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	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
WASH7P	653635	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14976G>A	uc009vis.2	-	3		c.369C>T			WASH7P_uc009vit.2_RNA|WASH7P_uc001aae.3_RNA|WASH7P_uc009viu.2_RNA|WASH7P_uc001aab.3_RNA|WASH7P_uc001aah.3_RNA|WASH7P_uc009vir.2_RNA|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_RNA|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						CTACCCTTGCGCCTCATGACC	0.582													4	36	---	---	---	---	PASS
PRAMEF11	440560	broad.mit.edu	37	1	12885289	12885289	+	Silent	SNP	G	T	T	rs148273194	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12885289G>T	uc001auk.2	-	4	1018	c.822C>A	c.(820-822)CTC>CTA	p.L274L		NM_001146344	NP_001139816	O60813	PRA11_HUMAN	PRAME family member 11	274	LRR 3.										0						GGCACTGGGAGAGATGCTTCA	0.458													5	214	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692													6	39	---	---	---	---	PASS
C1orf213	148898	broad.mit.edu	37	1	23696047	23696047	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23696047A>G	uc001bgw.2	+	1	584	c.257A>G	c.(256-258)TAT>TGT	p.Y86C	ZNF436_uc001bgt.2_5'Flank|ZNF436_uc001bgu.2_5'UTR|C1orf213_uc001bgv.2_Intron	NM_138479	NP_612488			hypothetical protein LOC148898 isoform 1												0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.97e-26)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;5.23e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		AAGCCCAGATATCGTAGGCTG	0.567													4	31	---	---	---	---	PASS
CD52	1043	broad.mit.edu	37	1	26646868	26646868	+	3'UTR	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26646868T>A	uc001bmc.2	+	2					UBXN11_uc001bma.2_5'Flank	NM_001803	NP_001794	P31358	CD52_HUMAN	CD52 antigen precursor						elevation of cytosolic calcium ion concentration|respiratory burst	anchored to membrane|integral to plasma membrane|membrane fraction					0		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	ATCCCCTCCATCTTTGGGAGG	0.547													9	51	---	---	---	---	PASS
CD52	1043	broad.mit.edu	37	1	26646869	26646869	+	3'UTR	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26646869C>A	uc001bmc.2	+	2					UBXN11_uc001bma.2_5'Flank	NM_001803	NP_001794	P31358	CD52_HUMAN	CD52 antigen precursor						elevation of cytosolic calcium ion concentration|respiratory burst	anchored to membrane|integral to plasma membrane|membrane fraction					0		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	TCCCCTCCATCTTTGGGAGGG	0.547													9	50	---	---	---	---	PASS
CD52	1043	broad.mit.edu	37	1	26646870	26646870	+	3'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26646870T>C	uc001bmc.2	+	2					UBXN11_uc001bma.2_5'Flank	NM_001803	NP_001794	P31358	CD52_HUMAN	CD52 antigen precursor						elevation of cytosolic calcium ion concentration|respiratory burst	anchored to membrane|integral to plasma membrane|membrane fraction					0		all_cancers(24;5.02e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	CCCCTCCATCTTTGGGAGGGG	0.547													9	50	---	---	---	---	PASS
RNU11	26824	broad.mit.edu	37	1	28975159	28975159	+	RNA	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28975159T>C	uc009vtj.1	+	1		c.48T>C				NR_004407				Homo sapiens RNA, U11 small nuclear (RNU11), non-coding RNA.												0						ACTCGATTGCTCTGCGTGCGG	0.478													52	175	---	---	---	---	PASS
TXLNA	200081	broad.mit.edu	37	1	32645838	32645838	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32645838C>A	uc001bui.2	+						TXLNA_uc001buj.2_5'UTR	NM_175852	NP_787048	P40222	TXLNA_HUMAN	taxilin						cell proliferation|exocytosis	cytoplasm|extracellular region	cytokine activity|high molecular weight B cell growth factor receptor binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCTTTGTGCGCCTGCTGTGGG	0.572													3	27	---	---	---	---	PASS
MTF1	4520	broad.mit.edu	37	1	38287820	38287820	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38287820G>T	uc001cce.1	-	9	1881	c.1740C>A	c.(1738-1740)ACC>ACA	p.T580T	MTF1_uc009vvj.1_Silent_p.T271T	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	580						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GTGGAGAACTGGTGGCACCAT	0.413													6	686	---	---	---	---	PASS
ZYG11A	440590	broad.mit.edu	37	1	53329658	53329658	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53329658G>T	uc001cuk.2	+	5	1528	c.1155G>T	c.(1153-1155)GTG>GTT	p.V385V	ZYG11A_uc001cul.2_Silent_p.V43V	NM_001004339	NP_001004339	Q6WRX3	ZY11A_HUMAN	zyg-11 homolog A	385							binding				0						TTCAGCTTGTGGCTATAGGAA	0.468													4	98	---	---	---	---	PASS
C8B	732	broad.mit.edu	37	1	57395015	57395015	+	3'UTR	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57395015C>A	uc001cyp.2	-	12					C8B_uc010oon.1_3'UTR|C8B_uc010ooo.1_3'UTR	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4						TAGGGCTGAGCTGGCATGAGT	0.478													16	65	---	---	---	---	PASS
JAK1	3716	broad.mit.edu	37	1	65303646	65303646	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65303646C>T	uc001dbu.1	-	22	3358	c.3109G>A	c.(3109-3111)GTC>ATC	p.V1037I	JAK1_uc009wam.1_Missense_Mutation_p.V1025I|JAK1_uc009wal.1_Missense_Mutation_p.V214I	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	1037	Protein kinase 2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		TCATCCTTGACGGTGTAATAC	0.413			Mis		ALL								5	138	---	---	---	---	PASS
TNNI3K	51086	broad.mit.edu	37	1	74818956	74818956	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74818956T>A	uc001dgf.1	+	10	990	c.939T>A	c.(937-939)TGT>TGA	p.C313*	TNNI3K_uc001dgc.1_Nonsense_Mutation_p.C414*|TNNI3K_uc001dgd.2_Nonsense_Mutation_p.C414*|TNNI3K_uc001dge.1_Nonsense_Mutation_p.C414*	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	313	ANK 8.					cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						TCAGTGCTTGTACCTATGGCA	0.294													5	343	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75102000	75102000	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75102000G>T	uc001dgg.2	-	6	786	c.567C>A	c.(565-567)ACC>ACA	p.T189T	C1orf173_uc001dgi.3_5'Flank	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	189										ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						CCAGCAATGAGGTTTTTGATC	0.343													70	367	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86315055	86315055	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86315055C>G	uc001dlj.2	-	38	3377	c.3335G>C	c.(3334-3336)AGA>ACA	p.R1112T	COL24A1_uc001dli.2_Missense_Mutation_p.R248T|COL24A1_uc010osd.1_Missense_Mutation_p.R412T|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	1112	Collagen-like 10.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		TGGACGACCTCTTTGCCCTGG	0.338													36	211	---	---	---	---	PASS
TMEM56	148534	broad.mit.edu	37	1	95614318	95614318	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95614318C>A	uc001drb.2	+	3	507	c.216C>A	c.(214-216)TTC>TTA	p.F72L	RWDD3_uc001drd.3_Missense_Mutation_p.F72L|TMEM56_uc001drc.2_Missense_Mutation_p.F72L	NM_152487	NP_689700	Q96MV1	TMM56_HUMAN	transmembrane protein 56	72	Helical; (Potential).|TLC.					integral to membrane					0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.133)		TTTTCTTATTCGATGAGGCTA	0.308													6	747	---	---	---	---	PASS
VAV3	10451	broad.mit.edu	37	1	108311072	108311072	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108311072G>C	uc001dvk.1	-	7	762	c.708C>G	c.(706-708)ATC>ATG	p.I236M	VAV3_uc010ouw.1_Missense_Mutation_p.I236M|VAV3_uc001dvl.1_Missense_Mutation_p.I60M|VAV3_uc010oux.1_Missense_Mutation_p.I236M	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	236	DH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		CAGGAATGTTGATGAATACTG	0.323													7	556	---	---	---	---	PASS
FNDC7	163479	broad.mit.edu	37	1	109273442	109273442	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109273442C>A	uc001dvx.2	+	9	1771	c.1771C>A	c.(1771-1773)CAC>AAC	p.H591N	FNDC7_uc010ova.1_Missense_Mutation_p.H358N	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	592	Fibronectin type-III 7.					extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TCATCAAAACCACTGCCTCCT	0.463													5	183	---	---	---	---	PASS
SLC16A4	9122	broad.mit.edu	37	1	110921782	110921782	+	Silent	SNP	A	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110921782A>C	uc001dzo.1	-	6	905	c.723T>G	c.(721-723)ACT>ACG	p.T241T	SLC16A4_uc009wfs.1_Silent_p.T193T|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Silent_p.T179T|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Silent_p.T131T	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	241	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CCTTCTGCGTAGTACTGTCCT	0.423													104	506	---	---	---	---	PASS
SLC16A1	6566	broad.mit.edu	37	1	113466326	113466326	+	Intron	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113466326C>T	uc001ecx.2	-						SLC16A1_uc001ecy.2_Intron|SLC16A1_uc001ecz.2_Intron|AFARP1_uc001eda.1_RNA	NM_003051	NP_003042	P53985	MOT1_HUMAN	solute carrier family 16, member 1						blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	integral to membrane|membrane fraction|plasma membrane	mevalonate transmembrane transporter activity|protein binding|secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Pyruvic acid(DB00119)	GACCACAGCACCCCGGTGGAA	0.602													4	19	---	---	---	---	PASS
PTPN22	26191	broad.mit.edu	37	1	114372312	114372312	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114372312T>C	uc001eds.2	-	18	2282	c.2152A>G	c.(2152-2154)ATA>GTA	p.I718V	PTPN22_uc009wgq.2_Missense_Mutation_p.I663V|PTPN22_uc010owo.1_Missense_Mutation_p.I474V|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Missense_Mutation_p.I718V|PTPN22_uc009wgs.2_Missense_Mutation_p.I591V	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type	718					negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATGTTTCTATAGATTGGGCC	0.343													5	367	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115151368	115151368	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115151368A>G	uc001efd.1	-	10	2198	c.1496T>C	c.(1495-1497)CTA>CCA	p.L499P	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.L442P	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	499										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCTTCTGTAGAGACACCAC	0.473													40	312	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118526527	118526527	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118526527G>T	uc001ehk.2	-	42	5847	c.5779C>A	c.(5779-5781)CTG>ATG	p.L1927M		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1927						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AGACTGTCCAGGTGATTATAC	0.294													6	637	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145297661	145297661	+	Missense_Mutation	SNP	C	A	A	rs4068083	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145297661C>A	uc001end.3	+	4	571	c.536C>A	c.(535-537)GCT>GAT	p.A179D	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.A179D|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	179											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTTGAGGAGGCTGAGAAAGTA	0.433													5	177	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145311931	145311931	+	Missense_Mutation	SNP	C	T	T	rs150825795	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145311931C>T	uc001end.3	+	14	2034	c.1999C>T	c.(1999-2001)CGT>TGT	p.R667C	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_5'UTR|NBPF10_uc010oyl.1_5'UTR|NBPF10_uc010oyj.1_5'UTR|NBPF10_uc010oym.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGAGCAACAGCGTGTTGGCTT	0.453													4	32	---	---	---	---	PASS
LOC200030	200030	broad.mit.edu	37	1	148346783	148346783	+	5'UTR	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148346783A>G	uc001eqf.2	-	1					LOC200030_uc001eqe.2_5'UTR|LOC200030_uc001eqg.2_5'UTR|NBPF14_uc009wkf.1_RNA|uc001erd.3_5'UTR|uc001erc.3_RNA|uc010paj.1_5'UTR|uc010pav.1_5'UTR|uc010paw.1_5'UTR	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GAAGAGGTGGAGTCAGGGACT	0.458													10	39	---	---	---	---	PASS
LOC200030	200030	broad.mit.edu	37	1	148346785	148346785	+	5'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148346785T>C	uc001eqf.2	-	1					LOC200030_uc001eqe.2_5'UTR|LOC200030_uc001eqg.2_5'UTR|NBPF14_uc009wkf.1_RNA|uc001erd.3_5'UTR|uc001erc.3_RNA|uc010paj.1_5'UTR|uc010pav.1_5'UTR|uc010paw.1_5'UTR	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						AGAGGTGGAGTCAGGGACTGG	0.453													10	39	---	---	---	---	PASS
PRPF3	9129	broad.mit.edu	37	1	150312943	150312943	+	Silent	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150312943C>T	uc001eum.3	+	9	1434	c.1272C>T	c.(1270-1272)CTC>CTT	p.L424L	PRPF3_uc009wlp.2_RNA|PRPF3_uc010pca.1_Silent_p.L383L|PRPF3_uc010pcb.1_Silent_p.L375L|PRPF3_uc009wlq.1_RNA	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog	424					nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		CAGCCCAGCTCAATCCTCCAG	0.269													149	291	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152328131	152328131	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152328131A>G	uc001ezw.3	-	3	2204	c.2131T>C	c.(2131-2133)TCA>CCA	p.S711P	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	711	Ser-rich.						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)			CCTGAACTTGACCCATGTTGA	0.478													6	203	---	---	---	---	PASS
ATF6	22926	broad.mit.edu	37	1	161761249	161761249	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161761249G>T	uc001gbr.2	+	5	473	c.406G>T	c.(406-408)GGT>TGT	p.G136C	ATF6_uc001gbq.1_Missense_Mutation_p.G136C	NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6	136	Cytoplasmic (Potential).|Transcription activation.				positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			TTCCTTATATGGTGAAAACTC	0.393													7	676	---	---	---	---	PASS
TADA1	117143	broad.mit.edu	37	1	166833059	166833059	+	Splice_Site	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166833059A>T	uc001gdw.2	-	4	514	c.330_splice	c.e4+1	p.D110_splice	TADA1_uc001gdv.2_5'Flank|TADA1_uc009wve.2_Missense_Mutation_p.V111E	NM_053053	NP_444281	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1-like						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1						AGAACAACCTACATCAAATTT	0.398													83	169	---	---	---	---	PASS
CD34	947	broad.mit.edu	37	1	208072364	208072364	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208072364G>T	uc001hgw.1	-	3	728	c.470C>A	c.(469-471)CCC>CAC	p.P157H	CD34_uc001hgx.1_Missense_Mutation_p.P157H|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	157	Extracellular (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GGGTTTAGTGGGAGATGTTGC	0.468													6	465	---	---	---	---	PASS
IARS2	55699	broad.mit.edu	37	1	220275605	220275605	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220275605C>A	uc001hmc.2	+	4	789	c.685C>A	c.(685-687)CAA>AAA	p.Q229K		NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	229					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	AACTTTTTACCAAATGTATGA	0.308													7	475	---	---	---	---	PASS
C1orf58	148362	broad.mit.edu	37	1	222906040	222906040	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222906040G>T	uc001hnq.1	+	13	1615	c.1220G>T	c.(1219-1221)GGG>GTG	p.G407V	C1orf58_uc010put.1_Missense_Mutation_p.G375V|C1orf58_uc010puu.1_3'UTR|C1orf58_uc010puv.1_Missense_Mutation_p.G375V|uc001hnr.1_Intron|uc001hns.1_5'Flank	NM_144695	NP_653296	Q5VW32	BROX_HUMAN	Bro1-domain-containing protein	407	BRO1.					membrane					0				GBM - Glioblastoma multiforme(131;0.0667)		AAGGACACTGGGTGCTACATC	0.358													5	341	---	---	---	---	PASS
C1orf124	83932	broad.mit.edu	37	1	231489083	231489083	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231489083A>G	uc001hur.2	+	5	1894	c.1446A>G	c.(1444-1446)AAA>AAG	p.K482K	C1orf124_uc001hus.2_3'UTR|C1orf124_uc001hut.2_3'UTR	NM_032018	NP_114407	Q9H040	CA124_HUMAN	hypothetical protein LOC83932 isoform a	482					DNA repair	nuclear speck	DNA binding|metal ion binding				0	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				ACAGCATCAAAGTCAAAAGCG	0.418													14	58	---	---	---	---	PASS
PLD5	200150	broad.mit.edu	37	1	242253369	242253369	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253369G>A	uc001hzn.1	-	10	1525	c.1398C>T	c.(1396-1398)GGC>GGT	p.G466G	PLD5_uc001hzl.3_Silent_p.G404G|PLD5_uc001hzm.3_Silent_p.G256G|PLD5_uc001hzo.1_Silent_p.G374G			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;	466						integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CAAGGCCCGTGCCAGCATTCT	0.423													38	312	---	---	---	---	PASS
HNRNPU	3192	broad.mit.edu	37	1	245017680	245017680	+	3'UTR	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245017680C>T	uc001iaz.1	-	14					HNRNPU_uc001iaw.1_RNA|HNRNPU_uc001iax.1_RNA|HNRNPU_uc001iay.1_3'UTR|HNRNPU_uc001iba.1_3'UTR	NM_031844	NP_114032	Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U						CRD-mediated mRNA stabilization	catalytic step 2 spliceosome|cell surface|CRD-mediated mRNA stability complex|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	ATP binding|DNA binding|protein binding|RNA binding				0	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			AAAAGTTAGCCTACTAAAGAA	0.333													8	592	---	---	---	---	PASS
ZNF669	79862	broad.mit.edu	37	1	247264073	247264073	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247264073G>T	uc001ice.2	-	4	1171	c.998C>A	c.(997-999)CCC>CAC	p.P333H	ZNF669_uc001icf.2_Missense_Mutation_p.P247H	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	333					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			ACATTTATAGGGTCTTTCTCC	0.413													6	266	---	---	---	---	PASS
TPO	7173	broad.mit.edu	37	2	1546455	1546455	+	3'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1546455T>C	uc002qww.2	+	17					TPO_uc010ewj.2_RNA|TPO_uc002qwu.2_3'UTR|TPO_uc002qwr.2_3'UTR|TPO_uc002qwx.2_3'UTR|TPO_uc010yio.1_3'UTR|TPO_uc010yip.1_3'UTR|TPO_uc002qwz.2_RNA	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CATTGCCTGATTTGTTCCTTC	0.398													5	53	---	---	---	---	PASS
C2orf18	54978	broad.mit.edu	37	2	27001276	27001276	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27001276G>A	uc002rhp.1	+	6	1089	c.1013G>A	c.(1012-1014)CGT>CAT	p.R338H	C2orf18_uc002rhq.1_Missense_Mutation_p.R255H|C2orf18_uc010eyo.1_Missense_Mutation_p.R285H|C2orf18_uc010ylc.1_Missense_Mutation_p.R191H	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor	338						integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCTACACCGTCCGCTGCTG	0.642													3	20	---	---	---	---	PASS
DHX57	90957	broad.mit.edu	37	2	39088979	39088979	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39088979C>A	uc002rrf.2	-	5	672	c.573G>T	c.(571-573)AGG>AGT	p.R191S	DHX57_uc002rre.2_5'UTR|DHX57_uc002rrg.2_Missense_Mutation_p.R191S	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	191	UBA.						ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				TGAAACCATACCTGTCAAGGG	0.393													15	49	---	---	---	---	PASS
KLRAQ1	129285	broad.mit.edu	37	2	48732717	48732717	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48732717C>A	uc002rwm.2	+	18	2135	c.1950C>A	c.(1948-1950)ACC>ACA	p.T650T	KLRAQ1_uc002rwl.2_Silent_p.T604T|KLRAQ1_uc002rwk.2_Intron|KLRAQ1_uc010yok.1_Intron	NM_001135629	NP_001129101	Q6ZMI0	KLRAQ_HUMAN	KLRAQ motif containing 1 isoform 1	650										ovary(1)	1						GGACTTTAACCAGGACATCTG	0.363													6	659	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61455816	61455816	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61455816C>A	uc002sbe.2	-	61	7429	c.7407G>T	c.(7405-7407)ATG>ATT	p.M2469I	USP34_uc002sbf.2_Missense_Mutation_p.M619I	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2469					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AAAAATGTACCATTGTAGATA	0.308													5	378	---	---	---	---	PASS
B3GNT2	10678	broad.mit.edu	37	2	62450134	62450134	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62450134A>G	uc002sbs.2	+	2	1017	c.779A>G	c.(778-780)AAT>AGT	p.N260S		NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	260	Lumenal (Potential).					Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			AATTACTTGAATAGTTTATCC	0.433													21	194	---	---	---	---	PASS
MRPL35	51318	broad.mit.edu	37	2	86433340	86433340	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86433340C>A	uc002srg.3	+	2	213	c.155C>A	c.(154-156)CCA>CAA	p.P52Q	MRPL35_uc002srf.3_Missense_Mutation_p.P52Q	NM_016622	NP_057706	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35 isoform a	52					translation	mitochondrial ribosome	structural constituent of ribosome				0						ATTCAGACACCAGTTGTTTCC	0.438													5	334	---	---	---	---	PASS
RMND5A	64795	broad.mit.edu	37	2	87820801	87820801	+	Intron	SNP	G	T	T	rs139041710	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87820801G>T	uc002srs.3	+						NCRNA00152_uc002ssk.3_RNA|NCRNA00152_uc010fgy.2_RNA|NCRNA00152_uc010fgz.2_RNA			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						TCACGACTCAGCCCCCTCCAG	0.507													6	119	---	---	---	---	PASS
ANKRD20B	729171	broad.mit.edu	37	2	95488787	95488787	+	RNA	SNP	G	T	T	rs78339506		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95488787G>T	uc010fhp.2	-	10		c.931C>A				NR_003366				Homo sapiens ankyrin repeat domain 20B (ANKRD20B), non-coding RNA.												0						TGCCTTTCTTGCTCTTCCTCT	0.323													19	405	---	---	---	---	PASS
RGPD3	653489	broad.mit.edu	37	2	107021431	107021431	+	3'UTR	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107021431C>T	uc010ywi.1	-	23						NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3						intracellular transport		binding			ovary(1)	1						CTGGTATCAACACTTCAAGCT	0.378													6	66	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109368077	109368077	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109368077C>T	uc002tem.3	+	11	1675	c.1549C>T	c.(1549-1551)CTT>TTT	p.L517F		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	517					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						ATGCCTGCCCCTTCCTGTGTG	0.398													6	214	---	---	---	---	PASS
ACOXL	55289	broad.mit.edu	37	2	111721267	111721267	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111721267G>T	uc002tgr.3	+	13	1350	c.1126G>T	c.(1126-1128)GGT>TGT	p.G376C	ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2	376					fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						CACTTTTGAAGGTGACGATGT	0.338													6	608	---	---	---	---	PASS
