Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MACF1	23499	broad.mit.edu	37	1	39798958	39798958	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:39798958C>T	uc010oiu.1	+	1	2149	c.2018C>T	c.(2017-2019)ACA>ATA	p.T673I	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	2238					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTAAAGAAAACATTTCTGGCT	0.383													4	42	---	---	---	---	PASS
ZMYND12	84217	broad.mit.edu	37	1	42898960	42898960	+	Splice_Site	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:42898960C>A	uc001chj.2	-	7	1100	c.830_splice	c.e7-1	p.D277_splice	ZMYND12_uc010ojt.1_Splice_Site_p.D167_splice	NM_032257	NP_115633	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12 isoform 1							intracellular	zinc ion binding			ovary(1)	1	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGGGCTTCATCTGCATTGGAA	0.463													6	107	---	---	---	---	PASS
C1orf168	199920	broad.mit.edu	37	1	57257917	57257917	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:57257917C>T	uc001cym.3	-	2	975	c.569G>A	c.(568-570)GGA>GAA	p.G190E	C1orf168_uc009vzu.1_RNA|C1orf168_uc009vzv.1_Missense_Mutation_p.G190E	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920	190										ovary(3)|skin(2)	5						AGTCTGGGCTCCTTTTGTTTC	0.463													7	96	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86252091	86252091	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:86252091T>C	uc001dlj.2	-	48	4047	c.4005A>G	c.(4003-4005)CCA>CCG	p.P1335P	COL24A1_uc001dli.2_Silent_p.P471P|COL24A1_uc010osd.1_Silent_p.P635P|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	1335	Collagen-like 15.				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)		CCTTTACTCCTGGAGGACCTG	0.468													15	80	---	---	---	---	PASS
REG4	83998	broad.mit.edu	37	1	120342441	120342441	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:120342441G>T	uc001eig.2	-	5	650	c.210C>A	c.(208-210)ATC>ATA	p.I70I	REG4_uc001eif.2_Silent_p.I70I	NM_001159352	NP_001152824	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	70	C-type lectin.					extracellular region	sugar binding			ovary(1)	1	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		TTAAACTCAGGATAGATGCCA	0.498													12	130	---	---	---	---	PASS
ADAM30	11085	broad.mit.edu	37	1	120437090	120437090	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:120437090C>T	uc001eij.2	-	1	2024	c.1870G>A	c.(1870-1872)GTC>ATC	p.V624I		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	624	Cys-rich.|Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		GAGCTATTGACGCAATTTTTT	0.453													5	58	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181686390	181686390	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:181686390G>A	uc001gow.2	+	11	1642	c.1477G>A	c.(1477-1479)GTG>ATG	p.V493M	CACNA1E_uc009wxs.2_Missense_Mutation_p.V400M	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	493	Helical; Name=S1 of repeat II.|II.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						CACTGCCTGTGTGGCCATTGT	0.547													11	60	---	---	---	---	PASS
CFHR3	10878	broad.mit.edu	37	1	196748418	196748418	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:196748418C>A	uc001gtl.2	+	2	272	c.185C>A	c.(184-186)CCT>CAT	p.P62H	CFHR3_uc001gtk.2_Missense_Mutation_p.P62H|CFHR3_uc010poy.1_Missense_Mutation_p.P62H|CFHR1_uc001gtm.2_Missense_Mutation_p.P25H	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	62	Sushi 1.					extracellular space					0						TTTGAGACTCCTTCAGGAAGT	0.393													6	36	---	---	---	---	PASS
F13B	2165	broad.mit.edu	37	1	197024916	197024916	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:197024916T>A	uc001gtt.1	-	8	1327	c.1283A>T	c.(1282-1284)TAT>TTT	p.Y428F		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	428	Sushi 7.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CAGTAAGTAATATTCATTGCA	0.423													4	61	---	---	---	---	PASS
C1orf53	388722	broad.mit.edu	37	1	197874996	197874996	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:197874996G>A	uc001guh.2	+	2	433	c.335G>A	c.(334-336)AGA>AAA	p.R112K		NM_001024594	NP_001019765	Q5VUE5	CA053_HUMAN	hypothetical protein LOC388722	112											0						CACTTGCAAAGAGGTGAATGT	0.438													9	93	---	---	---	---	PASS
PIGR	5284	broad.mit.edu	37	1	207104843	207104843	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:207104843C>G	uc001hez.2	-	10	2382	c.2198G>C	c.(2197-2199)AGG>ACG	p.R733T	PIGR_uc009xbz.2_Missense_Mutation_p.R733T	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor precursor	733	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CCTCCTCACCCTTTTTGCCTT	0.343													5	74	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216166446	216166446	+	Missense_Mutation	SNP	G	T	T	rs111033412		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:216166446G>T	uc001hku.1	-	35	7108	c.6721C>A	c.(6721-6723)CCC>ACC	p.P2241T		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2241	Fibronectin type-III 9.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACGCCTTCGGGTATGTCCTCG	0.507										HNSCC(13;0.011)	OREG0014251	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	104	---	---	---	---	PASS
TGFB2	7042	broad.mit.edu	37	1	218610736	218610736	+	Missense_Mutation	SNP	G	T	T	rs147678881		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:218610736G>T	uc001hlm.2	+	6	1637	c.984G>T	c.(982-984)AGG>AGT	p.R328S	TGFB2_uc001hln.2_Missense_Mutation_p.R356S|TGFB2_uc010pue.1_RNA|TGFB2_uc001hlo.2_RNA	NM_003238	NP_003229	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 2	328					activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		ATTTCAAGAGGGATCTAGGGT	0.408													4	80	---	---	---	---	PASS
COG2	22796	broad.mit.edu	37	1	230798897	230798897	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:230798897C>T	uc001htw.2	+	4	462	c.311C>T	c.(310-312)TCG>TTG	p.S104L	COG2_uc001htx.2_Missense_Mutation_p.S104L|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	104					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGCCTTAGATCGTCTGTCAGT	0.308													4	27	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112224	248112224	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:248112224T>A	uc001idt.1	+	1	65	c.65T>A	c.(64-66)ATT>AAT	p.I22N	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CCATCAAGAATTGACCTTTTC	0.398													11	144	---	---	---	---	PASS
