q	SH3KBP1_uc004czl.2_Missense_Mutation_p.R65Q	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a	102	SH3 2.				apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0						CACCTGGCACCGGCGCCTCCG	0.532000												
MAGEE2	139599	broad.mit.edu	37	X	75004861	75004861	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:75004861C>T	uc004ecj.1	-	1	211	c.26G>A	c.(25-27)CGC>CAC	p.R9H		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	9										ovary(1)|skin(1)	2						GCTACAGTGGCGTGCATTCTG	0.572000												
BRWD3	254065	broad.mit.edu	37	X	79975125	79975125	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:79975125C>T	uc004edt.2	-	18	2170	c.1907G>A	c.(1906-1908)GGG>GAG	p.G636E	BRWD3_uc010nmi.1_RNA|BRWD3_uc004edo.2_Missense_Mutation_p.G232E|BRWD3_uc004edp.2_Missense_Mutation_p.G465E|BRWD3_uc004edq.2_Missense_Mutation_p.G232E|BRWD3_uc010nmj.1_Missense_Mutation_p.G232E|BRWD3_uc004edr.2_Missense_Mutation_p.G306E|BRWD3_uc004eds.2_Missense_Mutation_p.G232E|BRWD3_uc004edu.2_Missense_Mutation_p.G306E|BRWD3_uc004edv.2_Missense_Mutation_p.G232E|BRWD3_uc004edw.2_Missense_Mutation_p.G232E|BRWD3_uc004edx.2_Missense_Mutation_p.G232E|BRWD3_uc004edy.2_Missense_Mutation_p.G232E|BRWD3_uc004edz.2_Missense_Mutation_p.G306E|BRWD3_uc004eea.2_Missense_Mutation_p.G306E|BRWD3_uc004eeb.2_Missense_Mutation_p.G232E	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	636										ovary(4)	4						GGTTTGCTGCCCAATTACCTG	0.373000												
NAP1L3	4675	broad.mit.edu	37	X	92926799	92926799	+	Missense_Mutation	SNP	T	T	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:92926799T>G	uc004efq.2	-	1	1810	c.1505A>C	c.(1504-1506)AAG>ACG	p.K502T	FAM133A_uc004efr.1_5'Flank	NM_004538	NP_004529	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	502					nucleosome assembly	chromatin assembly complex				ovary(1)|skin(1)	2						TCTGTATTTCTTGTTTCCATA	0.318000												
LAMP2	3920	broad.mit.edu	37	X	119575715	119575715	+	Missense_Mutation	SNP	C	C	G			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:119575715C>G	uc004est.3	-	8	1143	c.963G>C	c.(961-963)TGG>TGC	p.W321C	LAMP2_uc004ess.3_Missense_Mutation_p.W321C|LAMP2_uc011mtz.1_Missense_Mutation_p.W210C|LAMP2_uc011mua.1_Missense_Mutation_p.W274C|LAMP2_uc010nqp.1_Missense_Mutation_p.W321C	NM_002294	NP_002285	P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2 isoform	321	Lumenal (Potential).|Second lumenal domain.		W -> R (in DAND).		platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane				ovary(1)	1						GGGGGGCATCCCAGTAGCTGA	0.378000												
FRMD7	90167	broad.mit.edu	37	X	131212786	131212786	+	Missense_Mutation	SNP	T	T	C			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:131212786T>C	uc004ewn.2	-	12	1437	c.1259A>G	c.(1258-1260)GAC>GGC	p.D420G	FRMD7_uc011muy.1_Missense_Mutation_p.D405G	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	420					regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)					AAAGACAGGGTCCATATAAAT	0.383000												
ARHGEF6	9459	broad.mit.edu	37	X	135764986	135764986	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:135764986G>T	uc004fab.2	-	13	1872	c.1410C>A	c.(1408-1410)TAC>TAA	p.Y470*	ARHGEF6_uc011mwd.1_Nonsense_Mutation_p.Y343*|ARHGEF6_uc011mwe.1_Nonsense_Mutation_p.Y316*	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	470	PH.				apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)					ATAACATAAGGTACCGCTCCT	0.353000												
IDS	3423	broad.mit.edu	37	X	148568478	148568478	+	Silent	SNP	G	G	A			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chrX:148568478G>A	uc011mxe.1	-	8	1356	c.1158C>T	c.(1156-1158)TCC>TCT	p.S386S	IDS_uc011mxd.1_Intron|IDS_uc011mxf.1_Silent_p.S296S|IDS_uc011mxg.1_Silent_p.S175S|IDS_uc010nsu.1_5'UTR|IDS_uc004fcw.3_Silent_p.S175S	NM_000202	NP_000193	P22304	IDS_HUMAN	iduronate-2-sulfatase isoform a precursor	386						lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACTGTGAGGCGGAATCAAAAG	0.433000												
TMEM177	80775	broad.mit.edu	37	2	120461483	120461483	+	RNA	DEL	A	A	-			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:120461483delA	uc002tme.2	+	13		c.1505delA						Q53S58	TM177_HUMAN	Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)					tggtttccttaaacttgtcca	0.005												
TMEM177	80775	broad.mit.edu	37	2	120461483	120461483	+	RNA	DEL	A	A	-			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr2:120461483delA	uc002tme.2	+	13		c.1505delA						Q53S58	TM177_HUMAN	Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)					tggtttccttaaacttgtcca	0.005												
HNF4A	3172	broad.mit.edu	37	20	43019236	43019236	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr20:43019236delA	uc010zwo.1	+	2	192	c.4delA	c.(4-6)AAGfs	p.K2fs	HNF4A_uc002xlt.2_Intron|HNF4A_uc002xlu.2_Intron|HNF4A_uc002xlv.2_Intron|uc002xlw.1_Intron|uc002xlx.2_Intron			P41235	HNF4A_HUMAN	Homo sapiens NR2A1 mRNA for hepatocyte nuclear factor 4, alpha, complete cds.	Error:Variant_position_missing_in_P41235_after_alignment					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CTCAAGGATGAAGAGGTTGTG	0.607												
CUL9	23113	broad.mit.edu	37	6	43188240	43188243	+	Frame_Shift_Del	DEL	TTGT	TTGT	-			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr6:43188239_43188242CTTGT>C	uc003ouk.3	+	31	6400_6403	c.6325_6328CTTGT>C	c.(6325-6330)cttgttfs	p.L2109fs	CUL9_uc003oul.3_Frame_Shift_Del_p.L2081fs|CUL9_uc010jyk.3_Frame_Shift_Del_p.L1261fs|CUL9_uc003oun.3_5'UTR	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	Homo sapiens cullin 9 (CUL9), mRNA.	2109					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CGAGCAGAACCTTGTTTTGAATTG	0.588												
MUC6	4588	broad.mit.edu	37	11	1016412	1016414	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-BR-4183-01A-02D-1126-08	TCGA-BR-4183-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08e915c4-e7ca-40b9-9175-8967169c7019	f03b244a-cd1c-4101-b0fe-2ced7638bb2a	g.chr11:1016411_1016413TGAG>T	uc001lsw.2	-	30	6439_6441	c.6388_6390CTCA>A	c.(6388-6390)tca>A	p.S2130del		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	Homo sapiens mucin 6, oligomeric mucus/gel-forming (MUC6), mRNA.	2130	Ser-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent	p.S2130delS(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGGAGAAAATGAGGAGGACAGC	0.522