R3HDM1	23518	broad.mit.edu	37	2	136389312	136389312	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136389312G>T	uc002tuo.2	+	8	892	c.522G>T	c.(520-522)TTG>TTT	p.L174F	R3HDM1_uc010fni.2_Missense_Mutation_p.L172F|R3HDM1_uc002tup.2_Missense_Mutation_p.L118F|R3HDM1_uc010zbh.1_Missense_Mutation_p.L6F	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	174	R3H.						nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		TGCTGAAATTGGAACAAGAAA	0.328													7	624	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166201197	166201197	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166201197G>A	uc002udc.2	+	16	2985	c.2695G>A	c.(2695-2697)GGC>AGC	p.G899S	SCN2A_uc002udd.2_Missense_Mutation_p.G899S|SCN2A_uc002ude.2_Missense_Mutation_p.G899S	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	899	II.|Helical; Name=S5 of repeat II; (Potential).				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	TGCTGTGGTCGGCATGCAGCT	0.438													34	216	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170028541	170028541	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170028541T>C	uc002ues.2	-	58	11460	c.11247A>G	c.(11245-11247)TCA>TCG	p.S3749S		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3749	LDL-receptor class A 31.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TTTCCTCATCTGAGTTATCTC	0.453													59	141	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170044544	170044544	+	Silent	SNP	G	T	T	rs143637076		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170044544G>T	uc002ues.2	-	49	9477	c.9264C>A	c.(9262-9264)ATC>ATA	p.I3088I		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3088	Extracellular (Potential).|LDL-receptor class A 25.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TCATCATCTCGATGCAGCGCC	0.512													4	103	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179575503	179575503	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179575503C>T	uc010zfg.1	-	95	24813	c.24589G>A	c.(24589-24591)GGA>AGA	p.G8197R	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.G4858R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	9124							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)			TGGTACTTTCCGCCACTTCGT	0.488													57	300	---	---	---	---	PASS
CCDC141	285025	broad.mit.edu	37	2	179734018	179734018	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179734018C>A	uc002unf.1	-	5	552	c.495G>T	c.(493-495)GAG>GAT	p.E165D		NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	165							protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TGTACTGAACCTCATCATTCA	0.323													5	296	---	---	---	---	PASS
HSPE1	3336	broad.mit.edu	37	2	198368149	198368149	+	3'UTR	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198368149C>T	uc002uul.2	+	4						NM_002157	NP_002148	P61604	CH10_HUMAN	heat shock 10kDa protein 1						activation of caspase activity|protein folding|response to unfolded protein	mitochondrial matrix	ATP binding|chaperone binding|unfolded protein binding				0			Epithelial(96;0.225)			GATATAAACACTTCCAAATAA	0.259													4	56	---	---	---	---	PASS
CFLAR	8837	broad.mit.edu	37	2	202025389	202025389	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202025389A>G	uc002uxb.3	+	9	1480	c.1028A>G	c.(1027-1029)GAT>GGT	p.D343G	CFLAR_uc010zhk.1_Missense_Mutation_p.D247G|CFLAR_uc002uxc.3_Missense_Mutation_p.D308G|CFLAR_uc010zhl.1_Missense_Mutation_p.D247G|CFLAR_uc010fsw.1_RNA|CFLAR_uc002uxd.3_Missense_Mutation_p.D343G|CFLAR_uc002uxf.2_Missense_Mutation_p.D343G|CFLAR_uc010fsy.2_Intron|CFLAR_uc010fsx.2_Intron|CFLAR_uc010zhm.1_Missense_Mutation_p.D247G|CFLAR_uc010fsz.2_Missense_Mutation_p.D98G|CFLAR_uc002uxg.2_Missense_Mutation_p.D98G|uc002uxh.1_5'Flank	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform	343	Interaction with caspase-3.|Interaction with TRAF1 and TRAF2.|Not proteolytically processed and involved in apoptosis inhibition.|Caspase.|Interaction with caspase-8 subunits p18 and p10.			D -> E (in Ref. 8; AAC15825).	anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						TTCATGGGAGATTCATGCCCT	0.532													18	85	---	---	---	---	PASS
BMPR2	659	broad.mit.edu	37	2	203424437	203424437	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203424437A>G	uc002uzf.3	+	13	4033	c.2885A>G	c.(2884-2886)GAT>GGT	p.D962G	BMPR2_uc010ftr.2_3'UTR	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	962	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						TCAACACAAGATGGCAAATCA	0.418													6	373	---	---	---	---	PASS
NRP2	8828	broad.mit.edu	37	2	206587273	206587273	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206587273T>C	uc002vaw.2	+	4	1296	c.505T>C	c.(505-507)TAT>CAT	p.Y169H	NRP2_uc002vat.2_Missense_Mutation_p.Y169H|NRP2_uc002vau.2_Missense_Mutation_p.Y169H|NRP2_uc002vav.2_Missense_Mutation_p.Y169H|NRP2_uc002vax.2_Missense_Mutation_p.Y169H|NRP2_uc002vay.2_Missense_Mutation_p.Y169H|NRP2_uc010fud.2_Missense_Mutation_p.Y169H	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	169	Extracellular (Potential).|CUB 2.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						TCCTGAGAAGTATCCACACAA	0.473													6	189	---	---	---	---	PASS
NCL	4691	broad.mit.edu	37	2	232322358	232322358	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232322358C>G	uc002vru.2	-	9	1584	c.1443G>C	c.(1441-1443)TGG>TGC	p.W481C	SNORA75_uc002vrv.1_5'Flank|SNORD20_uc002vrw.1_5'Flank	NM_005381	NP_005372	P19338	NUCL_HUMAN	nucleolin	481					angiogenesis	cell cortex|nucleolus|ribonucleoprotein complex	nucleotide binding|protein C-terminus binding|RNA binding|telomeric DNA binding			ovary(2)|pancreas(1)	3		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TCTTACCACTCCAAGTGCTAT	0.368													49	382	---	---	---	---	PASS
STK25	10494	broad.mit.edu	37	2	242438498	242438498	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242438498A>G	uc002wbm.2	-	6	948	c.677T>C	c.(676-678)CTG>CCG	p.L226P	STK25_uc002wbk.2_Missense_Mutation_p.L45P|STK25_uc002wbl.2_Missense_Mutation_p.L45P|STK25_uc002wbn.2_Missense_Mutation_p.L226P|STK25_uc002wbo.2_Missense_Mutation_p.L149P|STK25_uc010zos.1_Missense_Mutation_p.L132P|STK25_uc010zot.1_Missense_Mutation_p.L152P|STK25_uc002wbp.2_Missense_Mutation_p.L226P|STK25_uc010fzo.2_Missense_Mutation_p.L149P|STK25_uc010zou.1_Missense_Mutation_p.L132P|STK25_uc010zov.1_Missense_Mutation_p.L132P	NM_006374	NP_006365	O00506	STK25_HUMAN	serine/threonine kinase 25	226	Protein kinase.				response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		CTTGGGAATCAGGAACAGGAC	0.607													6	83	---	---	---	---	PASS
TTLL3	26140	broad.mit.edu	37	3	9868880	9868880	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9868880T>C	uc003btg.2	+	9	1290	c.1074T>C	c.(1072-1074)TAT>TAC	p.Y358Y	ARPC4_uc003btc.1_Intron|TTLL3_uc003btd.3_Silent_p.Y325Y|TTLL3_uc003btf.3_Intron|TTLL3_uc010hco.1_Silent_p.Y294Y|TTLL3_uc003bth.3_Silent_p.Y146Y|TTLL3_uc011atj.1_Silent_p.Y294Y|TTLL3_uc003btj.3_Silent_p.Y146Y|TTLL3_uc003bti.3_Silent_p.Y146Y|TTLL3_uc003btk.2_Silent_p.Y161Y	NM_001025930	NP_001021100	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	358	TTL.				axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity			large_intestine(2)	2	Medulloblastoma(99;0.227)					GCGACAGCTATATCCGCTTTT	0.383													30	36	---	---	---	---	PASS
FANCD2	2177	broad.mit.edu	37	3	10078005	10078005	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10078005C>A	uc003buw.2	+	7	551	c.473C>A	c.(472-474)CCA>CAA	p.P158Q	FANCD2_uc003bux.1_Missense_Mutation_p.P158Q|FANCD2_uc003buy.1_Missense_Mutation_p.P158Q|FANCD2_uc003buv.2_Missense_Mutation_p.P158Q	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform	158	Interaction with FANCE.				DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GAGAAGTTGCCAGAATATTTT	0.318			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				6	706	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191570	10191570	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191570T>G	uc003bvc.2	+	3	776	c.563T>G	c.(562-564)CTG>CGG	p.L188R	VHL_uc003bvd.2_Missense_Mutation_p.L147R	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	188			L -> Q (in VHLD; type I).|L -> P (in VHLD; type I-II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L188fs*14(2)|p.L188P(2)|p.L188Q(2)|p.D187_L188del(2)|p.L188V(1)|p.D187_N193del(1)|p.E189fs*27(1)|p.Y185fs*11(1)|p.L188R(1)|p.D187fs*14(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACGAAGATCTGGAAGACCAC	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				38	50	---	---	---	---	PASS
METTL6	131965	broad.mit.edu	37	3	15467794	15467794	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15467794C>A	uc003bzs.1	-	2	483	c.225G>T	c.(223-225)GAG>GAT	p.E75D	METTL6_uc011avp.1_Missense_Mutation_p.E75D|METTL6_uc003bzt.1_Missense_Mutation_p.E75D|EAF1_uc003bzu.2_5'Flank|EAF1_uc011avq.1_5'Flank	NM_152396	NP_689609	Q8TCB7	METL6_HUMAN	methyltransferase like 6	75							methyltransferase activity				0						ATTAGCTTACCTCTCTACATG	0.269													5	328	---	---	---	---	PASS
TBC1D5	9779	broad.mit.edu	37	3	17413582	17413582	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17413582G>T	uc003cbf.2	-	13	2645	c.980C>A	c.(979-981)CCA>CAA	p.P327Q	TBC1D5_uc010hev.2_Missense_Mutation_p.P327Q|TBC1D5_uc003cbe.2_Missense_Mutation_p.P327Q|TBC1D5_uc010hew.1_Missense_Mutation_p.P279Q	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	327	Rab-GAP TBC.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						ATATATCTGTGGTGCAATTTC	0.229													5	308	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47165360	47165360	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47165360G>A	uc003cqs.2	-	3	819	c.766C>T	c.(766-768)CAG>TAG	p.Q256*	SETD2_uc003cqv.2_Nonsense_Mutation_p.Q245*	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	256					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATAGTGTCCTGCTTAGTATCT	0.363			N|F|S|Mis		clear cell renal carcinoma								150	200	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47165361	47165361	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47165361C>G	uc003cqs.2	-	3	818	c.765G>C	c.(763-765)AAG>AAC	p.K255N	SETD2_uc003cqv.2_Missense_Mutation_p.K244N	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	255					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TAGTGTCCTGCTTAGTATCTG	0.363			N|F|S|Mis		clear cell renal carcinoma								150	200	---	---	---	---	PASS
CADM2	253559	broad.mit.edu	37	3	86115873	86115873	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86115873C>A	uc003dqj.2	+	10	1874	c.1248C>A	c.(1246-1248)GCC>GCA	p.A416A	CADM2_uc003dqk.2_Silent_p.A385A|CADM2_uc003dql.2_Silent_p.A418A|uc003dqm.1_5'Flank	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D	416	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		CTGATACAGCCATTATCAATG	0.388													5	183	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113022837	113022837	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113022837T>G	uc003ead.1	-	14	2559	c.2546A>C	c.(2545-2547)AAA>ACA	p.K849T	WDR52_uc010hqj.1_5'UTR|WDR52_uc010hqk.1_RNA			Q96MT7	WDR52_HUMAN	RecName: Full=WD repeat protein 52.; Flags: Fragment;	Error:Variant_position_missing_in_Q96MT7_after_alignment										central_nervous_system(1)	1						TTTGTTAAGTTTTTGCTGCTT	0.448													91	485	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	C	C	rs79365690		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113049451A>C	uc003ead.1	-	8	1236	c.1223T>G	c.(1222-1224)GTT>GGT	p.V408G	WDR52_uc010hqk.1_5'Flank			Q96MT7	WDR52_HUMAN	RecName: Full=WD repeat protein 52.; Flags: Fragment;	Error:Variant_position_missing_in_Q96MT7_after_alignment										central_nervous_system(1)	1						TTCCTCAACAACAGCCACTTT	0.408													30	258	---	---	---	---	PASS
ARGFX	503582	broad.mit.edu	37	3	121305227	121305227	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121305227C>G	uc003eef.2	+	5	823	c.728C>G	c.(727-729)TCC>TGC	p.S243C		NM_001012659	NP_001012677	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	243						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(114;0.152)		AATGAGATATCCAGCTCTTCT	0.473													76	177	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121412704	121412704	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121412704A>G	uc003eei.3	-	13	6777	c.6651T>C	c.(6649-6651)GAT>GAC	p.D2217D	GOLGB1_uc010hrc.2_Silent_p.D2222D|GOLGB1_uc003eej.3_Silent_p.D2183D|GOLGB1_uc011bjm.1_Silent_p.D2103D|GOLGB1_uc010hrd.1_Silent_p.D2181D	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	2217	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		TTTGAATCGCATCACTAAACT	0.403													165	377	---	---	---	---	PASS
IQCB1	9657	broad.mit.edu	37	3	121526191	121526191	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121526191C>A	uc010hre.1	-	7	802	c.587G>T	c.(586-588)AGT>ATT	p.S196I	IQCB1_uc003eek.2_Missense_Mutation_p.R196I|IQCB1_uc010hrf.1_RNA	NM_001023570	NP_001018864	Q15051	IQCB1_HUMAN	IQ motif containing B1 isoform a	196					cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)		ACCAAGTCACCTGTTGATCTG	0.299													7	593	---	---	---	---	PASS
SLC15A2	6565	broad.mit.edu	37	3	121613330	121613330	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121613330C>G	uc003eep.2	+	1	160	c.7C>G	c.(7-9)CCT>GCT	p.P3A	SLC15A2_uc011bjn.1_Missense_Mutation_p.P3A	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	3					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	AGCCATGAATCCTTTCCAGAA	0.493													18	169	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123418999	123418999	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123418999C>T	uc003ego.2	-	18	3598	c.3316G>A	c.(3316-3318)GAT>AAT	p.D1106N	MYLK_uc011bjw.1_Missense_Mutation_p.D1106N|MYLK_uc003egp.2_Missense_Mutation_p.D1037N|MYLK_uc003egq.2_Missense_Mutation_p.D1106N|MYLK_uc003egr.2_Missense_Mutation_p.D1037N|MYLK_uc003egs.2_Missense_Mutation_p.D930N|MYLK_uc003egt.2_Missense_Mutation_p.D297N	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1106	Actin-binding (calcium/calmodulin- insensitive) (By similarity).|Ig-like C2-type 7.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		ACATGAACATCTTGCAGCTTC	0.547													19	128	---	---	---	---	PASS
ROPN1	54763	broad.mit.edu	37	3	123698012	123698012	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123698012C>A	uc003eha.2	-						ROPN1_uc003ehb.1_RNA|ROPN1_uc003ehc.1_RNA	NM_017578	NP_060048	Q9HAT0	ROP1A_HUMAN	ropporin						signal transduction		cAMP-dependent protein kinase regulator activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.148)		TTATGAGCACCACTGGCTTAT	0.418													5	251	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130380932	130380932	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130380932C>G	uc010htl.2	+	34	6313	c.6282C>G	c.(6280-6282)AGC>AGG	p.S2094R	COL6A6_uc003eni.3_Missense_Mutation_p.S193R	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	2094	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						GGGAAACCAGCCACTTAGATG	0.423													96	208	---	---	---	---	PASS
ATP2C1	27032	broad.mit.edu	37	3	130720168	130720168	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130720168A>G	uc003enl.2	+	28	2956	c.2734A>G	c.(2734-2736)ACA>GCA	p.T912A	ATP2C1_uc011blg.1_Missense_Mutation_p.T946A|ATP2C1_uc011blh.1_Missense_Mutation_p.T907A|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Missense_Mutation_p.T896A|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Missense_Mutation_p.T912A|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Missense_Mutation_p.T912A|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Missense_Mutation_p.T912A|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_Missense_Mutation_p.T590A	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a	912	Cytoplasmic (By similarity).				actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TGTTAGTTCGACATCATCATC	0.383									Hailey-Hailey_disease				21	676	---	---	---	---	PASS
P2RY12	64805	broad.mit.edu	37	3	151056476	151056476	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151056476A>G	uc003eyw.1	-	2	374	c.158T>C	c.(157-159)ATC>ACC	p.I53T	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron|P2RY12_uc011boa.1_Missense_Mutation_p.I53T|P2RY12_uc003eyx.1_Missense_Mutation_p.I53T	NM_176876	NP_795345	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y12	53	Cytoplasmic (Potential).				platelet activation	integral to membrane|plasma membrane	guanyl-nucleotide exchange factor activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TTTACTCCGGATTTGAAAGAA	0.373													40	227	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164725710	164725710	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164725710G>T	uc003fei.2	-	36	4318	c.4256C>A	c.(4255-4257)CCT>CAT	p.P1419H		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1419	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TGGGAAATAAGGTGGATAATT	0.229										HNSCC(35;0.089)			6	737	---	---	---	---	PASS
WDR49	151790	broad.mit.edu	37	3	167272564	167272564	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167272564C>A	uc003fev.1	-	6	980	c.674G>T	c.(673-675)TGT>TTT	p.C225F	WDR49_uc003feu.1_Missense_Mutation_p.C50F|WDR49_uc011bpd.1_Missense_Mutation_p.C278F|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	225	WD 4.									large_intestine(1)|ovary(1)|skin(1)	3						TGTATGGTGACAATATCCATT	0.348													10	606	---	---	---	---	PASS
SLC7A14	57709	broad.mit.edu	37	3	170198546	170198546	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170198546G>T	uc003fgz.2	-	7	1841	c.1525C>A	c.(1525-1527)CCC>ACC	p.P509T	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	509						integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CCGTAATTGGGGTGGTTGACG	0.458													5	267	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172502593	172502593	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172502593G>T	uc003fii.2	+	16	1870	c.1732G>T	c.(1732-1734)GAT>TAT	p.D578Y	ECT2_uc010hwv.1_Missense_Mutation_p.D609Y|ECT2_uc003fih.2_Missense_Mutation_p.D577Y|ECT2_uc003fij.1_Missense_Mutation_p.D578Y|ECT2_uc003fik.1_Missense_Mutation_p.D578Y|ECT2_uc003fil.1_Missense_Mutation_p.D609Y	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	578	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			ACTTTTAAATGGTACTTGTCT	0.343													6	603	---	---	---	---	PASS
ACTL6A	86	broad.mit.edu	37	3	179298972	179298972	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179298972C>A	uc003fjw.2	+	11	1163	c.990C>A	c.(988-990)ACC>ACA	p.T330T	ACTL6A_uc003fjx.2_Silent_p.T288T|ACTL6A_uc003fjy.2_Silent_p.T288T	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1	330					chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			ATGTTGTCACCACAAGTGTTG	0.408													6	696	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182554180	182554180	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182554180G>T	uc003flb.2	+	6	731	c.474G>T	c.(472-474)TTG>TTT	p.L158F	ATP11B_uc003fla.2_Missense_Mutation_p.L158F	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	158	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			CTGCAGACTTGGTGCTTCTGT	0.398													7	517	---	---	---	---	PASS
CLCN2	1181	broad.mit.edu	37	3	184073108	184073108	+	Intron	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184073108T>G	uc003foi.2	-						CLCN2_uc003foh.2_Intron|CLCN2_uc010hya.1_Intron|CLCN2_uc011brl.1_Intron|CLCN2_uc011brm.1_Intron|CLCN2_uc011brn.1_3'UTR	NM_004366	NP_004357	P51788	CLCN2_HUMAN	chloride channel 2							chloride channel complex	voltage-gated chloride channel activity				0	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	gcgtggcaggtgcttagaaGG	0.239													10	40	---	---	---	---	PASS
TPRG1	285386	broad.mit.edu	37	3	188933093	188933093	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188933093G>A	uc003frv.1	+	8	1450	c.223G>A	c.(223-225)GAG>AAG	p.E75K	TPRG1_uc003frw.1_Missense_Mutation_p.E75K	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	75											0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		GGGGGCCATTGAGACTGCCAT	0.483													9	135	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195410627	195410627	+	Missense_Mutation	SNP	A	G	G	rs6583272	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195410627A>G	uc003fuw.2	+	13	1718	c.524A>G	c.(523-525)CAG>CGG	p.Q175R	SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						CCTCAGGTGCAGATTGATGAG	0.473													9	133	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505774	195505774	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505774G>T	uc011bto.1	-	3	12753	c.12293C>A	c.(12292-12294)CCT>CAT	p.P4098H	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	983	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGGTGACAGGAAGAGGGGT	0.587													7	84	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505839	195505839	+	Silent	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505839A>T	uc011bto.1	-	3	12688	c.12228T>A	c.(12226-12228)GGT>GGA	p.G4076G	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATG	0.597													4	54	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195507324	195507324	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195507324G>C	uc011bto.1	-	3	11203	c.10743C>G	c.(10741-10743)CAC>CAG	p.H3581Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	502					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGAGG	0.572													9	83	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509127	195509127	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509127A>G	uc011bto.1	-	3	9400	c.8940T>C	c.(8938-8940)ACT>ACC	p.T2980T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	850	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGCTAGTGACAGGAA	0.587													3	11	---	---	---	---	PASS
SDHAP1	255812	broad.mit.edu	37	3	195698212	195698212	+	RNA	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195698212C>A	uc003fvx.3	-	11		c.1661G>T			SDHAP1_uc011btp.1_RNA	NR_003264				Homo sapiens full length insert cDNA clone ZC24D06.												0						TGCTGAGTCGCAGTTCCGATG	0.438													5	99	---	---	---	---	PASS
TFRC	7037	broad.mit.edu	37	3	195780320	195780320	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195780320A>G	uc003fvz.3	-	18	2292	c.2009T>C	c.(2008-2010)GTC>GCC	p.V670A	TFRC_uc003fwa.3_Missense_Mutation_p.V670A|TFRC_uc010hzy.2_Missense_Mutation_p.V589A|TFRC_uc011btr.1_Missense_Mutation_p.V388A	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor	670	Extracellular (Potential).|Ligand-binding.				cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		TTTCTTCATGACAAATCTGTC	0.403			T	BCL6	NHL								9	492	---	---	---	---	PASS