PGBD2	267002	broad.mit.edu	37	1	249212547	249212547	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr1:249212547G>T	uc001ifh.2	+	3	1911	c.1764G>T	c.(1762-1764)GAG>GAT	p.E588D	PGBD2_uc001ifg.2_Missense_Mutation_p.E337D|PGBD2_uc009xhd.2_Missense_Mutation_p.E585D	NM_170725	NP_733843	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	588										ovary(1)	1	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GCTTCAGGGAGTACCACATCC	0.488													8	65	---	---	---	---	PASS
SH3YL1	26751	broad.mit.edu	37	2	233210	233210	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:233210C>A	uc002qvx.2	-	6	508	c.424G>T	c.(424-426)GCC>TCC	p.A142S	SH3YL1_uc002qvy.2_Missense_Mutation_p.A142S|SH3YL1_uc002qvz.2_RNA|SH3YL1_uc002qwa.2_RNA|SH3YL1_uc010ewe.2_Missense_Mutation_p.A46S|SH3YL1_uc002qvu.2_RNA|SH3YL1_uc002qvv.2_Missense_Mutation_p.A46S|SH3YL1_uc002qvw.2_RNA	NM_015677	NP_056492	Q96HL8	SH3Y1_HUMAN	SH3 domain containing, Ysc84-like 1 isoform 1	142										ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		CTTCTCAGGGCCACGTTTCCT	0.483													3	12	---	---	---	---	PASS
ADCY3	109	broad.mit.edu	37	2	25045432	25045432	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:25045432G>A	uc002rfs.3	-	18	3150	c.2951C>T	c.(2950-2952)GCT>GTT	p.A984V	ADCY3_uc002rfr.3_Missense_Mutation_p.A571V|ADCY3_uc010ykm.1_Missense_Mutation_p.A985V	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	984	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GACTCCTGAAGCCGCCATATA	0.537													9	64	---	---	---	---	PASS
FAM179A	165186	broad.mit.edu	37	2	29245097	29245097	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:29245097C>A	uc010ezl.2	+	11	1785	c.1434C>A	c.(1432-1434)GCC>GCA	p.A478A	FAM179A_uc010ymm.1_Silent_p.A423A|FAM179A_uc002rmr.3_Silent_p.A5A	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	478							binding			ovary(3)|skin(1)	4						ATCTTAGAGCCTGTAAGGAGT	0.542													4	62	---	---	---	---	PASS
GALNT14	79623	broad.mit.edu	37	2	31178795	31178795	+	Missense_Mutation	SNP	C	T	T	rs150208592		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:31178795C>T	uc002rnr.2	-	5	1134	c.515G>A	c.(514-516)CGC>CAC	p.R172H	GALNT14_uc002rnq.2_Missense_Mutation_p.R152H|GALNT14_uc002rns.2_Missense_Mutation_p.R177H|GALNT14_uc010ymr.1_Missense_Mutation_p.R137H|GALNT14_uc010ezo.1_Missense_Mutation_p.R139H|GALNT14_uc010ezp.1_Missense_Mutation_p.R143H	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	172	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					TTCATTATTGCGCAAGCATTT	0.527													6	185	---	---	---	---	PASS
POLE4	56655	broad.mit.edu	37	2	75187240	75187240	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:75187240A>G	uc002snf.2	+	3	339	c.307A>G	c.(307-309)ATA>GTA	p.I103V		NM_019896	NP_063949	Q9NR33	DPOE4_HUMAN	DNA-directed DNA polymerase epsilon 4	103					histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex	DNA-directed DNA polymerase activity|protein binding|sequence-specific DNA binding				0						AGATAATGCAATAGAAGCTGT	0.438													11	92	---	---	---	---	PASS
CNGA3	1261	broad.mit.edu	37	2	99013218	99013218	+	Missense_Mutation	SNP	G	T	T	rs104893619		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:99013218G>T	uc002syt.2	+	8	2002	c.1585G>T	c.(1585-1587)GTG>TTG	p.V529L	CNGA3_uc002syu.2_Missense_Mutation_p.V511L|CNGA3_uc010fij.2_Missense_Mutation_p.V533L	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	529	cGMP.		V -> M (in ACHM2).		signal transduction|visual perception	integral to membrane	cGMP binding	p.V529M(1)		ovary(5)|upper_aerodigestive_tract(1)	6						CAAGCTGGCCGTGGTGGCTGA	0.552													9	75	---	---	---	---	PASS
SMPD4	55627	broad.mit.edu	37	2	130918802	130918802	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:130918802T>C	uc002tqq.1	-	11	1545	c.1025A>G	c.(1024-1026)TAC>TGC	p.Y342C	SMPD4_uc002tqp.1_Missense_Mutation_p.Y35C|SMPD4_uc010yzy.1_Intron|SMPD4_uc010yzz.1_Intron|SMPD4_uc002tqr.1_Intron|SMPD4_uc002tqs.1_Missense_Mutation_p.Y210C|SMPD4_uc002tqt.1_Intron|SMPD4_uc010zaa.1_Intron|SMPD4_uc010zab.1_Intron|SMPD4_uc010zac.1_Missense_Mutation_p.T56A|SMPD4_uc010zad.1_Intron	NM_017951	NP_060421	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4 isoform 2	303					sphingomyelin catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|trans-Golgi network	metal ion binding|protein binding|sphingomyelin phosphodiesterase activity|sphingomyelin phosphodiesterase D activity				0	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GGCGGGGCTGTAGAGGGCGCT	0.582													6	73	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168104927	168104927	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:168104927C>A	uc002udx.2	+	8	7043	c.7025C>A	c.(7024-7026)CCA>CAA	p.P2342Q	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.P2167Q|XIRP2_uc010fpq.2_Missense_Mutation_p.P2120Q|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2167	Pro-rich.				actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						GAAAGTTTTCCAGGCCTCCCT	0.463													10	113	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179480100	179480100	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:179480100A>G	uc010zfg.1	-	208	41092	c.40868T>C	c.(40867-40869)ATA>ACA	p.I13623T	uc002ump.1_RNA|TTN_uc010zfh.1_Missense_Mutation_p.I7318T|TTN_uc010zfi.1_Missense_Mutation_p.I7251T|TTN_uc010zfj.1_Missense_Mutation_p.I7126T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14550							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)			TCTTTCAACTATATATCCTTT	0.403													14	95	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179586757	179586757	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:179586757G>A	uc010zfg.1	-	75	19125	c.18901C>T	c.(18901-18903)CGA>TGA	p.R6301*	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Nonsense_Mutation_p.R2962*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7228							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)			CAAGTGATTCGCATCGGTTGA	0.408													8	148	---	---	---	---	PASS
COL5A2	1290	broad.mit.edu	37	2	189904261	189904261	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:189904261C>G	uc002uqk.2	-	51	3937	c.3662G>C	c.(3661-3663)GGC>GCC	p.G1221A	COL5A2_uc010frx.2_Missense_Mutation_p.G797A	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	1221					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			ACCCGGAGGGCCAGGTGGGCC	0.478													3	16	---	---	---	---	PASS