HTRA3	94031	broad.mit.edu	37	4	8288470	8288470	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8288470A>G	uc003gla.2	+	3	872	c.668A>G	c.(667-669)GAC>GGC	p.D223G	HTRA3_uc003gkz.2_Missense_Mutation_p.D223G	NM_053044	NP_444272	P83110	HTRA3_HUMAN	HtrA serine peptidase 3 precursor	223	Serine protease.				proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity			ovary(1)	1						AAAGACATCGACAAGAAGTCG	0.622													4	16	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48525026	48525026	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48525026G>C	uc003gyh.1	-	54	8018	c.7413C>G	c.(7411-7413)TGC>TGG	p.C2471W	FRYL_uc003gyf.1_5'Flank|FRYL_uc003gyg.1_Missense_Mutation_p.C1167W|FRYL_uc003gyi.1_Missense_Mutation_p.C1359W|FRYL_uc003gyj.1_Missense_Mutation_p.C766W	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	2471					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						TGCTACTAGAGCACTGGTACT	0.532													35	127	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55973949	55973949	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55973949A>C	uc003has.2	-	10	1669	c.1367T>G	c.(1366-1368)ATC>AGC	p.I456S	KDR_uc003hat.1_Missense_Mutation_p.I456S|KDR_uc011bzx.1_Missense_Mutation_p.I456S	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	456	Ig-like C2-type 5.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	ATACCAGTGGATGTGATGCGG	0.512			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			12	174	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55984862	55984862	+	Silent	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55984862T>A	uc003has.2	-	3	569	c.267A>T	c.(265-267)ACA>ACT	p.T89T	KDR_uc003hat.1_Silent_p.T89T|KDR_uc011bzx.1_Silent_p.T89T	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	89	Ig-like C2-type 1.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	CTTTTGGAATTGTGAGTGTCT	0.493			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			5	176	---	---	---	---	PASS
REST	5978	broad.mit.edu	37	4	57797456	57797456	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57797456C>T	uc003hch.2	+	4	2779	c.2432C>T	c.(2431-2433)TCC>TTC	p.S811F	REST_uc003hci.2_Missense_Mutation_p.S811F|REST_uc010ihf.2_Missense_Mutation_p.S485F	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	811	Pro-rich.				cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)					GAGCCAATTTCCAAAAAGCCT	0.517													11	56	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62761552	62761552	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62761552G>T	uc010ihh.2	+	8	1856	c.1683G>T	c.(1681-1683)AAG>AAT	p.K561N	LPHN3_uc003hcq.3_Missense_Mutation_p.K561N|LPHN3_uc003hcs.1_Missense_Mutation_p.K390N	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	561	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	p.K561N(1)		lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						TAACACAGAAGGTAAATCTTG	0.368													5	186	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73957762	73957762	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73957762G>T	uc003hgp.2	-	29	5700	c.5583C>A	c.(5581-5583)TCC>TCA	p.S1861S	ANKRD17_uc003hgo.2_Silent_p.S1748S|ANKRD17_uc003hgq.2_Silent_p.S1610S|ANKRD17_uc003hgr.2_Silent_p.S1860S	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	1861					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTTGTGAGTGGATGCAGAAG	0.428													5	234	---	---	---	---	PASS
HERC5	51191	broad.mit.edu	37	4	89383309	89383309	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89383309C>G	uc003hrt.2	+	4	643	c.490C>G	c.(490-492)CAG>GAG	p.Q164E		NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5	164	RCC1 2.				innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		TGCCTGGGGACAGAACCTGCA	0.463													7	187	---	---	---	---	PASS
RAP1GDS1	5910	broad.mit.edu	37	4	99355174	99355174	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99355174G>A	uc003htx.3	+	13	1718	c.1528G>A	c.(1528-1530)GCT>ACT	p.A510T	RAP1GDS1_uc003htw.3_Missense_Mutation_p.A511T|RAP1GDS1_uc003htv.3_Missense_Mutation_p.A510T|RAP1GDS1_uc003htz.3_Missense_Mutation_p.A461T|RAP1GDS1_uc003hty.3_Missense_Mutation_p.A462T|RAP1GDS1_uc003hua.3_Missense_Mutation_p.A419T	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform	510	ARM 5.						binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		GCAGAATGAAGCTCTTGTTGC	0.348			T	NUP98	T-ALL								59	226	---	---	---	---	PASS
RAP1GDS1	5910	broad.mit.edu	37	4	99355175	99355175	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99355175C>G	uc003htx.3	+	13	1719	c.1529C>G	c.(1528-1530)GCT>GGT	p.A510G	RAP1GDS1_uc003htw.3_Missense_Mutation_p.A511G|RAP1GDS1_uc003htv.3_Missense_Mutation_p.A510G|RAP1GDS1_uc003htz.3_Missense_Mutation_p.A461G|RAP1GDS1_uc003hty.3_Missense_Mutation_p.A462G|RAP1GDS1_uc003hua.3_Missense_Mutation_p.A419G	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform	510	ARM 5.						binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		CAGAATGAAGCTCTTGTTGCT	0.353			T	NUP98	T-ALL								58	226	---	---	---	---	PASS
PRDM5	11107	broad.mit.edu	37	4	121737604	121737604	+	Intron	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121737604T>A	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron|PRDM5_uc010inf.2_Missense_Mutation_p.E259V	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2						CAACGACTCCTCACCAGTGTG	0.537													8	44	---	---	---	---	PASS
TTC29	83894	broad.mit.edu	37	4	147860970	147860970	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147860970G>T	uc003ikw.3	-	3	305	c.78C>A	c.(76-78)TCC>TCA	p.S26S	TTC29_uc010ipc.2_RNA|TTC29_uc003ikx.3_Silent_p.S52S|TTC29_uc010ipd.1_Silent_p.S26S	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	26							binding				0	all_hematologic(180;0.151)					GAATTTTTCTGGAGGAGCAAG	0.423													5	315	---	---	---	---	PASS
FGG	2266	broad.mit.edu	37	4	155533576	155533576	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155533576G>T	uc003ioj.2	-	2	231	c.90C>A	c.(88-90)ACC>ACA	p.T30T	FGG_uc003iog.2_Silent_p.T30T|FGG_uc003ioh.2_Silent_p.T30T|FGG_uc010ipx.2_5'UTR|FGG_uc010ipy.2_5'UTR|FGG_uc003ioi.2_5'Flank|FGG_uc003iok.2_Silent_p.T30T	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B	30					platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	AGTTGTCTCTGGTAGCAACAT	0.338													5	377	---	---	---	---	PASS
FNIP2	57600	broad.mit.edu	37	4	159753253	159753253	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159753253T>C	uc003iqe.3	+	5	700	c.517T>C	c.(517-519)TCT>CCT	p.S173P	FNIP2_uc003iqd.2_Missense_Mutation_p.S173P	NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	173					DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TAAAGTCTTCTCTGCTAGAAT	0.393													7	539	---	---	---	---	PASS
DDX4	54514	broad.mit.edu	37	5	55059868	55059868	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55059868G>T	uc003jqg.3	+	6	384	c.310G>T	c.(310-312)GGT>TGT	p.G104C	DDX4_uc010ivz.2_Missense_Mutation_p.G104C|DDX4_uc003jqh.3_Missense_Mutation_p.G104C|DDX4_uc003jqj.2_5'Flank	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform	104	Gly-rich.				multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GTTTGAAGATGGTGATAGCTC	0.313													9	836	---	---	---	---	PASS
RAD17	5884	broad.mit.edu	37	5	68689235	68689235	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68689235C>A	uc003jwo.2	+	12	1425	c.1363C>A	c.(1363-1365)CAA>AAA	p.Q455K	RAD17_uc003jwg.2_Missense_Mutation_p.Q444K|RAD17_uc003jwh.2_Missense_Mutation_p.Q444K|RAD17_uc003jwi.2_Missense_Mutation_p.Q444K|RAD17_uc003jwj.2_Missense_Mutation_p.Q444K|RAD17_uc003jwk.2_Missense_Mutation_p.Q444K|RAD17_uc003jwl.2_Missense_Mutation_p.Q444K|RAD17_uc003jwm.2_Missense_Mutation_p.Q279K|RAD17_uc003jwn.2_Missense_Mutation_p.Q358K|RAD17_uc003jwp.2_Missense_Mutation_p.Q15K	NM_133339	NP_579917	O75943	RAD17_HUMAN	RAD17 homolog isoform 2	455	Interaction with MCM7.				cell cycle|DNA damage checkpoint|DNA repair|DNA replication|DNA replication checkpoint|mitotic cell cycle checkpoint|negative regulation of DNA replication|regulation of phosphorylation	nucleoplasm	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		ATATCTTCACCAAAACTACAT	0.338								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					6	605	---	---	---	---	PASS
UTP15	84135	broad.mit.edu	37	5	72864335	72864335	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72864335G>A	uc003kcw.1	+	4	497	c.274G>A	c.(274-276)GGT>AGT	p.G92S	UTP15_uc011cso.1_Missense_Mutation_p.G73S|UTP15_uc011csp.1_5'UTR|UTP15_uc010ize.1_Missense_Mutation_p.G92S|ANKRA2_uc003kcu.1_5'Flank|ANKRA2_uc003kcv.2_5'Flank	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	92	WD 2.				rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		TCGACAAGATGGTAGATTGCT	0.423													64	375	---	---	---	---	PASS
DHFR	1719	broad.mit.edu	37	5	79933760	79933760	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79933760G>T	uc003kgy.1	-	4	803	c.311C>A	c.(310-312)CCA>CAA	p.P104Q	DHFR_uc011ctl.1_Missense_Mutation_p.P184Q|DHFR_uc011ctm.1_Missense_Mutation_p.P52Q|DHFR_uc010jap.1_Intron|DHFR_uc003kgx.1_Missense_Mutation_p.P253Q	NM_000791	NP_000782	P00374	DYR_HUMAN	dihydrofolate reductase	104	DHFR.				folic acid metabolic process|glycine biosynthetic process|nucleotide biosynthetic process|one-carbon metabolic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|response to methotrexate|tetrahydrofolate metabolic process	cytosol	dihydrofolate reductase activity|drug binding|folate reductase activity|NADP binding				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.69e-46)|Epithelial(54;7.49e-41)|all cancers(79;1.54e-35)	Dapsone(DB00250)|Dimethyl sulfoxide(DB01093)|Lamotrigine(DB00555)|Methotrexate(DB00563)|NADH(DB00157)|Pemetrexed(DB00642)|Proguanil(DB01131)|Pyrimethamine(DB00205)|Trimethoprim(DB00440)|Trimetrexate(DB01157)	TGCTAATTCTGGTTGTTCAGT	0.348													6	671	---	---	---	---	PASS
ANKRD32	84250	broad.mit.edu	37	5	93985202	93985202	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93985202G>T	uc003kkr.3	+	6	718	c.638G>T	c.(637-639)TGG>TTG	p.W213L	ANKRD32_uc011cul.1_RNA	NM_032290	NP_115666	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	213										ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		AATTCTGTTTGGACTGAACAT	0.333													6	544	---	---	---	---	PASS
SLC25A46	91137	broad.mit.edu	37	5	110082047	110082047	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110082047G>T	uc003koz.2	+	4	529	c.462G>T	c.(460-462)CAG>CAT	p.Q154H	SLC25A46_uc011cvi.1_Missense_Mutation_p.Q63H	NM_138773	NP_620128	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	154	Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		ACAAAACTCAGGTGAGAATTT	0.289													7	680	---	---	---	---	PASS
CHSY3	337876	broad.mit.edu	37	5	129520692	129520692	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129520692G>C	uc003kvd.2	+	3	1857	c.1857G>C	c.(1855-1857)AAG>AAC	p.K619N		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	619	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		ACAATGAAAAGAAAGTACACA	0.348													23	147	---	---	---	---	PASS
FNIP1	96459	broad.mit.edu	37	5	131042127	131042127	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131042127C>G	uc003kvs.1	-	9	1033	c.891G>C	c.(889-891)TTG>TTC	p.L297F	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.L269F|FNIP1_uc010jdm.1_Missense_Mutation_p.L252F|FNIP1_uc003kvu.2_Missense_Mutation_p.L297F	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	297					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		CCCCATTTTCCAAACTTGTTG	0.433													40	265	---	---	---	---	PASS
DDX46	9879	broad.mit.edu	37	5	134120175	134120175	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134120175C>A	uc003kzw.2	+	10	1454	c.1286C>A	c.(1285-1287)CCC>CAC	p.P429H	DDX46_uc003kzv.1_RNA	NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	429	Helicase ATP-binding.				mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTTCTGTTGCCCATGTTTAGA	0.408													6	488	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140593646	140593646	+	5'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140593646T>C	uc003lja.1	+	1						NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACTGGGGACTTTACAGTCCCA	0.517													5	182	---	---	---	---	PASS
PCDH12	51294	broad.mit.edu	37	5	141337480	141337480	+	5'UTR	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141337480C>T	uc003llx.2	-	1						NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor						neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACAAGTCCTCCAGTGTTTCC	0.517													6	21	---	---	---	---	PASS
CSF1R	1436	broad.mit.edu	37	5	149449864	149449864	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149449864G>T	uc003lrl.2	-	8	1395	c.1200C>A	c.(1198-1200)TAC>TAA	p.Y400*	CSF1R_uc011dcd.1_Nonsense_Mutation_p.Y252*|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Nonsense_Mutation_p.Y400*	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor	400	Extracellular (Potential).				cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CCTCTGGGGGGTCTGAGGAAG	0.592													11	67	---	---	---	---	PASS
CPEB4	80315	broad.mit.edu	37	5	173380335	173380335	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173380335C>A	uc003mcs.3	+						CPEB4_uc010jju.1_3'UTR|CPEB4_uc010jjv.2_Intron|CPEB4_uc011dfg.1_Intron|CPEB4_uc003mct.3_Intron|CPEB4_uc003mcu.3_Intron	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GTGTGATTACCAATATTAGAA	0.353													4	110	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176636690	176636690	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176636690G>A	uc003mfr.3	+	5	1428	c.1290G>A	c.(1288-1290)CAG>CAA	p.Q430Q	NSD1_uc003mft.3_Silent_p.Q161Q|NSD1_uc003mfs.1_Silent_p.Q327Q|NSD1_uc011dfx.1_Silent_p.Q78Q	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	430					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TTGCAGAACAGTATGATGTTC	0.373			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			54	249	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38866076	38866076	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38866076C>A	uc003ooe.1	+	59	8932	c.8332C>A	c.(8332-8334)CAG>AAG	p.Q2778K		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CCAGTTTTACCAGAGACAGTT	0.328													6	378	---	---	---	---	PASS
VNN2	8875	broad.mit.edu	37	6	133065495	133065495	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133065495G>T	uc003qdt.2	-	7	1518	c.1507C>A	c.(1507-1509)CTG>ATG	p.L503M	VNN2_uc003qds.2_Missense_Mutation_p.L212M|VNN2_uc010kgb.2_Missense_Mutation_p.L282M|VNN2_uc003qdv.2_Missense_Mutation_p.L450M	NM_004665	NP_004656	O95498	VNN2_HUMAN	vanin 2 isoform 1 precursor	503					cellular component movement|pantothenate metabolic process	anchored to membrane|plasma membrane	pantetheine hydrolase activity				0				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		AATATTAGCAGGTAAGTTATT	0.393													5	265	---	---	---	---	PASS
SOD2	6648	broad.mit.edu	37	6	160105889	160105889	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160105889T>C	uc003qsg.2	-	4	674	c.520A>G	c.(520-522)ACA>GCA	p.T174A	SOD2_uc003qsh.2_Missense_Mutation_p.T135A|SOD2_uc003qsi.1_Missense_Mutation_p.T174A|SOD2_uc011efu.1_Intron|SOD2_uc011efv.1_Missense_Mutation_p.T135A	NM_001024465	NP_001019636	P04179	SODM_HUMAN	manganese superoxide dismutase isoform A	174					age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		ATCTAACCTGTTGTTCCTTGC	0.398													6	237	---	---	---	---	PASS
THSD7A	221981	broad.mit.edu	37	7	11485849	11485849	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11485849T>G	uc003ssf.3	-	13	3155	c.2903A>C	c.(2902-2904)AAC>ACC	p.N968T		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	968	TSP type-1 10.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTCTGACCAGTTCCCCACAGG	0.393										HNSCC(18;0.044)			10	398	---	---	---	---	PASS
DGKB	1607	broad.mit.edu	37	7	14797292	14797292	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14797292A>G	uc003ssz.2	-	2	322	c.135T>C	c.(133-135)TAT>TAC	p.Y45Y	DGKB_uc011jxt.1_Silent_p.Y45Y|DGKB_uc003sta.2_Silent_p.Y45Y|DGKB_uc011jxu.1_Silent_p.Y45Y|DGKB_uc011jxv.1_Silent_p.Y45Y	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1	45					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	CTTCAGGATTATACTTTGCAA	0.274													7	510	---	---	---	---	PASS
AVL9	23080	broad.mit.edu	37	7	32620436	32620436	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32620436G>T	uc003tcv.1	+	15	1911	c.1765G>T	c.(1765-1767)GGC>TGC	p.G589C	AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Silent_p.V372V	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	589						integral to membrane					0						TAGTGAACGTGGCAAAAAAAT	0.313													6	532	---	---	---	---	PASS
AVL9	23080	broad.mit.edu	37	7	32695599	32695599	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32695599C>A	uc011kai.1	+						uc003tcw.2_RNA	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						GATTACCTACCTCTCCATGAC	0.333													57	202	---	---	---	---	PASS
AVL9	23080	broad.mit.edu	37	7	32956881	32956881	+	Intron	SNP	A	G	G	rs116875310	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32956881A>G	uc011kai.1	+						RP9P_uc003tdc.2_RNA|RP9P_uc003tdd.2_RNA|RP9P_uc011kaj.1_RNA	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						CTATCCTGCTACTTTCTCTGA	0.507													4	146	---	---	---	---	PASS
MRPL32	64983	broad.mit.edu	37	7	42974658	42974658	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42974658G>A	uc003tia.2	+	2	282	c.235G>A	c.(235-237)GCA>ACA	p.A79T	C7orf25_uc010kxr.2_5'Flank|PSMA2_uc003thy.2_5'Flank|PSMA2_uc010kxt.2_5'Flank|PSMA2_uc003thz.1_5'Flank|MRPL32_uc003tib.2_RNA|MRPL32_uc003tic.2_Missense_Mutation_p.A26T	NM_031903	NP_114109	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32 precursor	79					translation	large ribosomal subunit|mitochondrial ribosome	structural constituent of ribosome				0						CTTTTGGATGGCAGCTCCCAA	0.428													99	223	---	---	---	---	PASS
MRPS17	51373	broad.mit.edu	37	7	56022934	56022934	+	3'UTR	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56022934T>A	uc003trd.2	+	3					MRPS17_uc003trb.2_3'UTR	NM_015969	NP_057053	Q9Y2R5	RT17_HUMAN	mitochondrial ribosomal protein S17 precursor						translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAAAAAGAAATTTTTCTAAGT	0.348													11	40	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	65226641	65226641	+	Intron	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65226641G>T	uc003tud.1	-						CCT6P1_uc003tug.2_RNA|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		AGGTTCTTGCGCAGAATTCTG	0.299													4	156	---	---	---	---	PASS
SBDSP1	155370	broad.mit.edu	37	7	72302284	72302284	+	RNA	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72302284C>A	uc003twf.2	+	3		c.636C>A			SBDSP1_uc011kel.1_RNA|SBDSP1_uc003twg.2_RNA|SBDSP1_uc003twh.2_RNA|SBDSP1_uc003twe.2_RNA	NR_001588				Homo sapiens Shwachman-Bodian-Diamond syndrome pseudogene, mRNA (cDNA clone IMAGE:4329436).												0						TGTGTGACTCCTGAAACAAAG	0.413													6	663	---	---	---	---	PASS
PEX1	5189	broad.mit.edu	37	7	92147044	92147044	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92147044T>C	uc003uly.2	-	5	881	c.785A>G	c.(784-786)GAG>GGG	p.E262G	PEX1_uc011khr.1_Missense_Mutation_p.E54G|PEX1_uc010ley.2_Missense_Mutation_p.E262G|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	262					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CCAAGATGTCTCTTGTTTCTT	0.358													7	459	---	---	---	---	PASS
PRKAR2B	5577	broad.mit.edu	37	7	106799894	106799894	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106799894C>G	uc003vdx.2	+	11	1299	c.1124C>G	c.(1123-1125)GCA>GGA	p.A375G		NM_002736	NP_002727	P31323	KAP3_HUMAN	cAMP-dependent protein kinase, regulatory	375	cAMP 2.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1						CTTTTCTCAGCAATGGATGTG	0.353													67	148	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107350559	107350559	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107350559C>T	uc003vep.2	+	19	2374	c.2150C>T	c.(2149-2151)ACA>ATA	p.T717I	SLC26A4_uc011kmb.1_Missense_Mutation_p.T304I|SLC26A4_uc011kmc.1_Missense_Mutation_p.T278I|SLC26A4_uc011kmd.1_Missense_Mutation_p.T286I	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	717	STAS.|Cytoplasmic (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						AGAAAGGACACATTCTTTTTG	0.373									Pendred_syndrome				6	531	---	---	---	---	PASS
DLD	1738	broad.mit.edu	37	7	107546742	107546742	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107546742G>T	uc003vet.2	+	8	723	c.613G>T	c.(613-615)GGT>TGT	p.G205C	DLD_uc010ljm.1_RNA|DLD_uc011kmg.1_Missense_Mutation_p.G157C|DLD_uc011kmh.1_Missense_Mutation_p.G182C|DLD_uc011kmi.1_Missense_Mutation_p.G106C	NM_000108	NP_000099	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase precursor	205					branched chain family amino acid catabolic process|cell redox homeostasis|lysine catabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	dihydrolipoyl dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)	GTCATCTACAGGTGCTTTATC	0.274													8	829	---	---	---	---	PASS
DLD	1738	broad.mit.edu	37	7	107555972	107555972	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107555972G>T	uc003vet.2	+	9	816	c.706G>T	c.(706-708)GGT>TGT	p.G236C	DLD_uc010ljm.1_RNA|DLD_uc011kmg.1_Missense_Mutation_p.G188C|DLD_uc011kmh.1_Missense_Mutation_p.G213C|DLD_uc011kmi.1_Missense_Mutation_p.G137C	NM_000108	NP_000099	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase precursor	236					branched chain family amino acid catabolic process|cell redox homeostasis|lysine catabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	dihydrolipoyl dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)	GCAAAGACTTGGTGCAGATGT	0.323													6	678	---	---	---	---	PASS
DLD	1738	broad.mit.edu	37	7	107557386	107557386	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107557386C>A	uc003vet.2	+	10	1133	c.1023C>A	c.(1021-1023)ACC>ACA	p.T341T	DLD_uc011kmg.1_Silent_p.T293T|DLD_uc011kmh.1_Silent_p.T318T|DLD_uc011kmi.1_Silent_p.T242T	NM_000108	NP_000099	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase precursor	341					branched chain family amino acid catabolic process|cell redox homeostasis|lysine catabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	dihydrolipoyl dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)	CAGTCAATACCAGATTTCAAA	0.333													7	480	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117267822	117267822	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117267822A>T	uc003vjd.2	+	22	3847	c.3715A>T	c.(3715-3717)AGG>TGG	p.R1239W	CFTR_uc011knq.1_Missense_Mutation_p.R645W	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	1239	Cytoplasmic (Potential).|ABC transporter 2.				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	TCCTGGCCAGAGGGTGAGATT	0.413									Cystic_Fibrosis				5	166	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121652506	121652506	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121652506G>T	uc003vjy.2	+	12	3801	c.3406G>T	c.(3406-3408)GGT>TGT	p.G1136C	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1136	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						TCAAGCATCTGGTGACACTTC	0.418													6	427	---	---	---	---	PASS