MYO1B	4430	broad.mit.edu	37	2	192206227	192206227	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:192206227T>C	uc010fsg.2	+	5	642	c.387T>C	c.(385-387)TGT>TGC	p.C129C	MYO1B_uc002usq.2_Silent_p.C129C|MYO1B_uc002usr.2_Silent_p.C129C|MYO1B_uc002uss.1_Silent_p.C129C	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1	129	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			CAGCTGTTTGTGGAAAAGGAG	0.393													7	61	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209217385	209217385	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:209217385C>T	uc002vcz.2	+	39	5881	c.5723C>T	c.(5722-5724)ACG>ATG	p.T1908M		NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1908	Catalytic.|PIPK.				cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						TAGAGGCCCACGGCGTTGGCC	0.328													8	47	---	---	---	---	PASS
UNC80	285175	broad.mit.edu	37	2	210642091	210642091	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:210642091C>G	uc010zjc.1	+	4	488	c.408C>G	c.(406-408)GAC>GAG	p.D136E	UNC80_uc002vdj.1_Missense_Mutation_p.D136E	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	136						integral to membrane					0						GGGGTACAGACCGAGGCTCCA	0.547													6	53	---	---	---	---	PASS
KCNE4	23704	broad.mit.edu	37	2	223917594	223917594	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:223917594G>T	uc002vnl.3	+	2	200	c.46G>T	c.(46-48)GCC>TCC	p.A16S		NM_080671	NP_542402	Q8WWG9	KCNE4_HUMAN	potassium voltage-gated channel, Isk-related	16						integral to membrane	voltage-gated potassium channel activity			ovary(1)	1		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)		CGGCACCGCCGCCTCCAGCAG	0.617													8	53	---	---	---	---	PASS
INPP5D	3635	broad.mit.edu	37	2	234102535	234102535	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr2:234102535G>T	uc010zmo.1	+	22	2677	c.2524G>T	c.(2524-2526)GAG>TAG	p.E842*	INPP5D_uc010zmp.1_Nonsense_Mutation_p.E841*	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	842					apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CCACCATGGGGAGTTGACAGG	0.617													5	42	---	---	---	---	PASS
CNTN6	27255	broad.mit.edu	37	3	1269556	1269556	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:1269556G>A	uc003boz.2	+	4	504	c.237G>A	c.(235-237)TTG>TTA	p.L79L	CNTN6_uc010hbo.2_Silent_p.L74L|CNTN6_uc011asj.1_Silent_p.L7L|CNTN6_uc003bpa.2_Silent_p.L79L	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	79	Ig-like C2-type 1.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		ACTACAGGTTGGATGGAGGCA	0.413													7	70	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	2942484	2942484	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:2942484T>A	uc003bpc.2	+	10	1277	c.1056T>A	c.(1054-1056)AAT>AAA	p.N352K	CNTN4_uc003bpb.1_Missense_Mutation_p.N24K|CNTN4_uc003bpd.1_Missense_Mutation_p.N352K|CNTN4_uc003bpe.2_Missense_Mutation_p.N24K|CNTN4_uc003bpf.2_Missense_Mutation_p.N24K	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	352	Ig-like C2-type 4.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GGCTAAAAAATGGCGAACCTC	0.393													3	51	---	---	---	---	PASS
ITPR1	3708	broad.mit.edu	37	3	4725142	4725142	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:4725142G>T	uc003bqa.2	+	27	3555	c.3207G>T	c.(3205-3207)ACG>ACT	p.T1069T	ITPR1_uc010hca.1_Silent_p.T1054T|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_5'UTR	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	1078	Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TCCACTTGACGATGCATGACT	0.602													15	73	---	---	---	---	PASS
DPPA4	55211	broad.mit.edu	37	3	109049432	109049432	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:109049432C>T	uc003dxq.3	-	5	673	c.618G>A	c.(616-618)TGG>TGA	p.W206*	DPPA4_uc011bho.1_Intron|DPPA4_uc011bhp.1_Nonsense_Mutation_p.W206*	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	206						nucleus	protein binding			upper_aerodigestive_tract(1)	1						AAATTCTCGCCCAGGAGGCCA	0.562													4	66	---	---	---	---	PASS
GRK7	131890	broad.mit.edu	37	3	141535837	141535837	+	Missense_Mutation	SNP	C	A	A	rs67254707		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:141535837C>A	uc011bnd.1	+	4	1691	c.1607C>A	c.(1606-1608)CCT>CAT	p.P536H		NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN	G-protein-coupled receptor kinase 7 precursor	536					visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						CCCAACAGACCTACGGGTTGT	0.458													8	96	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164716462	164716462	+	Splice_Site	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:164716462C>T	uc003fei.2	-	38	4469	c.4407_splice	c.e38-1	p.D1469_splice		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase						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)	CTGCAATGCACTAATATAGTA	0.338										HNSCC(35;0.089)			4	44	---	---	---	---	PASS
SERPINI1	5274	broad.mit.edu	37	3	167508224	167508224	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:167508224G>T	uc003ffa.3	+	3	513	c.315G>T	c.(313-315)GTG>GTT	p.V105V	SERPINI1_uc003ffb.3_Silent_p.V105V	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor	105					central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						GCCAATATGTGATGAAAATTG	0.318													4	68	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173996989	173996989	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:173996989G>T	uc003fio.1	+	6	1621	c.1198G>T	c.(1198-1200)GTA>TTA	p.V400L	NLGN1_uc010hww.1_Missense_Mutation_p.V440L|NLGN1_uc003fip.1_Missense_Mutation_p.V400L	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	417	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TGAAAATATAGTAGATAGCGA	0.353													15	73	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	182933804	182933804	+	Nonsense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:182933804T>A	uc003fli.1	-	22	2539	c.2449A>T	c.(2449-2451)AAG>TAG	p.K817*		NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	817	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TCACAGGACTTGATCAAATCC	0.448													21	74	---	---	---	---	PASS
DVL3	1857	broad.mit.edu	37	3	183884310	183884310	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:183884310G>T	uc003fms.2	+	9	1120	c.980G>T	c.(979-981)GGG>GTG	p.G327V	DVL3_uc011bqw.1_Missense_Mutation_p.G327V|DVL3_uc003fmt.2_Intron|DVL3_uc003fmu.2_Missense_Mutation_p.G159V	NM_004423	NP_004414	Q92997	DVL3_HUMAN	dishevelled 3	327					canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent	cytoplasm	beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity			ovary(1)|lung(1)|breast(1)	3	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			CACAAACCGGGGTATGGATGG	0.542													12	64	---	---	---	---	PASS
EPHB3	2049	broad.mit.edu	37	3	184298229	184298229	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr3:184298229A>T	uc003foz.2	+	12	2649	c.2212A>T	c.(2212-2214)ATG>TTG	p.M738L		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	738	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GCTGGTGGGCATGTTGCGGGG	0.597													13	65	---	---	---	---	PASS
HTRA3	94031	broad.mit.edu	37	4	8307739	8307739	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:8307739G>A	uc003gla.2	+	9	1442	c.1238G>A	c.(1237-1239)GGG>GAG	p.G413E		NM_053044	NP_444272	P83110	HTRA3_HUMAN	HtrA serine peptidase 3 precursor	413	PDZ.				proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity			ovary(1)	1						AAGGTCAACGGGCGTCCTCTA	0.642													4	60	---	---	---	---	PASS
LGI2	55203	broad.mit.edu	37	4	25005391	25005391	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:25005391G>T	uc003grf.2	-	8	1419	c.1320C>A	c.(1318-1320)ATC>ATA	p.I440I		NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	440	EAR 5.					extracellular region					0		Breast(46;0.173)				GGGAGTCCCCGATGAAGCGGG	0.537													14	155	---	---	---	---	PASS
GRXCR1	389207	broad.mit.edu	37	4	42965125	42965125	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:42965125G>T	uc003gwt.2	+	2	601	c.601G>T	c.(601-603)GTG>TTG	p.V201L		NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	201	Glutaredoxin.				cell redox homeostasis|inner ear receptor stereocilium organization|sensory perception of sound|vestibular receptor cell development	kinocilium|stereocilium	electron carrier activity|protein disulfide oxidoreductase activity			ovary(1)	1						CCTCCCTGTTGTGTTCATTGA	0.428													30	239	---	---	---	---	PASS
SMR3A	26952	broad.mit.edu	37	4	71232480	71232480	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:71232480T>C	uc003hfg.1	+	3	255	c.174T>C	c.(172-174)TAT>TAC	p.Y58Y	SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3	58	Pro-rich.					extracellular region					0		all_hematologic(202;0.196)				CTCCACCCTATGGTCCAGGGA	0.567													4	82	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123283401	123283401	+	Silent	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:123283401A>G	uc003ieh.2	+	84	15062	c.15017A>G	c.(15016-15018)TAA>TGA	p.*5006*	KIAA1109_uc003iem.2_Silent_p.*1362*	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	5006					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						GAAGAACACTAAAAAAGTAAT	0.289													4	44	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126372912	126372912	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:126372912T>A	uc003ifj.3	+	9	10741	c.10741T>A	c.(10741-10743)TAT>AAT	p.Y3581N	FAT4_uc011cgp.1_Missense_Mutation_p.Y1879N|FAT4_uc003ifi.1_Missense_Mutation_p.Y1059N	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3581	Cadherin 34.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TGCAGACTTCTATCTGTCTGT	0.463													15	80	---	---	---	---	PASS
GAB1	2549	broad.mit.edu	37	4	144381636	144381636	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:144381636A>T	uc003ije.2	+	8	2158	c.1799A>T	c.(1798-1800)GAC>GTC	p.D600V	GAB1_uc003ijd.2_Missense_Mutation_p.D630V|GAB1_uc011chq.1_Missense_Mutation_p.D497V	NM_002039	NP_002030	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1 isoform b	600					cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			breast(2)|lung(1)|skin(1)	4	all_hematologic(180;0.158)					TCCAGTGAAGACCCAGTATGT	0.418													15	95	---	---	---	---	PASS
ARFIP1	27236	broad.mit.edu	37	4	153784805	153784805	+	Silent	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:153784805A>G	uc003imz.2	+	3	417	c.141A>G	c.(139-141)CAA>CAG	p.Q47Q	ARFIP1_uc003inb.2_Silent_p.Q47Q|ARFIP1_uc003ina.2_Silent_p.Q47Q|ARFIP1_uc003inc.2_Silent_p.Q47Q|ARFIP1_uc011cij.1_Intron	NM_001025595	NP_001020766	P53367	ARFP1_HUMAN	ADP-ribosylation factor interacting protein 1	47					intracellular protein transport|regulation of protein secretion	cytosol|Golgi membrane				ovary(1)	1	all_hematologic(180;0.093)					CAGAAACCCAAATTACATCTC	0.368													10	44	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187541112	187541112	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr4:187541112C>A	uc003izf.2	-	10	6816	c.6628G>T	c.(6628-6630)GAA>TAA	p.E2210*		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2210	Extracellular (Potential).|Cadherin 20.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						TTCAGGCCTTCCGGGCTGTTA	0.488										HNSCC(5;0.00058)			14	88	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32091056	32091056	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:32091056A>C	uc003jhl.2	+	20	7890	c.7502A>C	c.(7501-7503)TAC>TCC	p.Y2501S	PDZD2_uc003jhm.2_Missense_Mutation_p.Y2501S	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2501					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						AGCGAGGATTACTCAGCAGGG	0.632													8	48	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33648940	33648940	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:33648940C>A	uc003jia.1	-	9	1629	c.1466G>T	c.(1465-1467)TGC>TTC	p.C489F	ADAMTS12_uc010iuq.1_Missense_Mutation_p.C489F	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	489	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TACTTCCTGGCAGAAGGTAGC	0.478										HNSCC(64;0.19)			13	55	---	---	---	---	PASS
TTC23L	153657	broad.mit.edu	37	5	34864559	34864559	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:34864559T>C	uc003jiu.2	+	6	657	c.554T>C	c.(553-555)TTC>TCC	p.F185S	TTC23L_uc003jiv.2_5'UTR|TTC23L_uc010iut.1_5'UTR	NM_144725	NP_653326	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	185	Potential.						binding			central_nervous_system(1)	1						GAAGCCTATTTCAACCTGCAG	0.433													5	57	---	---	---	---	PASS
LIFR	3977	broad.mit.edu	37	5	38510628	38510628	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:38510628C>G	uc010ive.1	-	7	1261	c.929G>C	c.(928-930)AGT>ACT	p.S310T	LIFR_uc003jli.2_Missense_Mutation_p.S310T	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	310	Extracellular (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					ATTTGTTCCACTACTTGCAGA	0.353			T	PLAG1	salivary adenoma								3	60	---	---	---	---	PASS
MAN2A1	4124	broad.mit.edu	37	5	109155491	109155491	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:109155491G>C	uc003kou.1	+	14	3194	c.2231G>C	c.(2230-2232)GGA>GCA	p.G744A		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	744	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GAAGATAGCGGAATTTTCACC	0.333													17	103	---	---	---	---	PASS