LRRC4	64101	broad.mit.edu	37	7	127669258	127669258	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127669258G>A	uc003vmk.2	-	2	1573	c.1436C>T	c.(1435-1437)ACG>ATG	p.T479M	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	479	Thr-rich.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)		ACCAGTGGACGTGGTAGGAAC	0.552													12	70	---	---	---	---	PASS
TNPO3	23534	broad.mit.edu	37	7	128607436	128607436	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128607436C>A	uc003vol.1	-	21	2983	c.2609G>T	c.(2608-2610)CGA>CTA	p.R870L	TNPO3_uc010llx.1_Missense_Mutation_p.R281L|TNPO3_uc003vom.1_Missense_Mutation_p.R804L|TNPO3_uc010lly.1_Missense_Mutation_p.R904L|TNPO3_uc010llz.1_Missense_Mutation_p.R806L	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3	870					splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5						TTCTAACCATCGACAAAAAGT	0.408													39	293	---	---	---	---	PASS
TRIM24	8805	broad.mit.edu	37	7	138265308	138265308	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138265308G>T	uc003vuc.2	+	16	2802	c.2587G>T	c.(2587-2589)GGA>TGA	p.G863*	TRIM24_uc003vub.2_Nonsense_Mutation_p.G829*	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha	863	PHD-type.				cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8						CCCTAACAGTGGAGAGTGGAT	0.398													6	470	---	---	---	---	PASS
CRYGN	155051	broad.mit.edu	37	7	151127152	151127152	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151127152G>T	uc003wke.2	-	4	627	c.531C>A	c.(529-531)TTC>TTA	p.F177L	CRYGN_uc003wkf.2_3'UTR|CRYGN_uc003wkg.2_RNA	NM_144727	NP_653328	Q8WXF5	CRGN_HUMAN	gammaN-crystallin	177											0			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTGCAGTCAGGAAAGGTGGCT	0.512													10	564	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3253877	3253877	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3253877G>A	uc011kwk.1	-	17	2825	c.2435C>T	c.(2434-2436)ACC>ATC	p.T812I	CSMD1_uc011kwj.1_Missense_Mutation_p.T204I|CSMD1_uc003wqe.2_5'UTR	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	812	Extracellular (Potential).|CUB 5.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GACCTCCAAGGTGTCATAATT	0.522													33	44	---	---	---	---	PASS
C8orf41	80185	broad.mit.edu	37	8	33356790	33356790	+	Silent	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33356790G>C	uc003xjl.3	-	7	1953	c.1428C>G	c.(1426-1428)CTC>CTG	p.L476L	C8orf41_uc010lvu.1_Intron|MAK16_uc003xjj.2_3'UTR|C8orf41_uc003xjk.3_Silent_p.L445L|C8orf41_uc010lvv.2_Silent_p.L311L|C8orf41_uc003xjm.3_Silent_p.L476L	NM_025115	NP_079391	Q6NXR4	CH041_HUMAN	hypothetical protein LOC80185	476							binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)		TTTTGGCCAGGAGACCCTGAA	0.388													8	184	---	---	---	---	PASS
GGH	8836	broad.mit.edu	37	8	63948282	63948282	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63948282T>C	uc003xuw.2	-	2	440	c.157A>G	c.(157-159)AGA>GGA	p.R53G		NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor	53	Gamma-glutamyl hydrolase.				glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	ATATAGTATCTTCCATAGTTT	0.323													6	333	---	---	---	---	PASS
PRDM14	63978	broad.mit.edu	37	8	70978469	70978469	+	Splice_Site	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70978469C>A	uc003xym.2	-	5	1385	c.1183_splice	c.e5+1	p.E395_splice		NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TGTGCACTCACCTTCAGAGGG	0.552													13	71	---	---	---	---	PASS
FABP4	2167	broad.mit.edu	37	8	82395438	82395438	+	5'UTR	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82395438A>G	uc003ycd.2	-	1						NM_001442	NP_001433	P15090	FABP4_HUMAN	fatty acid binding protein 4, adipocyte						triglyceride catabolic process	cytoplasm|nucleus|soluble fraction	fatty acid binding|protein binding|transporter activity			breast(1)	1			Epithelial(68;0.213)			TCAAGGTGAGAAGGAAGCTGC	0.393													6	385	---	---	---	---	PASS
RALYL	138046	broad.mit.edu	37	8	85799840	85799840	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85799840A>G	uc003ycq.3	+	9	1103	c.687A>G	c.(685-687)GAA>GAG	p.E229E	RALYL_uc003ycr.3_Silent_p.E229E|RALYL_uc003ycs.3_Silent_p.E229E|RALYL_uc010lzy.2_Silent_p.E218E|RALYL_uc003yct.3_Silent_p.E242E|RALYL_uc003ycu.3_Silent_p.E156E|RALYL_uc003ycv.3_Intron	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2	229	Potential.						identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						CCCCCCCAGAAGCTCAGAAGA	0.468													5	155	---	---	---	---	PASS
ATP6V0D2	245972	broad.mit.edu	37	8	87155145	87155145	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87155145G>T	uc003ydp.1	+	5	670	c.601G>T	c.(601-603)GGT>TGT	p.G201C		NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0	201					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0						TAAGAATCATGGTGATGTCAC	0.289													6	549	---	---	---	---	PASS
TAF2	6873	broad.mit.edu	37	8	120814248	120814248	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120814248A>G	uc003you.2	-	6	848	c.578T>C	c.(577-579)GTT>GCT	p.V193A		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	193					G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GTATGAATCAACACAAGGGAA	0.343													25	216	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139824101	139824101	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139824101C>T	uc003yvd.2	-	9	1837	c.1390G>A	c.(1390-1392)GGC>AGC	p.G464S		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	464	Pro-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGTTCACTGCCTGGGGTGGGA	0.602										HNSCC(7;0.00092)			12	64	---	---	---	---	PASS
PUF60	22827	broad.mit.edu	37	8	144898884	144898884	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144898884C>T	uc003yzs.2	-	12	1550	c.1486G>A	c.(1486-1488)GTC>ATC	p.V496I	SCRIB_uc003yzo.1_5'Flank|SCRIB_uc003yzp.1_5'Flank|PUF60_uc003yzr.2_Missense_Mutation_p.V436I|PUF60_uc003yzt.2_Missense_Mutation_p.V479I|PUF60_uc003yzq.2_Missense_Mutation_p.V453I	NM_078480	NP_510965	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa isoform a	496	RRM 3; atypical.|Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptosis|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nucleus|ribonucleoprotein complex	DNA binding|nucleotide binding|protein binding|RNA binding				0	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TAGATGATGACGCGGTTCACG	0.517													7	243	---	---	---	---	PASS
IL33	90865	broad.mit.edu	37	9	6252967	6252967	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6252967G>C	uc003zjt.2	+	5	502	c.445G>C	c.(445-447)GAC>CAC	p.D149H	IL33_uc011lmg.1_Intron|IL33_uc011lmh.1_Intron|IL33_uc003zju.1_Missense_Mutation_p.D149H	NM_033439	NP_254274	O95760	IL33_HUMAN	interleukin 33 precursor	149					positive regulation of chemokine secretion|positive regulation of inflammatory response|positive regulation of macrophage activation|positive regulation of transcription from RNA polymerase II promoter	extracellular space	cytokine activity				0		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		ATATGTTGAAGACTTGAAAAA	0.259													51	227	---	---	---	---	PASS
C9orf93	203238	broad.mit.edu	37	9	15724841	15724841	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15724841G>A	uc003zmd.2	+	14	1874	c.1559G>A	c.(1558-1560)CGA>CAA	p.R520Q	C9orf93_uc010mih.1_Missense_Mutation_p.R528Q|C9orf93_uc003zme.2_Missense_Mutation_p.R435Q|C9orf93_uc011lmu.1_Missense_Mutation_p.R528Q	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238	520	Potential.										0				GBM - Glioblastoma multiforme(50;4.84e-07)		TGTGCAGACCGAGAGGCTTTA	0.393													31	193	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106864804	106864804	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106864804C>A	uc004bbv.2	+	9	1258	c.970C>A	c.(970-972)CTG>ATG	p.L324M	SMC2_uc004bbu.1_Missense_Mutation_p.L324M|SMC2_uc004bbw.2_Missense_Mutation_p.L324M|SMC2_uc011lvl.1_Missense_Mutation_p.L324M|SMC2_uc010mtg.1_Missense_Mutation_p.L179M|SMC2_uc010mth.1_Missense_Mutation_p.L274M|SMC2_uc004bbx.2_Missense_Mutation_p.L324M	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	324	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						GAAGAAAAATCTGGCATGTGA	0.403													65	256	---	---	---	---	PASS
CDK5RAP2	55755	broad.mit.edu	37	9	123205921	123205921	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123205921T>A	uc004bkf.2	-	23	3306	c.3125A>T	c.(3124-3126)GAT>GTT	p.D1042V	CDK5RAP2_uc010mvi.2_Intron|CDK5RAP2_uc004bke.2_Missense_Mutation_p.D327V|CDK5RAP2_uc004bkg.2_Missense_Mutation_p.D1042V|CDK5RAP2_uc011lxw.1_Missense_Mutation_p.D307V|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_Missense_Mutation_p.D307V|CDK5RAP2_uc011lya.1_Missense_Mutation_p.D307V|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.D812V|CDK5RAP2_uc004bki.2_Missense_Mutation_p.D809V	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1042	Interaction with MAPRE1.				brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4						TCTTTGCTGATCACTGTCCAT	0.378													155	202	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	390776	390776	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:390776G>T	uc001ifp.2	-	28	3516	c.3426C>A	c.(3424-3426)TCC>TCA	p.S1142S	DIP2C_uc009xhi.1_Silent_p.S528S	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1142						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TCCCAGTTGTGGACACGCTGA	0.587													10	53	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5784120	5784120	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5784120G>T	uc001iij.2	+	14	3013	c.2388G>T	c.(2386-2388)TGG>TGT	p.W796C	C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	796										ovary(1)|central_nervous_system(1)	2						TTCATATGTGGGTAGCTCTGT	0.373													7	438	---	---	---	---	PASS
ITGA8	8516	broad.mit.edu	37	10	15561362	15561362	+	Missense_Mutation	SNP	G	A	A	rs141983422		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15561362G>A	uc001ioc.1	-	29	3032	c.3032C>T	c.(3031-3033)CCA>CTA	p.P1011L	ITGA8_uc010qcb.1_Missense_Mutation_p.P996L	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	1011	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						TACCCATAATGGGATTGAGAA	0.348													9	290	---	---	---	---	PASS
CSGALNACT2	55454	broad.mit.edu	37	10	43659419	43659419	+	Missense_Mutation	SNP	G	T	T	rs80035763	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43659419G>T	uc001jan.2	+	5	1421	c.1086G>T	c.(1084-1086)TTG>TTT	p.L362F		NM_018590	NP_061060	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate	362	Lumenal (Potential).				chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1						GAGAGGTCTTGATGTTTTTCT	0.433													10	595	---	---	---	---	PASS
HELLS	3070	broad.mit.edu	37	10	96334424	96334424	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96334424T>C	uc001kjt.2	+	9	924	c.819T>C	c.(817-819)CCT>CCC	p.P273P	HELLS_uc001kjs.2_Silent_p.P257P|HELLS_uc009xul.2_Silent_p.P273P|HELLS_uc009xum.2_Silent_p.P273P|HELLS_uc009xun.2_Silent_p.P149P|HELLS_uc009xuo.2_Silent_p.P273P|HELLS_uc001kju.2_5'UTR|HELLS_uc009xup.2_RNA|HELLS_uc009xuq.2_Silent_p.P135P|HELLS_uc009xur.2_RNA	NM_018063	NP_060533	Q9NRZ9	HELLS_HUMAN	helicase, lymphoid-specific	273	Helicase ATP-binding.				cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		TACCAGGACCTTTTCTTGTCT	0.383													7	470	---	---	---	---	PASS
PI4K2A	55361	broad.mit.edu	37	10	99344532	99344532	+	Silent	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99344532C>T	uc010qoy.1	+	1	431	c.72C>T	c.(70-72)GTC>GTT	p.V24V	DHDPSL_uc001knx.2_Silent_p.V24V|DHDPSL_uc001kny.2_Silent_p.V24V|DHDPSL_uc001knz.2_Silent_p.V24V	NM_018425	NP_060895	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	Error:Variant_position_missing_in_Q9BTU6_after_alignment					phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		ATGTGGGGGTCTGGGCCTCAG	0.597													12	37	---	---	---	---	PASS
ATRNL1	26033	broad.mit.edu	37	10	116881513	116881513	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116881513G>C	uc001lcg.2	+	3	814	c.428G>C	c.(427-429)AGC>ACC	p.S143T	ATRNL1_uc001lce.2_RNA|ATRNL1_uc001lcf.2_Missense_Mutation_p.S143T|ATRNL1_uc009xyq.2_Missense_Mutation_p.S143T	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	143	CUB.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ACAGAATGTAGCTGGGATCAT	0.289													80	285	---	---	---	---	PASS
CUZD1	50624	broad.mit.edu	37	10	124591749	124591749	+	3'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124591749T>C	uc001lgq.2	-	9					CUZD1_uc001lgp.2_3'UTR|CUZD1_uc009yad.2_3'UTR|CUZD1_uc009yaf.2_3'UTR|CUZD1_uc001lgr.2_3'UTR|CUZD1_uc010qty.1_3'UTR|CUZD1_uc009yae.2_3'UTR|CUZD1_uc001lgs.2_3'UTR|CUZD1_uc010qtz.1_3'UTR	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor						cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		GCATTTCCTTTGGCATCCTGG	0.443													68	265	---	---	---	---	PASS
MUC6	4588	broad.mit.edu	37	11	1021245	1021245	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1021245C>T	uc001lsw.2	-	27	3610	c.3559G>A	c.(3559-3561)GAC>AAC	p.D1187N		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1187					maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		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)		TCCTCGTGGTCGAAGTACTCA	0.642													38	15	---	---	---	---	PASS
OR51T1	401665	broad.mit.edu	37	11	4903717	4903717	+	Silent	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4903717C>T	uc010qyp.1	+	1	669	c.669C>T	c.(667-669)ATC>ATT	p.I223I		NM_001004759	NP_001004759	Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T,	196	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		AACCTTGGATCAGCAGTTTTT	0.443													46	235	---	---	---	---	PASS
OR52E8	390079	broad.mit.edu	37	11	5878157	5878157	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5878157G>T	uc010qzr.1	-	1	776	c.776C>A	c.(775-777)CCA>CAA	p.P259Q	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	259	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAAATGCTGGTGTAAAAAA	0.433													5	301	---	---	---	---	PASS
TMEM41B	440026	broad.mit.edu	37	11	9309300	9309300	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9309300T>C	uc001mhm.2	-	5	824	c.516A>G	c.(514-516)AGA>AGG	p.R172R	TMEM41B_uc001mhn.1_Silent_p.R172R	NM_015012	NP_055827	Q5BJD5	TM41B_HUMAN	transmembrane protein 41B isoform 1	172						integral to membrane					0				all cancers(16;9.96e-08)|Epithelial(150;4.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0972)		ATACAACTGGTCTCCCAACTA	0.343													9	368	---	---	---	---	PASS
FAR1	84188	broad.mit.edu	37	11	13734528	13734528	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13734528G>T	uc001mld.2	+	8	1058	c.903G>T	c.(901-903)ATG>ATT	p.M301I	FAR1_uc009ygp.2_Missense_Mutation_p.M301I	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	301					ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						GAAACATCATGGTGTATAATT	0.343													7	629	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20676549	20676549	+	3'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20676549T>C	uc001mqd.2	+	16					SLC6A5_uc009yic.2_3'UTR	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter						synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	ATGAGAGTGATTATGTAGAAA	0.453													5	26	---	---	---	---	PASS
SLC17A6	57084	broad.mit.edu	37	11	22364813	22364813	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22364813C>A	uc001mqk.2	+	3	773	c.360C>A	c.(358-360)GAC>GAA	p.D120E		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	120	Vesicular (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						TCAACTGGGACCCGGAAACCG	0.517													18	75	---	---	---	---	PASS
ANO3	63982	broad.mit.edu	37	11	26677727	26677727	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26677727G>T	uc001mqt.3	+	25	2777	c.2632G>T	c.(2632-2634)GGT>TGT	p.G878C	ANO3_uc010rdr.1_Missense_Mutation_p.G862C|ANO3_uc010rds.1_Missense_Mutation_p.G717C|ANO3_uc010rdt.1_Missense_Mutation_p.G732C	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	878	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						GAGTGAGCTTGGTATGGGAAA	0.388													6	736	---	---	---	---	PASS
KIF18A	81930	broad.mit.edu	37	11	28057941	28057941	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28057941T>C	uc001msc.2	-	14	2401	c.2219A>G	c.(2218-2220)AAC>AGC	p.N740S		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	740					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						ATTATCACTGTTTATGTTTGA	0.353													7	586	---	---	---	---	PASS
CKAP5	9793	broad.mit.edu	37	11	46802036	46802036	+	Splice_Site	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46802036C>A	uc001ndi.1	-	19	2360	c.2250_splice	c.e19-1	p.G750_splice	CKAP5_uc009ylg.1_Splice_Site_p.G636_splice|CKAP5_uc001ndj.1_Splice_Site_p.G750_splice	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						GACATTCAACCTAGAAGAAAC	0.338													5	314	---	---	---	---	PASS
GLYAT	10249	broad.mit.edu	37	11	58477555	58477555	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58477555C>A	uc001nnb.2	-	6	730	c.575G>T	c.(574-576)AGG>ATG	p.R192M		NM_201648	NP_964011	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase isoform a	192					acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process	mitochondrial matrix	glycine N-acyltransferase activity|glycine N-benzoyltransferase activity				0		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TCTCTGGCTCCTCTCATTACC	0.502													17	73	---	---	---	---	PASS
MS4A6E	245802	broad.mit.edu	37	11	60102420	60102420	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60102420G>C	uc001npd.2	+	1	66	c.52G>C	c.(52-54)GTC>CTC	p.V18L		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	18	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						CCCATCAAATGTCATCAACTT	0.418													69	400	---	---	---	---	PASS
MTA2	9219	broad.mit.edu	37	11	62362921	62362921	+	Missense_Mutation	SNP	C	T	T	rs139421444		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62362921C>T	uc001ntq.1	-	14	1679	c.1298G>A	c.(1297-1299)AGT>AAT	p.S433N	MTA2_uc010rlx.1_Missense_Mutation_p.S260N	NM_004739	NP_004730	O94776	MTA2_HUMAN	metastasis-associated protein 2	433					chromatin assembly or disassembly	NuRD complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						AGGAGAGAGACTTTGAGCTTC	0.502													60	116	---	---	---	---	PASS
PICALM	8301	broad.mit.edu	37	11	85712158	85712158	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85712158C>A	uc001pbm.2	-	10	1223	c.937G>T	c.(937-939)GGT>TGT	p.G313C	PICALM_uc001pbl.2_Missense_Mutation_p.G313C|PICALM_uc001pbn.2_Missense_Mutation_p.G313C|PICALM_uc010rtl.1_Missense_Mutation_p.G262C|PICALM_uc010rtk.1_5'UTR|PICALM_uc001pbo.1_5'UTR	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	313					clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				AGAGATAGACCAGTGCTTGCC	0.428			T	MLLT10|MLL	TALL|AML|								6	523	---	---	---	---	PASS
BIRC2	329	broad.mit.edu	37	11	102233644	102233644	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102233644G>T	uc001pgy.2	+	4	2412	c.1013G>T	c.(1012-1014)CGA>CTA	p.R338L	BIRC2_uc010ruq.1_Missense_Mutation_p.R289L|BIRC2_uc010rur.1_Missense_Mutation_p.R338L	NM_001166	NP_001157	Q13490	BIRC2_HUMAN	baculoviral IAP repeat-containing protein 2	338					cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		TTCTTGATACGAATGAAAGGC	0.264													5	582	---	---	---	---	PASS
NPAT	4863	broad.mit.edu	37	11	108044559	108044559	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108044559G>A	uc001pjz.3	-	13	1254	c.1152C>T	c.(1150-1152)CCC>CCT	p.P384P	NPAT_uc001pka.2_Silent_p.P179P	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	384					positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TACAAAAAGCGGGCTGACCAG	0.388													5	262	---	---	---	---	PASS
NNMT	4837	broad.mit.edu	37	11	114183068	114183068	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114183068G>C	uc001por.1	+	5	928	c.664G>C	c.(664-666)GAG>CAG	p.E222Q	NNMT_uc001pos.1_Missense_Mutation_p.E222Q	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	222					xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	GGAGGCAGTAGAGGCTGCTGT	0.542													3	33	---	---	---	---	PASS
SLC6A12	6539	broad.mit.edu	37	12	319083	319083	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:319083T>C	uc001qhz.2	-	4	613	c.70A>G	c.(70-72)AAG>GAG	p.K24E	SLC6A12_uc001qia.2_Missense_Mutation_p.K24E|SLC6A12_uc001qib.2_Missense_Mutation_p.K24E|SLC6A12_uc009zdh.1_Missense_Mutation_p.K24E|SLC6A12_uc009zdi.1_RNA	NM_003044	NP_003035	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter	24	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			TGGTCCAACTTCTCTCCCTCC	0.622													33	62	---	---	---	---	PASS
CLEC1B	51266	broad.mit.edu	37	12	10151706	10151706	+	5'UTR	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10151706C>G	uc001qwu.2	-	1					CLEC1B_uc009zhd.2_5'UTR	NM_016509	NP_057593	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B isoform						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0						GCATGGCTTCCCGAGTACTGC	0.393													13	567	---	---	---	---	PASS
RECQL	5965	broad.mit.edu	37	12	21628646	21628646	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21628646G>T	uc001rex.2	-	10	1410	c.1062C>A	c.(1060-1062)ACC>ACA	p.T354T	RECQL_uc001rey.2_Silent_p.T354T	NM_032941	NP_116559	P46063	RECQ1_HUMAN	RecQ protein-like	354	Helicase C-terminal.				DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			ovary(1)|lung(1)	2						TATGAACTGTGGTCTTATCTT	0.353								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					7	489	---	---	---	---	PASS
ZCRB1	85437	broad.mit.edu	37	12	42711610	42711610	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42711610G>T	uc001rmz.2	-	4	413	c.204C>A	c.(202-204)ACC>ACA	p.T68T	PPHLN1_uc001rmy.2_Intron	NM_033114	NP_149105	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	68	RRM.				mRNA processing	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding			skin(1)	1	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		TTATTGCCCTGGTACAGTTTT	0.383													7	602	---	---	---	---	PASS
SLC38A4	55089	broad.mit.edu	37	12	47172347	47172347	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47172347T>C	uc001rpi.2	-	11	1329	c.930A>G	c.(928-930)GGA>GGG	p.G310G	SLC38A4_uc001rpj.2_Silent_p.G310G	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	310	Extracellular (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)					CATATTCTACTCCACTGTCAT	0.473													6	256	---	---	---	---	PASS