SLC12A2	6558	broad.mit.edu	37	5	127520118	127520118	+	Silent	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:127520118A>G	uc003kus.2	+	25	3524	c.3360A>G	c.(3358-3360)CAA>CAG	p.Q1120Q	SLC12A2_uc010jdf.2_RNA|SLC12A2_uc010jdg.2_Silent_p.Q1104Q	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12	1120	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	ATAAAGAGCAAGATATTGCAG	0.313													7	54	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127636600	127636600	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:127636600G>T	uc003kuu.2	-	48	6514	c.6075C>A	c.(6073-6075)GGC>GGA	p.G2025G		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2025	EGF-like 34; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GAGAGCAAGAGCCGGGAAGGG	0.413													4	48	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127648420	127648420	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:127648420G>A	uc003kuu.2	-	37	5224	c.4785C>T	c.(4783-4785)ACC>ACT	p.T1595T		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1595	TB 6.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CCCCGATCTCGGTGTTGCAAG	0.562													25	153	---	---	---	---	PASS
MATR3	9782	broad.mit.edu	37	5	138653312	138653312	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:138653312G>C	uc003ldu.2	+	10	1637	c.1210G>C	c.(1210-1212)GAT>CAT	p.D404H	MATR3_uc010jfb.2_Missense_Mutation_p.D404H|MATR3_uc003ldt.2_Missense_Mutation_p.D66H|MATR3_uc003ldw.2_Missense_Mutation_p.D404H|MATR3_uc003ldx.2_Missense_Mutation_p.D404H|MATR3_uc010jfc.2_Missense_Mutation_p.D404H|MATR3_uc003ldy.2_Missense_Mutation_p.D81H|MATR3_uc011czb.1_Missense_Mutation_p.D116H|MATR3_uc003ldz.2_Missense_Mutation_p.D404H|MATR3_uc003lea.2_Missense_Mutation_p.D404H|MATR3_uc003leb.2_Missense_Mutation_p.D66H|MATR3_uc003lec.2_Missense_Mutation_p.D81H	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3	404	RRM 1.					nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TCACATCATGGATTTTCAACG	0.348													3	42	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140208977	140208977	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:140208977C>A	uc003lho.2	+	1	1328	c.1301C>A	c.(1300-1302)TCG>TAG	p.S434*	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Nonsense_Mutation_p.S434*|PCDHA6_uc011dab.1_Nonsense_Mutation_p.S434*	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	434	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTCGCCTTCGCTGTGGGCC	0.612													17	66	---	---	---	---	PASS
GRIA1	2890	broad.mit.edu	37	5	153149968	153149968	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:153149968G>C	uc003lva.3	+	13	2628	c.2263G>C	c.(2263-2265)GCC>CCC	p.A755P	GRIA1_uc003luy.3_Missense_Mutation_p.A755P|GRIA1_uc003luz.3_Missense_Mutation_p.A660P|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.A675P|GRIA1_uc011dcx.1_Missense_Mutation_p.A686P|GRIA1_uc011dcy.1_Missense_Mutation_p.A765P|GRIA1_uc011dcz.1_Missense_Mutation_p.A765P	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	755	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CAAGGGGTCTGCCCTGAGGTA	0.512													3	21	---	---	---	---	PASS
GABRP	2568	broad.mit.edu	37	5	170222260	170222260	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:170222260C>A	uc003mau.2	+	5	487	c.289C>A	c.(289-291)CTG>ATG	p.L97M	GABRP_uc011dev.1_Missense_Mutation_p.L97M	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	97	Extracellular (Potential).					cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGACCAGCGGCTGGTGTTTGA	0.557													5	104	---	---	---	---	PASS
ATP6V0E1	8992	broad.mit.edu	37	5	172410956	172410956	+	Silent	SNP	T	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr5:172410956T>G	uc003mcd.1	+	1	194	c.93T>G	c.(91-93)GGT>GGG	p.G31G		NM_003945	NP_003936	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0	31					ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCCTAAGGGTCCTAACCGGG	0.647													12	98	---	---	---	---	PASS
TRIM10	10107	broad.mit.edu	37	6	30128523	30128523	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:30128523G>T	uc003npo.3	-	1	189	c.113C>A	c.(112-114)GCC>GAC	p.A38D	TRIM10_uc003npn.2_Missense_Mutation_p.A38D|TRIM15_uc010jrx.2_5'Flank	NM_006778	NP_006769	Q9UDY6	TRI10_HUMAN	tripartite motif-containing 10 isoform 1	38	RING-type.					cytoplasm	zinc ion binding				0						GGTAAGGCAGGCCCGGCAGAA	0.622													9	73	---	---	---	---	PASS
AIM1	202	broad.mit.edu	37	6	106999847	106999847	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:106999847A>G	uc003prh.2	+	12	4696	c.4209A>G	c.(4207-4209)ATA>ATG	p.I1403M	AIM1_uc003pri.2_Missense_Mutation_p.I207M	NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	1403	Beta/gamma crystallin 'Greek key' 8.						sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTCAACCTATATGTTTGGTAA	0.338													14	87	---	---	---	---	PASS
FAM184A	79632	broad.mit.edu	37	6	119324136	119324136	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:119324136C>A	uc003pyj.2	-	9	2364	c.2016G>T	c.(2014-2016)TTG>TTT	p.L672F	FAM184A_uc003pyk.3_Missense_Mutation_p.L552F|FAM184A_uc003pyl.3_Missense_Mutation_p.L552F	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1	672	Potential.									ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						CTTTCAACTGCAAAAGTTGAG	0.348													13	82	---	---	---	---	PASS
MAP3K5	4217	broad.mit.edu	37	6	136913588	136913588	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:136913588T>C	uc003qhc.2	-	22	3404	c.3043A>G	c.(3043-3045)ACA>GCA	p.T1015A	MAP3K5_uc011edj.1_Missense_Mutation_p.T262A|MAP3K5_uc011edk.1_Missense_Mutation_p.T861A	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	1015					activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AAAAAGAGTGTCCGAATTCCC	0.443													14	132	---	---	---	---	PASS
C6orf72	116254	broad.mit.edu	37	6	149893447	149893447	+	Silent	SNP	A	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:149893447A>C	uc003qmq.1	+	2	174	c.147A>C	c.(145-147)ACA>ACC	p.T49T	C6orf72_uc010kie.1_Intron	NM_138785	NP_620140	Q9NU53	CF072_HUMAN	hypothetical protein LOC116254 precursor	49	Extracellular (Potential).					integral to membrane					0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.66e-12)|GBM - Glioblastoma multiforme(68;0.171)		ATGTAACTACACTGAAAGATG	0.353													3	40	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169641988	169641988	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr6:169641988A>G	uc003qwt.2	-	6	1008	c.760T>C	c.(760-762)TAC>CAC	p.Y254H		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	254					cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GGGCCCACGTACTCGGTGGTG	0.637													6	50	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17861181	17861181	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:17861181T>C	uc003stw.1	-	18	2042	c.1829A>G	c.(1828-1830)TAT>TGT	p.Y610C	SNX13_uc003stv.2_Missense_Mutation_p.Y599C|SNX13_uc010kuc.2_Missense_Mutation_p.Y396C|SNX13_uc010kub.2_Missense_Mutation_p.Y5C			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	610	PX.				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					ATAACGACGATAGGTTTTCCA	0.398													7	79	---	---	---	---	PASS