SCN8A	6334	broad.mit.edu	37	12	52180598	52180598	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52180598C>A	uc001ryw.2	+	22	4393	c.4215C>A	c.(4213-4215)GCC>GCA	p.A1405A	SCN8A_uc010snl.1_Silent_p.A1229A|SCN8A_uc001rza.1_RNA	NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	1405	III.				axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)	GATACCTGGCCCTTCTTCAAG	0.398													5	258	---	---	---	---	PASS
ACVR1B	91	broad.mit.edu	37	12	52380781	52380781	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52380781C>A	uc001rzn.2	+						ACVR1B_uc001rzl.2_Missense_Mutation_p.P439H|ACVR1B_uc001rzm.2_Intron|ACVR1B_uc010snn.1_Intron	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor						G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	GCTGGATCACCCAAAGCTGTT	0.473													8	812	---	---	---	---	PASS
RAP1B	5908	broad.mit.edu	37	12	69050104	69050104	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69050104G>T	uc001sub.2	+	6	506	c.343G>T	c.(343-345)GGT>TGT	p.G115C	RAP1B_uc010ste.1_Missense_Mutation_p.G49C|RAP1B_uc001suc.2_Missense_Mutation_p.G115C|RAP1B_uc010stf.1_Missense_Mutation_p.G96C|RAP1B_uc010stg.1_Missense_Mutation_p.G73C|RAP1B_uc010sth.1_Missense_Mutation_p.G73C|RAP1B_uc010sti.1_Missense_Mutation_p.G68C	NM_001089704	NP_001083173	P61224	RAP1B_HUMAN	SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;	115					blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)		GATTCTTGTTGGTAATAAGTG	0.313													7	763	---	---	---	---	PASS
NUP107	57122	broad.mit.edu	37	12	69090672	69090672	+	Silent	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69090672G>T	uc001suf.2	+	6	637	c.522G>T	c.(520-522)GTG>GTT	p.V174V	NUP107_uc001sug.2_Silent_p.V21V|NUP107_uc010stj.1_Silent_p.V145V	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	174					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TTGATCTTGTGGAAGAGTATG	0.348													7	585	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	80696423	80696423	+	IGR	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80696423G>T								PPP1R12A (367188 upstream) : PTPRQ (141703 downstream)																							GAAACAATCAGGTTTTTTTCT	0.294													4	98	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	80707313	80707313	+	IGR	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80707313G>T								PPP1R12A (378078 upstream) : PTPRQ (130813 downstream)																							CTGCAATCTTGGTGGCGACTG	0.358													7	761	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88483076	88483076	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88483076C>A	uc001tar.2	-	31	4106	c.3762G>T	c.(3760-3762)TTG>TTT	p.L1254F	CEP290_uc001taq.2_Missense_Mutation_p.L314F	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1254	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TTCTTCCCTCCAAACGAGCAT	0.438													6	635	---	---	---	---	PASS
CDK17	5128	broad.mit.edu	37	12	96688871	96688871	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96688871C>A	uc001tep.1	-	10	1392	c.903G>T	c.(901-903)TTG>TTT	p.L301F	CDK17_uc009ztk.2_Missense_Mutation_p.L301F|CDK17_uc010svb.1_Missense_Mutation_p.L248F	NM_002595	NP_002586	Q00537	CDK17_HUMAN	PCTAIRE protein kinase 2	301	Protein kinase.						ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7						GGCAATATGCCAAACCACGTA	0.343													6	563	---	---	---	---	PASS
UHRF1BP1L	23074	broad.mit.edu	37	12	100478292	100478292	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100478292T>A	uc001tgq.2	-	10	1479	c.1250A>T	c.(1249-1251)AAA>ATA	p.K417I	UHRF1BP1L_uc001tgr.2_Missense_Mutation_p.K417I|UHRF1BP1L_uc001tgp.2_Missense_Mutation_p.K67I	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	417										ovary(2)	2						TGTTGGGGATTTAGGAGGTGA	0.378													169	391	---	---	---	---	PASS
SLC17A8	246213	broad.mit.edu	37	12	100813894	100813894	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100813894C>T	uc010svi.1	+	12	2040	c.1727C>T	c.(1726-1728)ACA>ATA	p.T576I	SLC17A8_uc009ztx.2_Missense_Mutation_p.T526I	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	576	Cytoplasmic (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						GAAGAGCTGACATCCTACCAG	0.428													34	172	---	---	---	---	PASS
NT5DC3	51559	broad.mit.edu	37	12	104208888	104208888	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104208888A>C	uc010swe.1	-	2	261	c.220T>G	c.(220-222)TCC>GCC	p.S74A		NM_001031701	NP_001026871	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	74							hydrolase activity|metal ion binding			ovary(2)|skin(1)	3						CTCATAATGGAAGGAACCAAT	0.279													86	196	---	---	---	---	PASS
CLIP1	6249	broad.mit.edu	37	12	122865038	122865038	+	5'UTR	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122865038G>T	uc001ucg.1	-	1					CLIP1_uc001uch.1_5'UTR|CLIP1_uc001uci.1_5'UTR|CLIP1_uc010tae.1_5'UTR	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TTTGCCTGTTGCCACTATCTT	0.413													72	147	---	---	---	---	PASS
CLIP1	6249	broad.mit.edu	37	12	122865040	122865040	+	5'UTR	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122865040C>A	uc001ucg.1	-	1					CLIP1_uc001uch.1_5'UTR|CLIP1_uc001uci.1_5'UTR|CLIP1_uc010tae.1_5'UTR	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		TGCCTGTTGCCACTATCTTTC	0.413													70	147	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23913396	23913396	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23913396C>A	uc001uon.2	-	10	5208	c.4619G>T	c.(4618-4620)AGG>ATG	p.R1540M	SACS_uc001uoo.2_Missense_Mutation_p.R1393M|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	1540					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTCTCCTAACCTAGTTATGTT	0.388													6	297	---	---	---	---	PASS
STARD13	90627	broad.mit.edu	37	13	33684212	33684212	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33684212G>T	uc001uuw.2	-	12	2971	c.2845C>A	c.(2845-2847)CCG>ACG	p.P949T	STARD13_uc001uuu.2_Missense_Mutation_p.P941T|STARD13_uc001uuv.2_Missense_Mutation_p.P831T|STARD13_uc001uux.2_Missense_Mutation_p.P914T|STARD13_uc010tec.1_RNA	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain	949	START.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		AGCTTCAGCGGGTTCCCGTCG	0.547											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	37	---	---	---	---	PASS
SUGT1	10910	broad.mit.edu	37	13	53231666	53231666	+	Splice_Site	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53231666G>C	uc001vhc.2	+	3	322	c.97_splice	c.e3-1	p.E33_splice	SUGT1_uc001vha.2_Splice_Site|SUGT1_uc001vhb.2_Splice_Site_p.E33_splice|SUGT1_uc010thb.1_Splice_Site|SUGT1_uc001vhd.2_Splice_Site	NM_001130912	NP_001124384	Q9Y2Z0	SUGT1_HUMAN	suppressor of G2 allele of SKP1 isoform a						mitosis	kinetochore|ubiquitin ligase complex	binding				0		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		TGTTTTTGTAGGAGCTGACTA	0.338													61	222	---	---	---	---	PASS
SCEL	8796	broad.mit.edu	37	13	78191761	78191761	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78191761G>T	uc001vki.2	+	25	1649	c.1479G>T	c.(1477-1479)AAG>AAT	p.K493N	SCEL_uc001vkj.2_Missense_Mutation_p.K473N|SCEL_uc010thx.1_Missense_Mutation_p.K451N	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1	493	16 X approximate tandem repeats.|13.				embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AACTCATCAAGGTGAATCCTG	0.284													5	299	---	---	---	---	PASS
DOCK9	23348	broad.mit.edu	37	13	99505670	99505670	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99505670A>T	uc001vnt.2	-	35	3996	c.3941T>A	c.(3940-3942)ATG>AAG	p.M1314K	DOCK9_uc001vnw.2_Missense_Mutation_p.M1313K|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Missense_Mutation_p.M1314K|DOCK9_uc010tip.1_Missense_Mutation_p.M1K|DOCK9_uc010tiq.1_Missense_Mutation_p.M292K	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1314					blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACCATCAGACATGCTCTTTAA	0.368													79	250	---	---	---	---	PASS
LOC643677	643677	broad.mit.edu	37	13	103401605	103401605	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103401605G>T	uc001vpm.2	-	4	1582	c.1442C>A	c.(1441-1443)CCA>CAA	p.P481Q		NM_001146197	NP_001139669			hypothetical protein LOC643677												0						TTTACTGTCTGGTGTTTTTCT	0.343													4	121	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20296229	20296229	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296229C>A	uc010tkv.1	+	1	622	c.622C>A	c.(622-624)CTC>ATC	p.L208I		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	208	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCTGATGACACTCCTGTGCTT	0.517													17	181	---	---	---	---	PASS
PRPF39	55015	broad.mit.edu	37	14	45583821	45583821	+	Intron	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45583821A>G	uc001wvz.3	+						PRPF39_uc001wvy.3_Intron|PRPF39_uc010and.2_Intron|PRPF39_uc001wwa.1_Missense_Mutation_p.S257G	NM_017922	NP_060392	Q86UA1	PRP39_HUMAN	PRP39 pre-mRNA processing factor 39 homolog						mRNA processing|RNA splicing	nucleus	binding			ovary(1)|breast(1)	2						GTATCAAGTGAGTCTGCATAA	0.294													7	446	---	---	---	---	PASS
ATP5S	27109	broad.mit.edu	37	14	50779730	50779730	+	5'UTR	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50779730C>T	uc001wxw.1	+	1					L2HGDH_uc010tqn.1_5'Flank|L2HGDH_uc001wxu.2_5'Flank|L2HGDH_uc010tqo.1_5'Flank|ATP5S_uc001wxv.2_5'UTR|ATP5S_uc001wxx.1_5'UTR	NM_001003803	NP_001003803	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial F0						ATP biosynthetic process	mitochondrial inner membrane|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity			ovary(1)|skin(1)	2	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		AACCGAGATACAGTTTTAAAT	0.343													32	173	---	---	---	---	PASS
FBXO34	55030	broad.mit.edu	37	14	55817459	55817459	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55817459G>T	uc001xbu.2	+	2	596	c.351G>T	c.(349-351)AAG>AAT	p.K117N	FBXO34_uc001xbv.2_5'Flank|FBXO34_uc010aoo.2_Missense_Mutation_p.K117N	NM_017943	NP_060413	Q9NWN3	FBX34_HUMAN	F-box only protein 34	117										ovary(2)|lung(2)|skin(1)	5						GAAATACCAAGGAAAAAATTG	0.408													27	91	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64519077	64519077	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64519077C>A	uc001xgm.2	+	48	8676	c.8446C>A	c.(8446-8448)CAA>AAA	p.Q2816K	SYNE2_uc001xgl.2_Missense_Mutation_p.Q2816K	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2816	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAATCAATACCAAATGCTGGT	0.348													4	164	---	---	---	---	PASS
EML1	2009	broad.mit.edu	37	14	100344947	100344947	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100344947A>G	uc001ygs.2	+	4	578	c.509A>G	c.(508-510)AAC>AGC	p.N170S	EML1_uc010avt.1_Missense_Mutation_p.N157S|EML1_uc010tww.1_Missense_Mutation_p.N158S|EML1_uc001ygq.2_Missense_Mutation_p.N189S|EML1_uc001ygr.2_Missense_Mutation_p.N189S	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	170						cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GGCAAAAAGAACAGTGAAAGG	0.512													5	103	---	---	---	---	PASS
WARS	7453	broad.mit.edu	37	14	100809696	100809696	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100809696A>G	uc001yhf.1	-	7	939	c.855T>C	c.(853-855)GCT>GCC	p.A285A	WARS_uc001yhe.1_Silent_p.A91A|WARS_uc001yhg.1_Silent_p.A285A|WARS_uc001yhh.1_Silent_p.A285A|WARS_uc001yhi.1_Silent_p.A244A|WARS_uc001yhj.1_Silent_p.A244A|WARS_uc001yhk.1_Silent_p.A244A|WARS_uc001yhl.1_Silent_p.A285A	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a	285					angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	AGGAGGGAGCAGCCTGGATGG	0.453													11	123	---	---	---	---	PASS
TECPR2	9895	broad.mit.edu	37	14	102916037	102916037	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102916037G>A	uc001ylw.1	+	14	3295	c.3147G>A	c.(3145-3147)TCG>TCA	p.S1049S	TECPR2_uc010awl.2_Silent_p.S1049S|TECPR2_uc010txx.1_Silent_p.S212S	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1049							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						CCACTCACTCGGTGGCCACAG	0.562													7	93	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	22473214	22473214	+	RNA	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22473214G>A	uc001yuj.1	-	2		c.57C>T								Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:H6.																		GCTGCACCTGGGACAGGACCC	0.592													4	70	---	---	---	---	PASS
CHRNA7	1139	broad.mit.edu	37	15	32449727	32449727	+	Intron	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32449727A>G	uc001zft.2	+						uc001zfv.1_RNA|CHRNA7_uc010bae.1_Intron|CHRNA7_uc010baf.2_Intron|CHRNA7_uc010bah.1_Intron|CHRNA7_uc010baj.1_Intron|CHRNA7_uc010bak.2_Intron|CHRNA7_uc001zfu.2_RNA	NM_000746	NP_000737	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7						activation of MAPK activity|calcium ion transport|cellular calcium ion homeostasis|memory|negative regulation of tumor necrosis factor production|positive regulation of angiogenesis|positive regulation of cell proliferation|response to hypoxia|response to nicotine	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|beta-amyloid binding|chloride channel regulator activity|nicotinic acetylcholine-activated cation-selective channel activity|protein homodimerization activity|toxin binding			ovary(1)	1		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Nicotine(DB00184)|Varenicline(DB01273)	GGAGGGCGGAACCGGCTGAAG	0.453													9	72	---	---	---	---	PASS
DLL4	54567	broad.mit.edu	37	15	41223809	41223809	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41223809G>A	uc001zng.1	+	4	823	c.503G>A	c.(502-504)CGC>CAC	p.R168H		NM_019074	NP_061947	Q9NR61	DLL4_HUMAN	delta-like 4 protein precursor	168	Extracellular (Potential).				blood circulation|cell communication|cell differentiation|Notch receptor processing|Notch signaling pathway	integral to membrane|plasma membrane	calcium ion binding|Notch binding			breast(2)	2		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		ACAAGGCTGCGCTACTCTTAC	0.552													12	25	---	---	---	---	PASS
NUSAP1	51203	broad.mit.edu	37	15	41672330	41672330	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41672330G>A	uc001zns.3	+	11	1502	c.1272G>A	c.(1270-1272)GAG>GAA	p.E424E	NUSAP1_uc001znq.3_Silent_p.E190E|NUSAP1_uc001znr.3_Silent_p.E423E|NUSAP1_uc010bce.2_Silent_p.E385E|NUSAP1_uc001znt.3_Silent_p.E409E|NUSAP1_uc001znv.3_Silent_p.E422E|NUSAP1_uc001znu.3_Silent_p.E423E|NUSAP1_uc010ucw.1_Silent_p.E361E|NUSAP1_uc001znw.3_Silent_p.E228E	NM_016359	NP_057443	Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	424	Potential.				cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		AACGAAAGGAGAAGAAAGCAA	0.398													23	417	---	---	---	---	PASS
ADAL	161823	broad.mit.edu	37	15	43644189	43644189	+	3'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43644189T>C	uc010udo.1	+	12					ADAL_uc001zri.1_3'UTR	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1						adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		TCAATCAAGTTCCTGCCATAT	0.353													6	28	---	---	---	---	PASS
DUT	1854	broad.mit.edu	37	15	48633488	48633488	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48633488G>T	uc001zws.2	+	5	651	c.559G>T	c.(559-561)GGT>TGT	p.G187C	DUT_uc001zwt.2_Missense_Mutation_p.G76C|DUT_uc001zwu.2_RNA|DUT_uc001zwv.2_Missense_Mutation_p.G99C|DUT_uc001zww.2_Missense_Mutation_p.G99C	NM_001025248	NP_001020419	P33316	DUT_HUMAN	deoxyuridine triphosphatase isoform 1 precursor	187	Substrate binding.				DNA replication|dUTP metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process	mitochondrion|nucleoplasm	dUTP diphosphatase activity|protein binding				0		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		TTCTCTAGCTGGTGTCATAGA	0.289								Modulation_of_nucleotide_pools					6	606	---	---	---	---	PASS
TSPAN3	10099	broad.mit.edu	37	15	77348509	77348509	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77348509A>T	uc002bcj.2	-	2	369	c.152T>A	c.(151-153)CTC>CAC	p.L51H	TSPAN3_uc002bck.2_Missense_Mutation_p.L51H|TSPAN3_uc010ump.1_Intron|TSPAN3_uc010bkx.2_Intron	NM_005724	NP_005715	O60637	TSN3_HUMAN	transmembrane 4 superfamily member 8 isoform 1	51	Helical; (Potential).					integral to membrane					0				all cancers(203;1.14e-19)		AGCAGGGATGAGCGTGTACAC	0.483													5	75	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15111002	15111002	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15111002G>T	uc002dda.3	+	10	1062	c.838G>T	c.(838-840)GGT>TGT	p.G280C	PDXDC1_uc010uzl.1_Missense_Mutation_p.G265C|PDXDC1_uc010uzm.1_Missense_Mutation_p.G189C|PDXDC1_uc002dcz.2_Missense_Mutation_p.G257C|PDXDC1_uc002ddb.3_Missense_Mutation_p.G253C|PDXDC1_uc010uzn.1_Missense_Mutation_p.G252C|PDXDC1_uc002ddc.2_Missense_Mutation_p.G280C	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	280					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	ATTGGCTCTGGGTTATGTCTC	0.363													8	818	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24226072	24226072	+	Intron	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24226072C>A	uc002dmd.2	+						PRKCB_uc002dme.2_Missense_Mutation_p.Q653K	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	GAATATTGACCAATCAGAATT	0.433													6	328	---	---	---	---	PASS
HIRIP3	8479	broad.mit.edu	37	16	30006027	30006027	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30006027G>A	uc002dve.2	-	4	900	c.439C>T	c.(439-441)CGG>TGG	p.R147W	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvg.1_5'Flank|INO80E_uc002dvh.1_5'Flank|INO80E_uc002dvi.1_5'Flank|INO80E_uc002dvj.1_5'Flank|INO80E_uc002dvk.1_5'Flank|HIRIP3_uc002dvf.2_Intron	NM_003609	NP_003600	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	147	Glu-rich.				chromatin assembly or disassembly	nucleus	protein binding			central_nervous_system(1)	1						TCCCTCTGCCGTTCCTCATCA	0.567													16	103	---	---	---	---	PASS
ITGAL	3683	broad.mit.edu	37	16	30516763	30516763	+	Silent	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30516763A>G	uc002dyi.3	+	20	2522	c.2346A>G	c.(2344-2346)AGA>AGG	p.R782R	ITGAL_uc002dyj.3_Silent_p.R698R|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	782	Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)	CAAACTTGAGAGTGTCCTTCT	0.463													6	304	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32077601	32077601	+	RNA	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32077601G>A	uc010vfu.1	+	1		c.43G>A								Homo sapiens mRNA for immunoglobulin heavy chain, VHDJH rearrangement : VHLI26.																		CCATCTCCAGGGACAACGCCA	0.502													4	86	---	---	---	---	PASS
LONP2	83752	broad.mit.edu	37	16	48303949	48303949	+	Silent	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48303949C>T	uc002efi.1	+	7	1094	c.1005C>T	c.(1003-1005)GCC>GCT	p.A335A	LONP2_uc010vgm.1_RNA|LONP2_uc002efj.1_Silent_p.A291A	NM_031490	NP_113678	Q86WA8	LONP2_HUMAN	peroxisomal LON protease-like	335					misfolded or incompletely synthesized protein catabolic process|protein targeting to peroxisome|signal peptide processing	nucleoid|peroxisomal matrix	ATP binding|ATP-dependent peptidase activity|enzyme binding|sequence-specific DNA binding|serine-type endopeptidase activity				0						TTAGGGCAGCCCGGATTCTTC	0.408													22	286	---	---	---	---	PASS
RPGRIP1L	23322	broad.mit.edu	37	16	53679899	53679899	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53679899G>T	uc002ehp.2	-	17	2385	c.2321C>A	c.(2320-2322)CCC>CAC	p.P774H	RPGRIP1L_uc002eho.3_Missense_Mutation_p.P774H|RPGRIP1L_uc010vgy.1_Missense_Mutation_p.P774H|RPGRIP1L_uc010cbx.2_Missense_Mutation_p.P774H|RPGRIP1L_uc010vgz.1_Missense_Mutation_p.P774H	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	774					negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)				AGCAGTTTTGGGTGCTTGCTG	0.383													5	232	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58585152	58585152	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58585152C>A	uc002env.2	-	24	3519	c.3226G>T	c.(3226-3228)GAT>TAT	p.D1076Y	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.D1071Y|CNOT1_uc002enx.2_Missense_Mutation_p.D1076Y|CNOT1_uc002enz.1_Missense_Mutation_p.D505Y|CNOT1_uc010vik.1_Missense_Mutation_p.D72Y|SNORA46_uc002eny.1_5'Flank	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1076					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AGCAACGTATCTATATTTGTA	0.323													27	392	---	---	---	---	PASS
CDH5	1003	broad.mit.edu	37	16	66422343	66422343	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66422343G>T	uc002eom.3	+	4	772	c.616G>T	c.(616-618)GGA>TGA	p.G206*	CDH5_uc002eon.1_Nonsense_Mutation_p.G206*	NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	206	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)		CGATAATTCTGGTCTGTGTGA	0.517													5	289	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													6	43	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													4	45	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268158A>C	uc010cfp.1	-	3		c.257T>G								Homo sapiens cDNA, FLJ98908.																		TTCTTCATTAAAACAGCTACT	0.333													4	101	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70942693	70942693	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70942693G>T	uc002ezr.2	-	48	8201	c.8073C>A	c.(8071-8073)TTC>TTA	p.F2691L		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2692										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				TCTGAATCTCGAAGACTTGGT	0.458													7	581	---	---	---	---	PASS
AP1G1	164	broad.mit.edu	37	16	71780730	71780730	+	Intron	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71780730C>G	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc002faz.2_5'UTR	NM_001128	NP_001119	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)				TATAGTTTTTCAAAAACAAAA	0.259													15	51	---	---	---	---	PASS
MAP1LC3B	81631	broad.mit.edu	37	16	87436808	87436808	+	3'UTR	SNP	G	C	C	rs7865	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87436808G>C	uc002fjx.2	+	4					MAP1LC3B_uc010chs.2_RNA	NM_022818	NP_073729	Q9GZQ8	MLP3B_HUMAN	microtubule-associated proteins 1A/1B light						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0249)		CACAGATCATGAAACAGTAGT	0.388													4	76	---	---	---	---	PASS
CHD3	1107	broad.mit.edu	37	17	7797756	7797756	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7797756G>A	uc002gje.2	+	8	1249	c.1099G>A	c.(1099-1101)GGG>AGG	p.G367R	CHD3_uc002gjd.2_Missense_Mutation_p.G426R|CHD3_uc002gjf.2_Missense_Mutation_p.G367R|CHD3_uc002gjg.1_Missense_Mutation_p.G195R	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	367					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)				TGCAGTGGCCGGGGAGGAGGA	0.438													20	72	---	---	---	---	PASS
AKAP10	11216	broad.mit.edu	37	17	19850777	19850777	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19850777A>G	uc002gwo.2	-	5	1056	c.919T>C	c.(919-921)TCT>CCT	p.S307P	AKAP10_uc002gwp.1_Missense_Mutation_p.S307P|AKAP10_uc010cqw.1_Missense_Mutation_p.S307P|AKAP10_uc010vze.1_Missense_Mutation_p.S228P	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor	307	RGS 1.				blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					GCATCTGGAGATATATATTTG	0.343													7	599	---	---	---	---	PASS
CCL15	6359	broad.mit.edu	37	17	34324761	34324761	+	3'UTR	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34324761G>T	uc010wcu.1	-	4					CCL14-CCL15_uc010wcs.1_RNA|CCL14-CCL15_uc010wct.1_RNA	NM_032965	NP_116741	Q16663	CCL15_HUMAN	chemokine (C-C motif) ligand 15 precursor						cell-cell signaling|cellular calcium ion homeostasis|immune response	extracellular space	chemoattractant activity|chemokine activity|heparin binding|signal transducer activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACTCACAGGAGGTGTTGGAGG	0.348													5	191	---	---	---	---	PASS
KRT33A	3883	broad.mit.edu	37	17	39503349	39503349	+	Silent	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39503349G>C	uc002hwk.1	-	4	751	c.714C>G	c.(712-714)ACC>ACG	p.T238T		NM_004138	NP_004129	O76009	KT33A_HUMAN	keratin 33A	238	Coil 2.|Rod.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)				CCCTGCGGTTGGTTTCCACCA	0.637													5	64	---	---	---	---	PASS
C17orf104	284071	broad.mit.edu	37	17	42745374	42745374	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42745374T>G	uc010czv.2	+	5	2095	c.2095T>G	c.(2095-2097)TCA>GCA	p.S699A	C17orf104_uc002igy.1_Missense_Mutation_p.S533A|C17orf104_uc002igz.3_Missense_Mutation_p.S533A|C17orf104_uc010wja.1_RNA|C17orf104_uc002iha.2_Missense_Mutation_p.S533A	NM_001145080	NP_001138552	A2RUB1	CQ104_HUMAN	hypothetical protein LOC284071	699										central_nervous_system(1)	1						ATTTGGCCATTCAGTTGTTCC	0.348													59	182	---	---	---	---	PASS
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	G	G	rs138671696	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62968690A>G	uc002jez.3	-	4		c.641T>C			AMZ2P1_uc002jfa.3_RNA|AMZ2P1_uc002jfb.3_RNA|AMZ2P1_uc010del.2_RNA					Homo sapiens cDNA FLJ32065 fis, clone OCBBF1000086, weakly similar to Archeobacterial metalloproteinase-like protein 2 (EC 3.-.-.-).												0						AAAATTCCACAAGTCTCTTGG	0.373													8	557	---	---	---	---	PASS
MAP2K6	5608	broad.mit.edu	37	17	67515735	67515735	+	Intron	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67515735T>C	uc002jij.2	+						MAP2K6_uc002jii.2_Intron|MAP2K6_uc002jik.2_3'UTR	NM_002758	NP_002749	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)					TGGAGCAAGGTTGGATTGAAA	0.388													6	25	---	---	---	---	PASS
C17orf99	100141515	broad.mit.edu	37	17	76157222	76157222	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76157222A>T	uc002jus.3	+	3	312	c.257A>T	c.(256-258)AAC>ATC	p.N86I	C17orf99_uc010wts.1_Missense_Mutation_p.N73I	NM_001163075	NP_001156547	Q6UX52	CQ099_HUMAN	hypothetical protein LOC100141515 precursor	86						extracellular region					0						TTCAACCTCAACGTCACACTC	0.587													8	57	---	---	---	---	PASS
METTL4	64863	broad.mit.edu	37	18	2538990	2538990	+	3'UTR	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2538990A>T	uc002klh.3	-	9					METTL4_uc010dkj.2_3'UTR	NM_022840	NP_073751	Q8N3J2	METL4_HUMAN	methyltransferase like 4						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		methyltransferase activity|nucleic acid binding			kidney(1)|skin(1)	2						ACTTTAATCAAGATCATAGTC	0.343													97	128	---	---	---	---	PASS
EMILIN2	84034	broad.mit.edu	37	18	2891708	2891708	+	Nonsense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2891708C>G	uc002kln.2	+	4	1742	c.1583C>G	c.(1582-1584)TCA>TGA	p.S528*		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor	528					cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		CCAGGAGTGTCAGGGTCAGGA	0.532													7	53	---	---	---	---	PASS
CTAGE1	64693	broad.mit.edu	37	18	19997027	19997027	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19997027T>C	uc002ktv.1	-	1	852	c.748A>G	c.(748-750)ATG>GTG	p.M250V		NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	250	Potential.					integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TCTTCAAGCATAGCAACCCCA	0.373													7	408	---	---	---	---	PASS
REEP6	92840	broad.mit.edu	37	19	1495634	1495634	+	Intron	SNP	G	A	A	rs2277748	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1495634G>A	uc002ltc.2	+						REEP6_uc010xgp.1_Missense_Mutation_p.V126M	NM_138393	NP_612402	Q96HR9	REEP6_HUMAN	receptor accessory protein 6							integral to membrane					0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		GGGCACAGCCGTGGAGCGCAT	0.637													7	106	---	---	---	---	PASS
MBD3L1	85509	broad.mit.edu	37	19	8953327	8953327	+	5'UTR	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8953327T>C	uc002mko.2	+	1						NM_145208	NP_660209	Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						ATGATTTATTTTAATAGTGTA	0.443													20	95	---	---	---	---	PASS
ZNF121	7675	broad.mit.edu	37	19	9676854	9676854	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9676854T>C	uc010xkp.1	-	4	1167	c.935A>G	c.(934-936)TAT>TGT	p.Y312C	ZNF121_uc010dwt.2_Missense_Mutation_p.Y312C|ZNF121_uc010xkq.1_Missense_Mutation_p.Y312C	NM_001008727	NP_001008727	P58317	ZN121_HUMAN	zinc finger protein 121	312	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CTTACATTCATAGGGCTTCTC	0.378													5	199	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10257171	10257171	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10257171T>G	uc002mng.2	-	27	2882	c.2702A>C	c.(2701-2703)GAG>GCG	p.E901A	DNMT1_uc002mnf.2_5'Flank|DNMT1_uc010xlc.1_Missense_Mutation_p.E917A|DNMT1_uc002mnh.2_Missense_Mutation_p.E796A|DNMT1_uc010xld.1_Missense_Mutation_p.E901A	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	901					chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	TTGCCTCATCTCAGCCAGACG	0.577													7	41	---	---	---	---	PASS
ZNF441	126068	broad.mit.edu	37	19	11892183	11892183	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11892183C>A	uc010dyj.2	+	4	1738	c.1544C>A	c.(1543-1545)CCC>CAC	p.P515H	ZNF441_uc002msn.3_Missense_Mutation_p.P471H	NM_152355	NP_689568	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	515	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TTTGATTCTCCCAGTTCATTT	0.398													4	119	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14758037	14758037	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14758037C>T	uc002mzi.3	-	8	986	c.838G>A	c.(838-840)GTG>ATG	p.V280M	EMR3_uc010dzp.2_Missense_Mutation_p.V228M|EMR3_uc010xnv.1_Missense_Mutation_p.V154M	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	280	Extracellular (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						GAGAGAGACACGTTCCTTTTG	0.448													31	128	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22155677	22155677	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22155677G>A	uc002nqp.2	-	5	2008	c.1859C>T	c.(1858-1860)CCC>CTC	p.P620L	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				ACATTTGTAGGGTTTCTCTCC	0.378													4	70	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22170044	22170044	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22170044C>G	uc002nqp.2	-	3	349	c.200G>C	c.(199-201)AGA>ACA	p.R67T	ZNF208_uc002nqo.1_Missense_Mutation_p.R67T|ZNF208_uc002nqq.2_RNA	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				CATCTCATGTCTCTTCATATT	0.418													24	154	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22574468	22574468	+	Silent	SNP	G	A	A	rs139959911	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22574468G>A	uc002nqt.2	-	4	1691	c.1569C>T	c.(1567-1569)TGC>TGT	p.C523C		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	523	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AGGCTTTGCCGCATTCTTCAC	0.383													14	59	---	---	---	---	PASS
ZNF45	7596	broad.mit.edu	37	19	44419197	44419197	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44419197G>T	uc002oxu.1	-	4	490	c.391C>A	c.(391-393)CAG>AAG	p.Q131K	ZNF45_uc002oxw.1_Missense_Mutation_p.Q131K|ZNF45_uc002oxv.1_Missense_Mutation_p.Q131K	NM_003425	NP_003416	Q02386	ZNF45_HUMAN	zinc finger protein 45	131					multicellular organismal development	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						TTTTCCAACTGGCAGCCTGTT	0.408													8	672	---	---	---	---	PASS
GRWD1	83743	broad.mit.edu	37	19	48954349	48954349	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48954349C>T	uc002pjd.2	+	6	1117	c.884C>T	c.(883-885)CCC>CTC	p.P295L		NM_031485	NP_113673	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	295	WD 2.					nucleolus				ovary(1)	1		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		CGGGCAGCCCCCAGCAAGGCC	0.667													4	19	---	---	---	---	PASS
AP2A1	160	broad.mit.edu	37	19	50309986	50309986	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50309986C>A	uc002ppn.2	+	24	3116	c.2905C>A	c.(2905-2907)CTG>ATG	p.L969M	AP2A1_uc002ppo.2_Missense_Mutation_p.L947M|AP2A1_uc010enk.2_Missense_Mutation_p.L100M	NM_014203	NP_055018	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1	969				ENFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEP VSRHLCELLAQQF -> GDREDTRVWGMPGTFLRPFVFLFL FICCCLHSGGLGGVPLPPFPPQAQRGEGPGKWMSPPLPPHP VVAPPTPSPSRGCVLL (in Ref. 4; AAH14214).	axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CTCCCGTCACCTGTGTGAGCT	0.652													8	35	---	---	---	---	PASS
LILRA1	11024	broad.mit.edu	37	19	55106239	55106239	+	Silent	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106239G>A	uc002qgh.1	+	4	362	c.180G>A	c.(178-180)CTG>CTA	p.L60L	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Silent_p.L60L	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	60	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)		AGTACCGTCTGTATAGAGAAA	0.572													6	193	---	---	---	---	PASS
LILRB4	11006	broad.mit.edu	37	19	55177763	55177763	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55177763G>A	uc002qgp.2	+	8	1309	c.947G>A	c.(946-948)AGG>AAG	p.R316K	LILRB4_uc002qgq.2_Missense_Mutation_p.R316K|LILRB4_uc002qgr.2_Missense_Mutation_p.R357K|LILRB4_uc010ert.2_Missense_Mutation_p.R357K|LILRB4_uc010eru.2_Missense_Mutation_p.R345K	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	316	Cytoplasmic (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)		GGCCTACAGAGGAGGTAATTC	0.617													39	173	---	---	---	---	PASS
ZNF544	27300	broad.mit.edu	37	19	58772269	58772269	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58772269T>C	uc010euo.2	+	7	771	c.297T>C	c.(295-297)GCT>GCC	p.A99A	ZNF544_uc010yhw.1_Intron|ZNF544_uc010yhx.1_Silent_p.A71A|ZNF544_uc010yhy.1_Silent_p.A71A|ZNF544_uc002qrt.3_5'UTR|ZNF544_uc002qru.3_5'UTR|uc002qrx.1_Intron	NM_014480	NP_055295	Q6NX49	ZN544_HUMAN	zinc finger protein 544	99					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AAGATCGAGCTAGGGAAGAAC	0.438													61	108	---	---	---	---	PASS
C20orf194	25943	broad.mit.edu	37	20	3355713	3355713	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3355713C>T	uc002wii.2	-	5	520	c.469G>A	c.(469-471)GAC>AAC	p.D157N	C20orf194_uc002wik.2_5'UTR|C20orf194_uc010gay.1_RNA	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943	157											0						CTACTACAGTCTCGAACCATG	0.408													33	328	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20493735	20493735	+	Silent	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20493735C>A	uc002wrz.2	-	32	4421	c.4278G>T	c.(4276-4278)CTG>CTT	p.L1426L	RALGAPA2_uc010gcx.2_Silent_p.L1130L|RALGAPA2_uc010zsg.1_Silent_p.L874L|RALGAPA2_uc002wsa.1_Silent_p.L198L	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1426					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						CAAACAGCTGCAGGTTTGGAC	0.537													8	190	---	---	---	---	PASS
CST11	140880	broad.mit.edu	37	20	23433266	23433266	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23433266G>C	uc002wtf.1	-	1	217	c.183C>G	c.(181-183)GAC>GAG	p.D61E	CST11_uc002wtg.1_Missense_Mutation_p.D61E	NM_130794	NP_570612	Q9H112	CST11_HUMAN	cystatin 11 isoform 1 precursor	61					defense response to bacterium	cytoplasm|nucleus	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGTGGTACTTGTCATCACTTT	0.507													5	140	---	---	---	---	PASS
RALGAPB	57148	broad.mit.edu	37	20	37202798	37202798	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37202798C>A	uc002xiw.2	+	29	4405	c.4148C>A	c.(4147-4149)ACA>AAA	p.T1383K	RALGAPB_uc002xix.2_Missense_Mutation_p.T1380K|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Missense_Mutation_p.T1162K	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	1383	Rap-GAP.				activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						TTAAGATCTACAACTCTTGAA	0.388													13	293	---	---	---	---	PASS
BCAS1	8537	broad.mit.edu	37	20	52612686	52612686	+	Intron	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52612686T>C	uc002xws.2	-						BCAS1_uc010zza.1_5'UTR|BCAS1_uc010zzb.1_Intron|BCAS1_uc010gim.2_Intron|BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Intron	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			ACCCCCTAATTCCAGCCATAC	0.453													8	42	---	---	---	---	PASS
TTC3	7267	broad.mit.edu	37	21	38463711	38463711	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38463711A>G	uc002yvz.2	+	7	704	c.599A>G	c.(598-600)GAA>GGA	p.E200G	TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Missense_Mutation_p.E200G|TTC3_uc002ywb.2_Missense_Mutation_p.E200G|TTC3_uc010gnf.2_5'UTR|TTC3_uc011aed.1_Intron|TTC3_uc010gne.1_Missense_Mutation_p.E200G	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	200					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)				TTCTTTACTGAATGTAAGTAT	0.289													7	475	---	---	---	---	PASS
PI4KA	5297	broad.mit.edu	37	22	21192985	21192985	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21192985A>C	uc002zsz.3	-	2	248	c.17T>G	c.(16-18)TTC>TGC	p.F6C	PI4KA_uc010gsq.1_Missense_Mutation_p.F64C	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	6					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GATCCCATGGAAATCCACTGG	0.388													50	232	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38120095	38120095	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38120095G>A	uc003atr.2	+	7	1803	c.1532G>A	c.(1531-1533)AGA>AAA	p.R511K	TRIOBP_uc003atu.2_Missense_Mutation_p.R339K|TRIOBP_uc003atq.1_Missense_Mutation_p.R511K|TRIOBP_uc003ats.1_Missense_Mutation_p.R339K	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	511					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GACAATCCCAGAGCCTCCAGA	0.592													4	179	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41084301	41084301	+	Splice_Site	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41084301G>T	uc004dfb.2	+	41	7606	c.6973_splice	c.e41-1	p.V2325_splice	USP9X_uc004dfc.2_Splice_Site_p.V2325_splice	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						CTTGTTTTTAGGTTGCATATT	0.363													7	467	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	48159154	48159154	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48159154G>A	uc010nib.1	-	6	466	c.379C>T	c.(379-381)CCA>TCA	p.P127S		NM_174962	NP_777622			synovial sarcoma, X breakpoint 9																		GATGCTTCTGGCACTTCCTTC	0.433													5	269	---	---	---	---	PASS
ZC3H12B	340554	broad.mit.edu	37	X	64717061	64717061	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64717061G>C	uc010nko.2	+	2	634	c.625G>C	c.(625-627)GAT>CAT	p.D209H		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	209							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3						ACTTGCTGTGGATTGGTTTCT	0.403													9	202	---	---	---	---	PASS
CDX4	1046	broad.mit.edu	37	X	72673463	72673463	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72673463G>A	uc011mqk.1	+	2	613	c.613G>A	c.(613-615)GAG>AAG	p.E205K		NM_005193	NP_005184	O14627	CDX4_HUMAN	caudal type homeobox 4	205	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(35;0.156)					GAGAAAATCAGAGCTGGCAGT	0.393													29	140	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86087134	86087134	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86087134G>T	uc004eew.2	+	12	1946	c.1776G>T	c.(1774-1776)ATG>ATT	p.M592I	DACH2_uc004eex.2_3'UTR|DACH2_uc010nmq.2_Missense_Mutation_p.M458I|DACH2_uc011mra.1_Missense_Mutation_p.M425I|DACH2_uc010nmr.2_Missense_Mutation_p.M373I	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	592					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						GTTTAGAAATGGCACAACAGT	0.333													6	341	---	---	---	---	PASS
UTY	7404	broad.mit.edu	37	Y	15409556	15409556	+	Intron	SNP	A	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15409556A>T	uc004fsx.1	-						UTY_uc004fsw.1_Intron|UTY_uc010nwx.1_Intron|UTY_uc004fsy.2_3'UTR	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3						chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						ACCCCCAAAGAGAAACTGCAG	0.363													82	112	---	---	---	---	PASS
CD24	100133941	broad.mit.edu	37	Y	21154403	21154403	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:21154403T>G	uc004ftz.1	-	1	303	c.193A>C	c.(193-195)ACA>CCA	p.T65P	TTTY14_uc004fty.2_Intron	NM_013230	NP_037362	P25063	CD24_HUMAN	CD24 antigen precursor	65					axon guidance|B cell receptor transport into membrane raft|cell activation|cell migration|cell-cell adhesion|chemokine receptor transport out of membrane raft|cholesterol homeostasis|elevation of cytosolic calcium ion concentration|induction of apoptosis by intracellular signals|negative regulation of transforming growth factor-beta3 production|positive regulation of activated T cell proliferation|positive regulation of MAP kinase activity|regulation of cytokine-mediated signaling pathway|regulation of epithelial cell differentiation|regulation of MAPKKK cascade|respiratory burst|response to estrogen stimulus|response to hypoxia|response to molecule of bacterial origin|T cell costimulation|Wnt receptor signaling pathway	anchored to membrane|cell surface|membrane raft|plasma membrane	protein kinase binding|protein tyrosine kinase activator activity|signal transducer activity				0						AGACTGGCTGTTGACTGCAGG	0.507													6	49	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2269	2269	+	5'Flank	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2269G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CACACCCAATTGGACCAATCT	0.398													25	143	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2585	2585	+	5'Flank	SNP	G	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2585G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		GGTACCCTAACCGTGCAaagg	0.289													7	133	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7042	7042	+	Silent	SNP	T	C	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7042T>C	uc011mfh.1	+	1	1189	c.141T>C	c.(139-141)TGT>TGC	p.C47C	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CTTCCACTATGTCCTATCAAT	0.453													57	49	---	---	---	---	PASS
KIAA0562	9731	broad.mit.edu	37	1	3750216	3750216	+	Intron	DEL	C	-	-	rs35801288		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3750216delC	uc001aky.2	-						KIAA0562_uc010nzm.1_Intron	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,							centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		ATAAAAAAAACATTGGAAAAA	0.279													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27537996	27537996	+	IGR	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27537996delT								SLC9A1 (56545 upstream) : WDTC1 (23011 downstream)																							ttttcttttcttttttttttt	0.129													3	5	---	---	---	---	
PPT1	5538	broad.mit.edu	37	1	40558459	40558460	+	Intron	INS	-	GCATGTGAAAA	GCATGTGAAAA	rs113022418		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40558459_40558460insGCATGTGAAAA	uc001cfb.2	-						PPT1_uc010ojf.1_5'Flank|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			gctaaccactggcatgtgaaat	0.000													9	4	---	---	---	---	
AK5	26289	broad.mit.edu	37	1	78022914	78022914	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78022914delT	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						tttattattatttttttttGT	0.438													4	3	---	---	---	---	
C1orf146	388649	broad.mit.edu	37	1	92697268	92697268	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92697268delT	uc001doq.2	+						C1orf146_uc010ote.1_Intron	NM_001012425	NP_001012425	Q5VVC0	CA146_HUMAN	hypothetical protein LOC388649											ovary(1)	1		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		TTTTCTAAAGTTTTTTTTTTT	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143397663	143397664	+	IGR	DEL	AA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143397663_143397664delAA								None (None upstream) : LOC100286793 (249975 downstream)																							TTAGAGAAACAAAGAGAAGTAC	0.248													6	3	---	---	---	---	
TDRD10	126668	broad.mit.edu	37	1	154517246	154517246	+	Intron	DEL	C	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154517246delC	uc009wow.2	+						TDRD10_uc001ffd.2_Intron|TDRD10_uc001ffe.2_Intron	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a								nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGATTGTCCTCTGTCTTTCTC	0.522													286	133	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175516482	175516483	+	Intron	INS	-	TCA	TCA	rs144624193	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175516482_175516483insTCA	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					AGTCTATAACTTCAACCCCTTC	0.485													2	4	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179619818	179619818	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179619818delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						TTTTTTATCATTTTTCCTTTA	0.070													13	9	---	---	---	---	
C1orf25	81627	broad.mit.edu	37	1	185093829	185093829	+	Intron	DEL	A	-	-	rs79409945		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185093829delA	uc001grf.3	-						C1orf25_uc010pon.1_Intron	NM_030934	NP_112196	Q7Z2T5	TRM1L_HUMAN	N2,N2-dimethylguanosine tRNA							intracellular	RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding				0						cccagtatccaaaaaaaaaac	0.134													8	4	---	---	---	---	