CDCA7L	55536	broad.mit.edu	37	7	21948030	21948030	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:21948030G>A	uc010kuk.2	-	4	519	c.399C>T	c.(397-399)AGC>AGT	p.S133S	CDCA7L_uc003sve.3_Silent_p.S99S|CDCA7L_uc010kul.2_Silent_p.S87S|CDCA7L_uc003svf.3_Silent_p.S132S|CDCA7L_uc011jyk.1_Silent_p.S133S	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1	133					positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						TTCTAGACCTGCTTCTTCTAG	0.453													4	44	---	---	---	---	PASS
VPS41	27072	broad.mit.edu	37	7	38937702	38937702	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:38937702C>G	uc003tgy.2	-	2	75	c.49G>C	c.(49-51)GAT>CAT	p.D17H	VPS41_uc003tgz.2_Missense_Mutation_p.D17H|VPS41_uc010kxn.2_Missense_Mutation_p.D17H	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	17					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						TCAGACTCATCTGTAGATTCT	0.428													3	39	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43506139	43506139	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:43506139A>C	uc003tid.1	+	15	3490	c.2885A>C	c.(2884-2886)GAG>GCG	p.E962A	HECW1_uc011kbi.1_Missense_Mutation_p.E928A	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	962					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						ACCAACCCCGAGTTCTTCACT	0.493													7	72	---	---	---	---	PASS
NPC1L1	29881	broad.mit.edu	37	7	44579469	44579469	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:44579469C>A	uc003tlb.2	-	2	583	c.527G>T	c.(526-528)CGC>CTC	p.R176L	NPC1L1_uc003tlc.2_Missense_Mutation_p.R176L|NPC1L1_uc011kbw.1_Missense_Mutation_p.R176L|NPC1L1_uc003tld.2_Missense_Mutation_p.R176L	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	176	Extracellular (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)	TGCAGGGACGCGCACACGGCT	0.622													4	49	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47988034	47988034	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:47988034C>A	uc003tny.1	-	1	4	c.4G>T	c.(4-6)GCC>TCC	p.A2S		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						GCCTCCTCGGCCATGTCCTGT	0.453													10	31	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72865253	72865253	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:72865253C>A	uc003tyc.2	-	14	3849	c.3504G>T	c.(3502-3504)CTG>CTT	p.L1168L		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1168					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCATCCCAAGCAGCACGTGCA	0.448													5	51	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72891444	72891444	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:72891444C>A	uc003tyc.2	-	7	2692	c.2347G>T	c.(2347-2349)GTG>TTG	p.V783L		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	783	Potential.				ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				tccttCAACACAGCAAGCCGT	0.318													6	54	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77973166	77973166	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:77973166G>T	uc003ugx.2	-	9	1591	c.1337C>A	c.(1336-1338)CCT>CAT	p.P446H	MAGI2_uc003ugy.2_Missense_Mutation_p.P446H|MAGI2_uc010ldx.1_Missense_Mutation_p.P55H|MAGI2_uc010ldy.1_Missense_Mutation_p.P55H|MAGI2_uc011kgr.1_Missense_Mutation_p.P278H|MAGI2_uc011kgs.1_Missense_Mutation_p.P283H	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	446	PDZ 2.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				AAACTCATCAGGCTCGTCTCC	0.473													3	47	---	---	---	---	PASS
HGF	3082	broad.mit.edu	37	7	81350120	81350120	+	Silent	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:81350120G>C	uc003uhl.2	-	10	1377	c.1212C>G	c.(1210-1212)TCC>TCG	p.S404S	HGF_uc003uhm.2_Silent_p.S399S	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	404	Kringle 4.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4						ATCTTGTTTGGGATAAGTTGC	0.328													3	39	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	96251955	96251955	+	RNA	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:96251955C>A	uc010lfm.1	-	5		c.591G>T								Homo sapiens cDNA, FLJ17342.																		TGTATCCAGCCCTGGAAAAAT	0.413													5	23	---	---	---	---	PASS
LMTK2	22853	broad.mit.edu	37	7	97823671	97823671	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:97823671G>T	uc003upd.1	+	11	4187	c.3894G>T	c.(3892-3894)CTG>CTT	p.L1298L		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1298					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					ACGAGGACCTGCGGGCCTTCA	0.632													3	46	---	---	---	---	PASS
LMTK2	22853	broad.mit.edu	37	7	97823674	97823674	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:97823674G>A	uc003upd.1	+	11	4190	c.3897G>A	c.(3895-3897)CGG>CGA	p.R1299R		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1299					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AGGACCTGCGGGCCTTCAACC	0.632													4	45	---	---	---	---	PASS
ZNF3	7551	broad.mit.edu	37	7	99669446	99669446	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:99669446T>C	uc003usq.2	-	6	968	c.661A>G	c.(661-663)ATC>GTC	p.I221V	ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Missense_Mutation_p.I221V|ZNF3_uc010lgj.2_Missense_Mutation_p.I185V|ZNF3_uc003uss.2_Missense_Mutation_p.I228V|ZNF3_uc003ust.3_Missense_Mutation_p.I221V	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2	221	C2H2-type 1.				cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CCAGTGTGGATTCTCTGATGT	0.463													10	65	---	---	---	---	PASS
DNAJB9	4189	broad.mit.edu	37	7	108212208	108212208	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:108212208G>T	uc003vfn.2	+	2	240	c.38G>T	c.(37-39)TGC>TTC	p.C13F	THAP5_uc003vfl.2_5'Flank|THAP5_uc003vfm.2_5'Flank	NM_012328	NP_036460	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	13					ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0						TTTGCAATCTGCATTTTAATG	0.348													9	70	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117171036	117171036	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:117171036C>G	uc003vjd.2	+	4	489	c.357C>G	c.(355-357)ATC>ATG	p.I119M	CFTR_uc011knq.1_Translation_Start_Site	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	119	Helical; Name=2; (Potential).|ABC transmembrane type-1 1.				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)	AACGCTCTATCGCGATTTATC	0.453									Cystic_Fibrosis				3	33	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149502592	149502592	+	Missense_Mutation	SNP	G	T	T	rs111879522		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:149502592G>T	uc010lpk.2	+	58	8405	c.8405G>T	c.(8404-8406)CGA>CTA	p.R2802L		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	2802	TSP type-1 7.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGTCGTTCCCGACTCTGCCCC	0.677													5	34	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149520539	149520539	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:149520539C>A	uc010lpk.2	+	93	13357	c.13357C>A	c.(13357-13359)CCA>ACA	p.P4453T	SSPO_uc010lpm.1_RNA|SSPO_uc003wgg.2_Intron|SSPO_uc003wgh.2_RNA|SSPO_uc003wgi.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	4453					cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCAGGACCTGCCACCCTGCCA	0.642													5	29	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151879119	151879119	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr7:151879119T>C	uc003wla.2	-	36	6045	c.5826A>G	c.(5824-5826)ACA>ACG	p.T1942T	MLL3_uc003wkz.2_Silent_p.T1003T	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1942	Pro-rich.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GCCTATTTGCTGTTGTCTCAT	0.453			N		medulloblastoma								9	100	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3216711	3216711	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:3216711G>T	uc011kwk.1	-	21	3660	c.3270C>A	c.(3268-3270)GGC>GGA	p.G1090G	CSMD1_uc011kwj.1_Silent_p.G482G|CSMD1_uc003wqe.2_Silent_p.G246G	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1090	Sushi 6.|Extracellular (Potential).					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)		ACACACGGCGGCCCCCACCCA	0.552													5	41	---	---	---	---	PASS
NEFM	4741	broad.mit.edu	37	8	24775515	24775515	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:24775515A>T	uc003xed.3	+	3	2180	c.2147A>T	c.(2146-2148)GAG>GTG	p.E716V	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Missense_Mutation_p.E340V	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	716	Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		cccaaggaagagaaggtagag	0.174													5	7	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77761753	77761753	+	Nonsense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:77761753T>A	uc003yav.2	+	8	3903	c.3516T>A	c.(3514-3516)TAT>TAA	p.Y1172*	ZFHX4_uc003yau.1_Nonsense_Mutation_p.Y1217*|ZFHX4_uc003yaw.1_Nonsense_Mutation_p.Y1172*	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1172	C2H2-type 8.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TCCAGTTCTATCAATGTCCTT	0.313										HNSCC(33;0.089)			5	54	---	---	---	---	PASS
FABP5	2171	broad.mit.edu	37	8	82196796	82196796	+	Silent	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:82196796A>G	uc003yca.1	+	4	450	c.402A>G	c.(400-402)GTA>GTG	p.V134V		NM_001444	NP_001435	Q01469	FABP5_HUMAN	fatty acid binding protein 5	134					epidermis development	cytoplasm	fatty acid binding|protein binding|transporter activity				0	Lung NSC(7;3.57e-05)|all_lung(9;0.00011)		Epithelial(68;0.102)			ATGAAAAAGTAGAATAAAAAT	0.348													5	28	---	---	---	---	PASS
RUNX1T1	862	broad.mit.edu	37	8	93029532	93029532	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:93029532T>C	uc003yfd.2	-	2	232	c.148A>G	c.(148-150)AGG>GGG	p.R50G	RUNX1T1_uc003yfc.1_Missense_Mutation_p.R23G|RUNX1T1_uc003yfe.1_Missense_Mutation_p.R13G|RUNX1T1_uc010mao.2_Missense_Mutation_p.R23G|RUNX1T1_uc011lgi.1_Missense_Mutation_p.R61G|RUNX1T1_uc003yfh.1_Missense_Mutation_p.R13G|RUNX1T1_uc003yfb.1_Missense_Mutation_p.R13G|RUNX1T1_uc003yff.1_Missense_Mutation_p.R13G|RUNX1T1_uc003yfg.1_Missense_Mutation_p.R13G	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	50					generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GGAGTCAGCCTAGATTGCGTC	0.473													4	49	---	---	---	---	PASS
MTDH	92140	broad.mit.edu	37	8	98703374	98703374	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:98703374T>A	uc003yhz.2	+	6	1334	c.1006T>A	c.(1006-1008)TGG>AGG	p.W336R	MTDH_uc010mbf.2_RNA	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	336	Cytoplasmic (Potential).				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)			TGGAAAAGACTGGGGAAGGAG	0.383													4	51	---	---	---	---	PASS
SCRIB	23513	broad.mit.edu	37	8	144894454	144894454	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr8:144894454G>A	uc003yzp.1	-	9	895	c.888C>T	c.(886-888)CTC>CTT	p.L296L	SCRIB_uc003yzo.1_Silent_p.L296L	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	296	LRR 12.|Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	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;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGTTCTCCGTGAGGATCAGCT	0.592													14	65	---	---	---	---	PASS
KANK1	23189	broad.mit.edu	37	9	713340	713340	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:713340G>T	uc003zgl.1	+	7	3223	c.2574G>T	c.(2572-2574)CAG>CAT	p.Q858H	KANK1_uc003zgm.2_Missense_Mutation_p.Q858H|KANK1_uc003zgn.1_Missense_Mutation_p.Q858H|KANK1_uc003zgo.1_Missense_Mutation_p.Q858H|KANK1_uc003zgp.1_Missense_Mutation_p.Q858H|KANK1_uc003zgq.2_Missense_Mutation_p.Q700H|KANK1_uc003zgr.1_Missense_Mutation_p.Q700H|KANK1_uc003zgs.1_Missense_Mutation_p.Q700H	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	858					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		CTCACTCACAGATGGGCTCCC	0.517													10	62	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:20414340G>A	uc003zoe.2	-	5	763	c.504C>T	c.(502-504)AGC>AGT	p.S168S	MLLT3_uc011lne.1_Silent_p.S136S|MLLT3_uc011lnf.1_Silent_p.S165S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.A130V	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	168	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.144			T	MLL	ALL								3	39	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32633524	32633524	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:32633524C>A	uc003zrg.1	-	1	2144	c.2054G>T	c.(2053-2055)CGC>CTC	p.R685L	uc003zrh.1_RNA	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	685					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTGAGGTGTGCGCATAAAAAA	0.453													19	86	---	---	---	---	PASS