CAPN2	824	broad.mit.edu	37	1	223949716	223949717	+	Intron	INS	-	T	T	rs146172055	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223949716_223949717insT	uc001hob.3	+						CAPN2_uc010puy.1_Intron|CAPN2_uc001hoc.2_Intron	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1						proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)		AAAAAAAAACCTTATATTAATT	0.391													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249096814	249096815	+	IGR	INS	-	A	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249096814_249096815insA								LOC646627 (193663 upstream) : SH3BP5L (7836 downstream)																							GGACCTGTCTGAAACAAGACTC	0.505													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2835356	2835358	+	IGR	DEL	TCT	-	-	rs66875467		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2835356_2835358delTCT								MYT1L (500311 upstream) : TSSC1 (357383 downstream)																							TGATTGTAGATCTTCTTCTCTTG	0.399													1	8	---	---	---	---	
RNF144A	9781	broad.mit.edu	37	2	7075204	7075205	+	Intron	INS	-	G	G	rs35268138		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7075204_7075205insG	uc002qys.2	+						RNF144A_uc002qyt.2_Intron|RNF144A_uc002qyu.2_Intron	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		cccttgagacatatgccatcag	0.000													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28467327	28467330	+	Intron	DEL	TTAT	-	-	rs71933719		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28467327_28467330delTTAT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					atgatttatcttatttgtttttca	0.098													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	44262526	44262526	+	IGR	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44262526delT								LRPPRC (39382 upstream) : PPM1B (133474 downstream)																							ttttattttctttttttttgt	0.174													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60843066	60843067	+	IGR	INS	-	TG	TG			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60843066_60843067insTG								BCL11A (62433 upstream) : PAPOLG (140316 downstream)																							Gtctgtctgtctctctctctct	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	61927745	61927745	+	IGR	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61927745delT								XPO1 (162327 upstream) : FAM161A (124240 downstream)																							AACTGTCTCATTTTTTTTCTC	0.199													7	4	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97817294	97817294	+	Intron	DEL	A	-	-	rs114282044	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97817294delA	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						AGTTTTATTCAGCAATACTCT	0.239													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130380380	130380382	+	IGR	DEL	AAG	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130380380_130380382delAAG								None (None upstream) : LOC389033 (300053 downstream)																							CAAGAGGACAAAGAAGAAGAGGG	0.498													4	2	---	---	---	---	
EPC2	26122	broad.mit.edu	37	2	149447555	149447556	+	Intron	INS	-	A	A	rs142314364	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149447555_149447556insA	uc010zbt.1	+							NM_015630	NP_056445	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)		TAATTTTGTTTAAAAAATTCTA	0.277													1	7	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163292254	163292254	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163292254delT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	AACTTGGTTCTTTTTTTTTTA	0.338													9	4	---	---	---	---	
GALNT3	2591	broad.mit.edu	37	2	166651613	166651613	+	5'Flank	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166651613delA	uc010fph.1	-						GALNT3_uc010fpi.1_5'Flank|GALNT3_uc002udi.2_5'Flank	NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3						protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3						TTTTTAAGACAAAAAAAAATT	0.393													6	4	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212252385	212252385	+	Intron	DEL	A	-	-	rs77289701		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212252385delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		CATGACCAATAATCAGGGAAG	0.348										TSP Lung(8;0.080)			6	12	---	---	---	---	
LOC643387	643387	broad.mit.edu	37	2	239140426	239140427	+	5'UTR	INS	-	C	C	rs144646397		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239140426_239140427insC	uc010znu.1	+	1					LOC151174_uc002vxy.2_5'Flank|LOC151174_uc002vxx.3_5'Flank	NR_026923				Homo sapiens TAR DNA binding protein pseuodgene (LOC643387), non-coding RNA.												0						aaaaaaacaaaaaacaaacaaa	0.554													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14123417	14123418	+	IGR	INS	-	A	A	rs2607754		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14123417_14123418insA								TPRXL (15938 upstream) : CHCHD4 (30160 downstream)																							catacacatacccacacacaca	0.252													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14123418	14123419	+	IGR	INS	-	A	A	rs59775566		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14123418_14123419insA								TPRXL (15939 upstream) : CHCHD4 (30159 downstream)																							atacacatacccacacacacac	0.252													11	6	---	---	---	---	
PXK	54899	broad.mit.edu	37	3	58377226	58377227	+	Intron	INS	-	T	T	rs144635538	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58377226_58377227insT	uc003djz.1	+						PXK_uc003djx.1_Intron|PXK_uc003djy.1_Intron|PXK_uc003dka.1_Intron|PXK_uc003dkb.1_Intron|PXK_uc003dkc.1_Intron|PXK_uc011bfe.1_Intron|PXK_uc010hnj.1_Intron|PXK_uc003dkd.1_Intron|PXK_uc010hnk.1_Intron	NM_017771	NP_060241	Q7Z7A4	PXK_HUMAN	PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		TTGGAGTTTACTTCCCAAAAAA	0.292													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	71843594	71843595	+	IGR	INS	-	GAA	GAA	rs148014095	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71843594_71843595insGAA								PROK2 (9237 upstream) : RYBP (580156 downstream)																							AGGAATCCCCCGAAGAAGTTCA	0.431													4	3	---	---	---	---	
PFN2	5217	broad.mit.edu	37	3	149684634	149684634	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149684634delA	uc003ext.1	-						PFN2_uc003exs.1_Intron|PFN2_uc003exu.1_Intron|PFN2_uc011bnu.1_Intron	NM_053024	NP_444252	P35080	PROF2_HUMAN	profilin 2 isoform a						actin cytoskeleton organization|regulation of actin polymerization or depolymerization	actin cytoskeleton|cytoplasm	actin binding|phosphatidylinositol-4,5-bisphosphate binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CTAGCTACAGAAAAAAAAAAA	0.308													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151886839	151886840	+	IGR	DEL	GT	-	-	rs10552404		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151886839_151886840delGT								SUCNR1 (287189 upstream) : LOC401093 (93573 downstream)																							AAGCCAAGGGgtgtgtgtgtgt	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194416832	194416833	+	IGR	DEL	AG	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194416832_194416833delAG								FAM43A (7068 upstream) : C3orf21 (372182 downstream)																							AAATATTAAAAGTCTTTGAGAT	0.421													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195428679	195428682	+	Intron	DEL	AAAT	-	-	rs112452749		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195428679_195428682delAAAT	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		TTCATTAATCAAATAATTCATGTA	0.368													5	6	---	---	---	---	
SDHAP1	255812	broad.mit.edu	37	3	195690462	195690463	+	Intron	INS	-	G	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195690462_195690463insG	uc003fvy.2	-						SDHAP1_uc003fvx.3_Intron					Homo sapiens full length insert cDNA clone ZC24D06.												0						catgcgcaacaggggactgtaa	0.045													11	7	---	---	---	---	
FYTTD1	84248	broad.mit.edu	37	3	197508926	197508926	+	3'UTR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197508926delA	uc003fyi.2	+	9					FYTTD1_uc011bui.1_3'UTR|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_3'UTR	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		ttttttttttaaaaaaaaaaa	0.284													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197781264	197781265	+	IGR	DEL	AG	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197781264_197781265delAG								LMLN (10675 upstream) : LOC348840 (3139 downstream)																							aaagaaaaaaagaaaGTGTTTA	0.124													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21001932	21001932	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21001932delA	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				tattctacagaaaaaaaagat	0.000													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21714405	21714405	+	Intron	DEL	A	-	-	rs28691092	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21714405delA	uc003gqi.1	-							NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				AGAGATTTTTAAAAAAAAAAA	0.353													5	3	---	---	---	---	
N4BP2	55728	broad.mit.edu	37	4	40105583	40105583	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40105583delT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron|N4BP2_uc010ifr.2_Intron	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						ATGCTAGttcttttttttttg	0.174													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863502	69863503	+	IGR	INS	-	CGGA	CGGA	rs78806655	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863502_69863503insCGGA								UGT2A3 (45993 upstream) : UGT2B7 (98690 downstream)																							aatggatgatttggatgttagc	0.045													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863503	69863504	+	IGR	INS	-	GATTC	GATTC	rs141141985	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863503_69863504insGATTC								UGT2A3 (45994 upstream) : UGT2B7 (98689 downstream)																							atggatgatttggatgttagct	0.045													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	73871288	73871289	+	IGR	DEL	CA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73871288_73871289delCA								ADAMTS3 (436772 upstream) : COX18 (49127 downstream)																							CACCCACTGTCACACACACAAA	0.426													4	2	---	---	---	---	
SEC31A	22872	broad.mit.edu	37	4	83801742	83801742	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83801742delA	uc003hnf.2	-						SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron|SEC31A_uc003hno.2_Intron	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				attctgtctcaaaaaaaaaaa	0.109													3	3	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159750098	159750098	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159750098delA	uc003iqe.3	+						FNIP2_uc003iqd.2_Intron	NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ATTATTGGGGAAAAAAAAAAG	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28018041	28018042	+	IGR	INS	-	T	T	rs150282831	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28018041_28018042insT								CDH9 (979352 upstream) : None (None downstream)																							tctcatatcacttttttttttg	0.000													3	4	---	---	---	---	
ERBB2IP	55914	broad.mit.edu	37	5	65274570	65274573	+	Intron	DEL	TAAT	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65274570_65274573delTAAT	uc003juk.1	+						ERBB2IP_uc003juh.1_Intron|ERBB2IP_uc003jui.1_Intron|ERBB2IP_uc003juj.1_Intron|ERBB2IP_uc011cqx.1_Intron|ERBB2IP_uc011cqy.1_Intron|ERBB2IP_uc011cqz.1_Intron	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2						basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		AAAAATCAAATAATTAAGCATGAT	0.422													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	107061613	107061635	+	IGR	DEL	CAGTGGGGACAATAAATAGGAAG	-	-	rs146006387	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107061613_107061635delCAGTGGGGACAATAAATAGGAAG								EFNA5 (55017 upstream) : FBXL17 (133105 downstream)																							AAGAACAGCTCAGTGGGGACAATAAATAGGAAGCTGGGGAACA	0.372													124	69	---	---	---	---	
SEMA6A	57556	broad.mit.edu	37	5	115803579	115803581	+	Intron	DEL	GTG	-	-	rs10551961		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115803579_115803581delGTG	uc010jck.2	-						SEMA6A_uc003krx.3_Intron|SEMA6A_uc003krv.3_5'UTR|SEMA6A_uc003krw.3_Intron|SEMA6A_uc010jcj.2_Intron	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		ACACGGCTTAgtggtggtggtgg	0.281													12	10	---	---	---	---	
PRDM6	93166	broad.mit.edu	37	5	122472556	122472557	+	Intron	INS	-	TG	TG	rs141615926	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122472556_122472557insTG	uc003kti.2	+						PRDM6_uc003ktj.2_Intron	NM_001136239	NP_001129711	Q9NQX0	PRDM6_HUMAN	PR domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding				0						CTGGCTGGCAATGTGCATGGGA	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124896803	124896804	+	IGR	DEL	AT	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124896803_124896804delAT								ZNF608 (812303 upstream) : GRAMD3 (798984 downstream)																							TTACACACACATATGAGTATGT	0.386													7	6	---	---	---	---	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139906281	139906282	+	Intron	INS	-	CTAA	CTAA	rs10636296		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139906281_139906282insCTAA	uc003lfs.1	+						ANKHD1_uc003lfr.2_Intron|ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1_uc003lfw.2_Intron|ANKHD1_uc010jfl.2_Intron|ANKHD1-EIF4EBP3_uc003lfx.1_5'Flank	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTGATTTTATCTATGTCATTT	0.267													10	5	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7240518	7240518	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7240518delT	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TCATTGATGGTTTTTTTTTTT	0.318													4	3	---	---	---	---	
DOPEY1	23033	broad.mit.edu	37	6	83862340	83862341	+	Intron	DEL	TT	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83862340_83862341delTT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron|DOPEY1_uc003pjt.2_Intron	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1						protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		tttctttttctttttttttttt	0.129													4	4	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90416123	90416124	+	Intron	INS	-	T	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90416123_90416124insT	uc003pnn.1	-							NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		cagattttcaattttttttttt	0.074													6	4	---	---	---	---	
KPNA5	3841	broad.mit.edu	37	6	117045743	117045746	+	Intron	DEL	TTTA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117045743_117045746delTTTA	uc003pxh.2	+							NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		TTACAATCTTTTTATTTATTTAGT	0.221													15	12	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	166952429	166952429	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166952429delT	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TGtttttttcttttttttttc	0.224													8	5	---	---	---	---	
C7orf50	84310	broad.mit.edu	37	7	1167234	1167234	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1167234delT	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726	Q9BRJ6	CG050_HUMAN	hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)		cctttctgtcttttttttttt	0.149													9	4	---	---	---	---	
SEPT7	989	broad.mit.edu	37	7	35904634	35904634	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35904634delT	uc010kxc.2	+						SEPT7_uc011kat.1_Intron|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_Intron|SEPT7_uc003tey.2_Intron	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1						cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0						TATTTTAGGATTTTTTTTTTT	0.274													15	10	---	---	---	---	
GBAS	2631	broad.mit.edu	37	7	56062938	56062938	+	Intron	DEL	A	-	-	rs34820247		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56062938delA	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474	O75323	NIPS2_HUMAN	nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCCATGGAAGAAGGAGGCCAG	0.493													16	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	74016919	74016919	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74016919delA								GTF2IRD1 (1 upstream) : GTF2I (55111 downstream)																							GTAAAAAAAGAAAAAAAAAAA	0.373													11	5	---	---	---	---	
PON1	5444	broad.mit.edu	37	7	94940479	94940479	+	Intron	DEL	G	-	-	rs77343187		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94940479delG	uc003uns.2	-						PON1_uc011kih.1_Intron	NM_000446	NP_000437	P27169	PON1_HUMAN	paraoxonase 1 precursor						aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)	TACTAAGTCTGGTTCTGAAGA	0.368													7	12	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126078884	126078884	+	3'UTR	DEL	T	-	-	rs34182595		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126078884delT	uc003vlr.2	-	10					GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_3'UTR|GRM8_uc010lkz.1_RNA	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	TTCAACAGCATTTTTTTTCAC	0.308										HNSCC(24;0.065)			16	20	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151531149	151531150	+	Intron	INS	-	A	A	rs138194213	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151531149_151531150insA	uc003wkk.2	-						PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		GTTTCTGGAGGAAAAAAAAAAT	0.490													12	8	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3165574	3165592	+	Intron	DEL	ATGTGATAATTCTAATAAT	-	-	rs11268389		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3165574_3165592delATGTGATAATTCTAATAAT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TAAGACACTCATGTGATAATTCTAATAATATGTGATAAT	0.338													4	4	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3977473	3977474	+	Intron	INS	-	A	A	rs145056751	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3977473_3977474insA	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		taataggtatcaaaaaaattag	0.074													6	4	---	---	---	---	
ERI1	90459	broad.mit.edu	37	8	8870531	8870532	+	Intron	INS	-	T	T	rs146429223	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8870531_8870532insT	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163	Q8IV48	ERI1_HUMAN	three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)	accattctcacttttttttttc	0.000													3	3	---	---	---	---	
KIAA1967	57805	broad.mit.edu	37	8	22477079	22477085	+	Intron	DEL	GCAGTCC	-	-	rs11277601		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22477079_22477085delGCAGTCC	uc003xch.2	+						KIAA1967_uc003xci.2_Intron|KIAA1967_uc003xcj.1_3'UTR	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein						apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		CCAGCAGGAGGCAGTCCGCAGTCCGCA	0.599													7	5	---	---	---	---	
EXTL3	2137	broad.mit.edu	37	8	28588314	28588315	+	Intron	INS	-	G	G	rs141340707	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28588314_28588315insG	uc003xgz.1	+							NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3							integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		GCGTTAGAATTGGGAGTCAGAA	0.416													3	6	---	---	---	---	
MTDH	92140	broad.mit.edu	37	8	98673139	98673140	+	Intron	INS	-	ATA	ATA	rs143868890	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98673139_98673140insATA	uc003yhz.2	+							NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			aaaCACTAGGGATAATCTATCA	0.282													21	13	---	---	---	---	
ARID3C	138715	broad.mit.edu	37	9	34625821	34625822	+	Intron	INS	-	GA	GA			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34625821_34625822insGA	uc011lon.1	-							NM_001017363	NP_001017363	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT- like)						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		GCTGGGGAAGGATTGGGGTCAT	0.406													110	103	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68417846	68417847	+	IGR	INS	-	T	T	rs149432770		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68417846_68417847insT								FAM27B (623657 upstream) : MIR1299 (584392 downstream)																							AGAACATGTGATTTTAAATCCA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420735	68420735	+	IGR	DEL	A	-	-	rs150487532		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420735delA								FAM27B (626546 upstream) : MIR1299 (581504 downstream)																							CAGGTGTTGCAGAAACTGGGC	0.363													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68494353	68494353	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68494353delA								FAM27B (700164 upstream) : MIR1299 (507886 downstream)																							ATTTGAGAGGAAAGCTGGTGC	0.383													3	3	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73409009	73409009	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73409009delT	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aie.2_Intron|TRPM3_uc004aif.2_Intron|TRPM3_uc004aig.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						GGATAGCAGATTTTTTTTTTT	0.303													4	2	---	---	---	---	
CENPP	401541	broad.mit.edu	37	9	95369491	95369492	+	Intron	INS	-	A	A	rs150950547	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95369491_95369492insA	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004asj.2_Intron	NM_001012267	NP_001012267	Q6IPU0	CENPP_HUMAN	centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2						ttgttttttttatcatgtgaat	0.020													1	7	---	---	---	---	
SMC2	10592	broad.mit.edu	37	9	106891784	106891784	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106891784delA	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_Intron	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						actccatctcaaaaaaaaaaa	0.114													14	8	---	---	---	---	
FKBP15	23307	broad.mit.edu	37	9	115930521	115930522	+	Intron	DEL	TA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115930521_115930522delTA	uc004bgs.2	-						FKBP15_uc004bgr.2_Intron|FKBP15_uc011lxc.1_Intron	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						GGACAGAGACTATGATTCTTTC	0.530													4	7	---	---	---	---	
FKBP15	23307	broad.mit.edu	37	9	115932150	115932151	+	In_Frame_Ins	INS	-	TTC	TTC	rs142392062	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115932150_115932151insTTC	uc004bgs.2	-	26	2956_2957	c.2838_2839insGAA	c.(2836-2841)insGAA	p.946_947insE	FKBP15_uc004bgr.2_In_Frame_Ins_p.383_384insE|FKBP15_uc011lxc.1_In_Frame_Ins_p.527_528insE|FKBP15_uc011lxd.1_In_Frame_Ins_p.878_879insE	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	946_947	Potential.				endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						tcttctgctttttcttcttctt	0.480													6	4	---	---	---	---	
OPTN	10133	broad.mit.edu	37	10	13154861	13154861	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13154861delT	uc001ilu.1	+						OPTN_uc001ilv.1_Intron|OPTN_uc001ilw.1_Intron|OPTN_uc001ilx.1_Intron|OPTN_uc001ily.1_Intron|OPTN_uc010qbr.1_Intron|OPTN_uc001ilz.1_Intron	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin						cell death|Golgi ribbon formation|Golgi to plasma membrane protein transport|protein targeting to Golgi|signal transduction	perinuclear region of cytoplasm|trans-Golgi network	protein C-terminus binding			ovary(2)	2						AGCTGTAGTCTTTTTTTTTTT	0.303													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47035930	47035931	+	Intron	DEL	CA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47035930_47035931delCA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						cataaatatccacacacacaca	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54391254	54391254	+	IGR	DEL	T	-	-	rs113267821		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54391254delT								DKK1 (313838 upstream) : MBL2 (133887 downstream)																							ctttccttacttttttttttc	0.000													4	2	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94239368	94239369	+	Intron	DEL	GT	-	-	rs3831274		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94239368_94239369delGT	uc001kia.2	-						IDE_uc010qnp.1_Intron|IDE_uc001khz.2_Intron	NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	gtgtgtgtgagtgtgtgtgtgt	0.317													8	4	---	---	---	---	
INPP5F	22876	broad.mit.edu	37	10	121583100	121583101	+	Intron	INS	-	A	A	rs76438649	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121583100_121583101insA	uc001leo.2	+						INPP5F_uc001lep.2_Intron	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AACAAACTTTTATTCCCCGATT	0.198													7	8	---	---	---	---	
NLRP14	338323	broad.mit.edu	37	11	7079850	7079855	+	Intron	DEL	TCTGGA	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7079850_7079855delTCTGGA	uc001mfb.1	+							NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		ctaactctactctggatcttgtttta	0.117													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30881963	30881964	+	Intron	INS	-	TTGTTT	TTGTTT	rs143609604	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30881963_30881964insTTGTTT	uc001mss.1	-											Homo sapiens mRNA for KIAA1493 protein, partial cds.																		TATTTTGGGGATTGTTTTTGTT	0.361													13	9	---	---	---	---	
PACSIN3	29763	broad.mit.edu	37	11	47208726	47208726	+	5'Flank	DEL	C	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47208726delC	uc001ndw.2	-						PACSIN3_uc001ndx.2_5'Flank|PACSIN3_uc001ndy.2_5'Flank|PACSIN3_uc001ndz.2_5'Flank|PACSIN3_uc001nea.2_5'Flank	NM_016223	NP_057307	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in						endocytosis|negative regulation of endocytosis|positive regulation of membrane protein ectodomain proteolysis	cytoplasm|plasma membrane	cytoskeletal protein binding				0						TAAATCCCTTCTCCCTCCTCT	0.537													6	5	---	---	---	---	
TMEM223	79064	broad.mit.edu	37	11	62558503	62558503	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62558503delT	uc001nve.2	-							NM_001080501	NP_001073970	A0PJW6	TM223_HUMAN	transmembrane protein 223							integral to membrane					0						TACTGAGCGCttttttttttg	0.264													8	4	---	---	---	---	
UCP3	7352	broad.mit.edu	37	11	73712720	73712721	+	Intron	INS	-	T	T	rs140851461	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73712720_73712721insT	uc001our.2	-							NM_003356	NP_003347	P55916	UCP3_HUMAN	uncoupling protein 3 isoform UCP3L						mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)					CTCTCTCTCTCTTTTTTTTTTC	0.356													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91379651	91379651	+	IGR	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91379651delT								MIR1261 (777281 upstream) : FAT3 (705611 downstream)																							CGAAACAAGCTTTTTTTTCCC	0.333													5	3	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99210643	99210644	+	Intron	INS	-	A	A	rs146793097	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99210643_99210644insA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		tcattttttagaaaaaaaaaat	0.000													2	4	---	---	---	---	
CHD4	1108	broad.mit.edu	37	12	6704291	6704291	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6704291delT	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						ATATACCTCCTTTTTTTTTTT	0.398													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	26326422	26326423	+	Intron	DEL	TT	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26326422_26326423delTT	uc001rhc.2	+											Homo sapiens cDNA clone IMAGE:5300499.																		TATCATGCTCTTTTTCTTTTTC	0.322													4	2	---	---	---	---	
ATP5B	506	broad.mit.edu	37	12	57038363	57038363	+	Intron	DEL	A	-	-	rs71642550		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57038363delA	uc001slr.2	-						SNORD59B_uc001sls.1_5'Flank	NM_001686	NP_001677	P06576	ATPB_HUMAN	mitochondrial ATP synthase beta subunit						angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1						ACTCCCTCTCAAAAAAAAAAA	0.194													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77076252	77076252	+	IGR	DEL	T	-	-	rs11370356		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77076252delT								OSBPL8 (122663 upstream) : ZDHHC17 (81602 downstream)																							ACAAAATTAAttttttttttt	0.184													6	4	---	---	---	---	
TMEM120B	144404	broad.mit.edu	37	12	122181462	122181462	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122181462delA	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294	A0PK00	T120B_HUMAN	transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		agactctctcaaaaaaaaaaa	0.224													9	4	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49034091	49034091	+	Intron	DEL	C	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49034091delC	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ctttctttttctttctttctt	0.070		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			13	9	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49034095	49034096	+	Intron	INS	-	T	T	rs68126210		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49034095_49034096insT	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ctttttctttctttctttctct	0.059		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79668173	79668173	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79668173delA								RNF219 (433473 upstream) : RBM26 (225927 downstream)																							gtatagtaataaaaaaaaaaG	0.154													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103622562	103622562	+	IGR	DEL	A	-	-	rs71721729		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103622562delA								LOC121952 (74179 upstream) : SLC10A2 (73788 downstream)																							AGCATGGGTGAAAAAAAGTGA	0.428													4	3	---	---	---	---	
GZMB	3002	broad.mit.edu	37	14	25101878	25101879	+	Intron	INS	-	T	T	rs144943417	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25101878_25101879insT	uc001wps.2	-						GZMB_uc010ama.2_Intron|GZMB_uc010amb.2_Intron	NM_004131	NP_004122	P10144	GRAB_HUMAN	granzyme B precursor						activation of pro-apoptotic gene products|cleavage of lamin|cytolysis|induction of apoptosis by intracellular signals	cytosol|immunological synapse|nucleus	protein binding|serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.028)		AGTTTGTATTCTATGCCAAAGT	0.495													5	9	---	---	---	---	
ATG2B	55102	broad.mit.edu	37	14	96772871	96772872	+	Intron	INS	-	AGG	AGG	rs147920063	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96772871_96772872insAGG	uc001yfi.2	-							NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B											ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TCTGAGTCTTTAGATGTGTCAC	0.277													3	11	---	---	---	---	
ADAM10	102	broad.mit.edu	37	15	58936414	58936414	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58936414delT	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		TTCTTTGCGGTTttttttttt	0.199													4	2	---	---	---	---	
MTFMT	123263	broad.mit.edu	37	15	65319541	65319541	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65319541delT	uc002aof.3	-							NM_139242	NP_640335	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)	tttctttttcttttttttttt	0.139													4	4	---	---	---	---	
GNPTG	84572	broad.mit.edu	37	16	1404194	1404195	+	Intron	DEL	TG	-	-	rs150776261		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1404194_1404195delTG	uc002clm.2	+						C16orf42_uc002cll.2_5'Flank	NM_032520	NP_115909	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphotransferase, gamma							extracellular region|Golgi apparatus	protein binding			central_nervous_system(1)	1		Hepatocellular(780;0.0893)				GGCAGGCCACTGTGTAACAGCG	0.599													21	22	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12657064	12657065	+	Intron	INS	-	TC	TC	rs10676403		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12657064_12657065insTC	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						CATGCTGGGATTGAGGCTCATA	0.584													4	3	---	---	---	---	
RPS15A	6210	broad.mit.edu	37	16	18796196	18796196	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18796196delA	uc002dfh.1	-						RPS15A_uc002dfi.1_Intron|RPS15A_uc002dfj.1_Intron|RPS15A_uc002dfk.1_Intron	NM_001019	NP_001010	P62244	RS15A_HUMAN	ribosomal protein S15a						endocrine pancreas development|positive regulation of cell cycle|positive regulation of cell proliferation|response to virus|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0						CCAATAACAGAAAAACTGAGT	0.383													70	41	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32152597	32152597	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32152597delA								ZNF267 (223971 upstream) : HERC2P4 (10013 downstream)																							TAAGGCACATAATGAGCAATT	0.318													7	6	---	---	---	---	
VPS35	55737	broad.mit.edu	37	16	46714944	46714945	+	Intron	INS	-	AC	AC	rs148688318	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46714944_46714945insAC	uc002eef.3	-						VPS35_uc002eed.2_5'Flank|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AAAAAAACTATacacacacaca	0.223													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55005874	55005875	+	IGR	DEL	TC	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55005874_55005875delTC								IRX5 (37481 upstream) : IRX6 (352596 downstream)																							tttctttctttctctctttctt	0.000													7	7	---	---	---	---	
CENPN	55839	broad.mit.edu	37	16	81053508	81053508	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81053508delT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094	Q96H22	CENPN_HUMAN	centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0						CTGAAAAGGATTTTTTTTTTT	0.174													6	3	---	---	---	---	
SPNS3	201305	broad.mit.edu	37	17	4350374	4350375	+	Intron	DEL	GT	-	-	rs3055435		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4350374_4350375delGT	uc002fxt.2	+						SPNS3_uc002fxu.2_Intron	NM_182538	NP_872344	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3						lipid transport|transmembrane transport	integral to membrane				large_intestine(1)	1						GGGACGGGGGGTGGTGGTCAGG	0.450													12	6	---	---	---	---	
ELAC2	60528	broad.mit.edu	37	17	12908601	12908606	+	Intron	DEL	GTAACT	-	-	rs10532461		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12908601_12908606delGTAACT	uc002gnz.3	-						ELAC2_uc002gnv.3_5'Flank|ELAC2_uc002gnw.3_5'Flank|ELAC2_uc002gnx.3_Intron|ELAC2_uc010vvo.1_Intron|ELAC2_uc010vvp.1_Intron|ELAC2_uc010vvq.1_Intron|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1						tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						ACCTAAACAGGTAACTGTCAGGTTGA	0.466									Hereditary_Prostate_Cancer				10	11	---	---	---	---	
LGALS9C	654346	broad.mit.edu	37	17	18387617	18387617	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18387617delA	uc002gtw.2	+						LGALS9C_uc010vyb.1_Intron	NM_001040078	NP_001035167	Q6DKI2	LEG9C_HUMAN	galectin 9 like								sugar binding			ovary(1)	1						tccgtttcccataactgctct	0.154													4	4	---	---	---	---	
ARHGAP23	57636	broad.mit.edu	37	17	36642474	36642474	+	Intron	DEL	T	-	-	rs113594815		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36642474delT	uc010wdp.1	+						ARHGAP23_uc002hqc.2_Intron	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23						signal transduction	intracellular	GTPase activator activity			lung(1)	1						GGttttactcttttttttttt	0.264													7	6	---	---	---	---	
HSF5	124535	broad.mit.edu	37	17	56554230	56554230	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56554230delT	uc002iwi.1	-							NM_001080439	NP_001073908	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTCTTGCTGTTTTTTTTTTC	0.428													8	4	---	---	---	---	
RGS9	8787	broad.mit.edu	37	17	63186049	63186049	+	Intron	DEL	T	-	-	rs112552969		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63186049delT	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron|RGS9_uc002jfg.2_Intron	NM_003835	NP_003826	O75916	RGS9_HUMAN	regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4						TCCTTAGAACTTTTTTTTTTT	0.483													7	5	---	---	---	---	
HGS	9146	broad.mit.edu	37	17	79667398	79667398	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79667398delA	uc002kbg.2	+							NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			actccatctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
ZFP161	7541	broad.mit.edu	37	18	5290766	5290769	+	3'UTR	DEL	CCAC	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5290766_5290769delCCAC	uc002kmq.2	-	4					ZFP161_uc002kmr.2_3'UTR|ZFP161_uc010dkp.2_3'UTR	NM_003409	NP_003400	O43829	ZF161_HUMAN	zinc finger protein 161 homolog						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CCATACGTTTCCACAAAAATATTG	0.441													2	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8954062	8954062	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8954062delA								MBD3L1 (46 upstream) : MUC16 (5459 downstream)																							GCCAATACTTAAAAAAAAAAA	0.269													4	2	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17993148	17993148	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17993148delT	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						CACTTCTATGttttttttttt	0.100													4	2	---	---	---	---	
TSHZ3	57616	broad.mit.edu	37	19	31770731	31770731	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31770731delA	uc002nsy.3	-							NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537						negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					ggagagaaagaaaaaaaaaaG	0.284													9	5	---	---	---	---	
C19orf54	284325	broad.mit.edu	37	19	41255310	41255310	+	Intron	DEL	C	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41255310delC	uc002oou.1	-						C19orf54_uc002oow.1_Intron|C19orf54_uc002oox.1_Intron|C19orf54_uc002ooy.1_Intron|C19orf54_uc010xvs.1_Intron|SNRPA_uc002ooz.2_5'Flank	NM_198476	NP_940878	Q5BKX5	CS054_HUMAN	hypothetical protein LOC284325												0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GACACGGGAACCCCCCCCCCA	0.572													15	9	---	---	---	---	
CCDC9	26093	broad.mit.edu	37	19	47770228	47770228	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47770228delT	uc010xym.1	+							NM_015603	NP_056418	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9												0		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		tctggttttcttttttttttt	0.239													5	5	---	---	---	---	
NUCB1	4924	broad.mit.edu	37	19	49414663	49414664	+	Intron	DEL	TT	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49414663_49414664delTT	uc002plb.3	+						NUCB1_uc002pla.2_Intron|NUCB1_uc002plc.2_Intron	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1 precursor							ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		ttttcttttctttttttttttt	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9000244	9000245	+	IGR	DEL	TT	-	-	rs10533993		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9000244_9000245delTT								PLCB1 (134699 upstream) : PLCB4 (49456 downstream)																							AGTTCCTCTCTTTATTTGTTTT	0.381													2	5	---	---	---	---	
TASP1	55617	broad.mit.edu	37	20	13568226	13568226	+	Intron	DEL	C	-	-	rs146633280		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13568226delC	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron|TASP1_uc010zrj.1_Intron	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0						accaaaaaaacatcaaagaaa	0.000													16	10	---	---	---	---	
NCOA6	23054	broad.mit.edu	37	20	33302801	33302803	+	3'UTR	DEL	CAT	-	-	rs138237168	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33302801_33302803delCAT	uc002xav.2	-	16					NCOA6_uc002xaw.2_3'UTR	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6						brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7						CGGCACAATACATCATTAGGAGA	0.350													8	5	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40820172	40820172	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40820172delT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCAAAAGAGATTTTGAGCAGA	0.498													4	2	---	---	---	---	
SERINC3	10955	broad.mit.edu	37	20	43135292	43135293	+	Intron	DEL	AT	-	-	rs35788400		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43135292_43135293delAT	uc002xme.2	-						SERINC3_uc002xmf.1_Intron|SERINC3_uc010ggs.1_Intron|SERINC3_uc010zwp.1_Intron	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1							integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			TTTTTTAATGATAGTGAAATTC	0.168													13	16	---	---	---	---	
TP53TG5	27296	broad.mit.edu	37	20	44006414	44006414	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44006414delA	uc002xny.2	-						SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein						intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1						tgactctaccaaaaaaaaaaa	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53294071	53294072	+	IGR	INS	-	G	G	rs140274215	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53294071_53294072insG								DOK5 (26362 upstream) : None (None downstream)																							cctaggggagagggtggcagcc	0.074													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10715466	10715466	+	IGR	DEL	A	-	-	rs145593257		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10715466delA								None (None upstream) : TPTE (191277 downstream)																							tgcagatcctaaaaaaagact	0.000													8	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11093134	11093135	+	Intron	INS	-	C	C	rs141935972		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11093134_11093135insC	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GTTCTCCCCTACCCCCCACAAC	0.401													4	2	---	---	---	---	
ETS2	2114	broad.mit.edu	37	21	40184706	40184708	+	Intron	DEL	AAT	-	-	rs66814912		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40184706_40184708delAAT	uc002yxg.2	+						ETS2_uc002yxf.2_Intron	NM_005239	NP_005230	P15036	ETS2_HUMAN	v-ets erythroblastosis virus E26 oncogene						positive regulation of transcription, DNA-dependent|skeletal system development	nucleus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)|pancreas(1)	4		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				cctgtctcaaaaTAATAATAATA	0.153													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	38426471	38426472	+	IGR	INS	-	C	C	rs143271740	by1000genomes	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38426471_38426472insC								POLR2F (42130 upstream) : PICK1 (26790 downstream)																							gctctcgggagccagtgtgcgc	0.193													4	2	---	---	---	---	
FAM116B	414918	broad.mit.edu	37	22	50751548	50751548	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50751548delA	uc011aru.1	-						FAM116B_uc011arv.1_Intron	NM_001001794	NP_001001794	Q8NEG7	F116B_HUMAN	family with sequence similarity 116, member B												0		all_cancers(38;4.34e-09)|all_epithelial(38;3.03e-08)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTGAGAGGGGATGGGTGAGCC	0.652													19	15	---	---	---	---	
GYG2	8908	broad.mit.edu	37	X	2774786	2774793	+	Intron	DEL	TATCTATG	-	-	rs80318590		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2774786_2774793delTATCTATG	uc004cqs.1	+						GYG2_uc004cqt.1_Intron|GYG2_uc004cqu.1_Intron|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Intron|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909	O15488	GLYG2_HUMAN	glycogenin 2 isoform b						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				atcatctatctatctatgtatctatcta	0.231													3	3	---	---	---	---	
CDKL5	6792	broad.mit.edu	37	X	18616437	18616437	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18616437delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)					ttagatagtcttttttttttt	0.020													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	35041277	35041277	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35041277delA								FAM47B (78243 upstream) : MAGEB16 (775182 downstream)																							atatagggttaaaaaaaaaaa	0.000													6	3	---	---	---	---	
PCDH19	57526	broad.mit.edu	37	X	99578759	99578759	+	Intron	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99578759delA	uc010nmz.2	-						PCDH19_uc004efw.3_Intron|PCDH19_uc004efx.3_Intron	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						ACTAAAACCCAAAAAAAAAAT	0.308													4	2	---	---	---	---	
XIAP	331	broad.mit.edu	37	X	123022776	123022776	+	Intron	DEL	T	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123022776delT	uc010nqu.2	+						XIAP_uc004etx.2_Intron|XIAP_uc010nqv.2_Intron	NM_001167	NP_001158	P98170	XIAP_HUMAN	baculoviral IAP repeat-containing protein 4						anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus	cytosol	caspase inhibitor activity|ligase activity|protein binding|zinc ion binding			ovary(1)|lung(1)	2						AGATTATCCCttttttttttt	0.169									X-linked_Lymphoproliferative_syndrome				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	140757920	140757920	+	IGR	DEL	A	-	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140757920delA								SPANXC (85060 upstream) : SPANXE (27649 downstream)																							CCAAAAAATGAAAAAAAAAAT	0.299													4	2	---	---	---	---	
HSFX2	100130086	broad.mit.edu	37	X	148685933	148685948	+	Intron	DEL	CTGCTGCCTTGCCCCT	-	-	rs72102447		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148685933_148685948delCTGCTGCCTTGCCCCT	uc004fdl.2	-						HSFX1_uc004fdm.2_Intron|TMEM185A_uc011mxp.1_Intron|TMEM185A_uc004fdo.2_Intron|TMEM185A_uc011mxq.1_Intron|TMEM185A_uc004fdp.3_Intron	NM_016153	NP_057237	Q9UBD0	HSFX1_HUMAN	heat shock transcription factor family, X linked							cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GGGGCTCAGCCTGCTGCCTTGCCCCTCTGCTGCCTT	0.528													8	5	---	---	---	---	