TMEM8B	51754	broad.mit.edu	37	9	35853663	35853663	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:35853663G>T	uc003zym.2	+	14	2260	c.1245G>T	c.(1243-1245)ATG>ATT	p.M415I	TMEM8B_uc003zyo.2_Missense_Mutation_p.M415I	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a	415	Helical; (Potential).				cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1						TTTGGCATATGCTCATTGCGG	0.587													12	64	---	---	---	---	PASS
CTSL1	1514	broad.mit.edu	37	9	90345351	90345351	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:90345351G>T	uc004aph.2	+	7	1190	c.840G>T	c.(838-840)GTG>GTT	p.V280V	CTSL1_uc004api.2_Silent_p.V280V|CTSL1_uc004apj.2_Silent_p.V225V|CTSL1_uc010mqh.2_Silent_p.V98V|CTSL1_uc004apk.2_Silent_p.V280V|CTSL1_uc004apl.2_Silent_p.V280V	NM_001912	NP_001903	P07711	CATL1_HUMAN	cathepsin L1 preproprotein	280					macrophage apoptosis|proteolysis	extracellular region|lysosome|nucleus	cysteine-type endopeptidase activity|histone binding			ovary(3)	3					Glucagon recombinant(DB00040)	GTGTGCTGGTGGTTGGCTACG	0.418													6	55	---	---	---	---	PASS
IPPK	64768	broad.mit.edu	37	9	95411767	95411767	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:95411767C>A	uc004asl.1	-	5	659	c.382G>T	c.(382-384)GAG>TAG	p.E128*		NM_022755	NP_073592	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	128					inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2						GGCCGGTGCTCTGCAAAGCGG	0.507													6	37	---	---	---	---	PASS
ZNF462	58499	broad.mit.edu	37	9	109692032	109692032	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr9:109692032C>G	uc004bcz.2	+	3	6128	c.5839C>G	c.(5839-5841)CAA>GAA	p.Q1947E	ZNF462_uc010mto.2_Missense_Mutation_p.Q1795E|ZNF462_uc004bda.2_Missense_Mutation_p.Q1795E|ZNF462_uc011lvz.1_5'Flank	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	1947					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5						AGATTTCAAACAAGAGAGGGT	0.488													4	27	---	---	---	---	PASS
NRG3	10718	broad.mit.edu	37	10	83635583	83635583	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr10:83635583C>T	uc001kco.2	+	1	514	c.487C>T	c.(487-489)CGG>TGG	p.R163W	NRG3_uc010qlz.1_Missense_Mutation_p.R163W|NRG3_uc001kcp.2_5'Flank|NRG3_uc001kcq.2_5'Flank	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	163	Ser/Thr-rich.|Extracellular (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CACCATCACGCGGGCGCCCAC	0.592													3	24	---	---	---	---	PASS
C10orf26	54838	broad.mit.edu	37	10	104572554	104572554	+	Silent	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr10:104572554C>T	uc001kwe.3	+	4	755	c.495C>T	c.(493-495)AGC>AGT	p.S165S	C10orf26_uc001kwf.3_Silent_p.S186S|C10orf26_uc009xxg.1_Intron	NM_017787	NP_060257	Q9NX94	OPA1L_HUMAN	hypothetical protein LOC54838 isoform 2	165	Pro-rich.					integral to membrane				central_nervous_system(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;6.14e-09)|all cancers(201;1.66e-07)|BRCA - Breast invasive adenocarcinoma(275;0.224)		CTGAGCCCAGCAGAAGCAGCA	0.652													4	26	---	---	---	---	PASS
TCERG1L	256536	broad.mit.edu	37	10	132944776	132944776	+	Silent	SNP	T	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr10:132944776T>G	uc001lkp.2	-	7	1268	c.1182A>C	c.(1180-1182)GCA>GCC	p.A394A	TCERG1L_uc009yax.1_RNA	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	394										large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		TACTTGCTGGTGCCTCCAGCT	0.493													11	35	---	---	---	---	PASS
EFCAB4A	283229	broad.mit.edu	37	11	828686	828686	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:828686C>G	uc001lrv.2	+	1	457	c.79C>G	c.(79-81)CGG>GGG	p.R27G	EFCAB4A_uc010qwt.1_Missense_Mutation_p.R27G|EFCAB4A_uc009ycm.1_Missense_Mutation_p.R27G|EFCAB4A_uc001lrw.2_5'Flank			Q8N4Y2	EFC4A_HUMAN	RecName: Full=EF-hand calcium-binding domain-containing protein 4A;	27					store-operated calcium entry		calcium ion binding				0		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCAGGGCCGCGGGCTGCAAT	0.652													5	51	---	---	---	---	PASS
STK33	65975	broad.mit.edu	37	11	8435164	8435164	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:8435164C>G	uc001mgi.1	-	11	2141	c.1222G>C	c.(1222-1224)GTT>CTT	p.V408L	STK33_uc001mgj.1_Missense_Mutation_p.V408L|STK33_uc001mgk.1_Missense_Mutation_p.V408L|STK33_uc010rbn.1_Missense_Mutation_p.V367L|STK33_uc001mgl.3_Missense_Mutation_p.V221L	NM_030906	NP_112168	Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	408						Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		TTTTCCTCAACACTTTCTGGG	0.378													11	113	---	---	---	---	PASS
OR5L2	26338	broad.mit.edu	37	11	55594722	55594722	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:55594722G>T	uc001nhy.1	+	1	28	c.28G>T	c.(28-30)GCT>TCT	p.A10S		NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L,	10	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)				CACCACTGTGGCTGAGTTCAT	0.413										HNSCC(27;0.073)			16	153	---	---	---	---	PASS
OR5W2	390148	broad.mit.edu	37	11	55681406	55681406	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:55681406T>A	uc010rir.1	-	1	653	c.653A>T	c.(652-654)TAT>TTT	p.Y218F		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	218	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GATATAACAATAAGAAATGAA	0.398													5	46	---	---	---	---	PASS
OR9Q2	219957	broad.mit.edu	37	11	57958868	57958868	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:57958868G>C	uc010rka.1	+	1	906	c.906G>C	c.(904-906)AGG>AGC	p.R302S		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	302	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)				AGGCCACTAGGAAAGCCCTGA	0.403													8	36	---	---	---	---	PASS
VWCE	220001	broad.mit.edu	37	11	61026208	61026208	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:61026208G>T	uc001nra.2	-	20	3086	c.2807C>A	c.(2806-2808)ACC>AAC	p.T936N	VWCE_uc001nrb.2_RNA	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	936						extracellular region	calcium ion binding			ovary(1)	1						GCCAGGGTGGGTGGTGGCTGC	0.652													9	51	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62297927	62297927	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:62297927G>A	uc001ntl.2	-	5	4262	c.3962C>T	c.(3961-3963)CCC>CTC	p.P1321L	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1321					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				GGAGATCTTGGGGGCCTTGAA	0.517													9	163	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62298339	62298339	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:62298339T>C	uc001ntl.2	-	5	3850	c.3550A>G	c.(3550-3552)AAG>GAG	p.K1184E	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1184					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				TCAGGCATCTTAAACTTGGGA	0.522													13	181	---	---	---	---	PASS
CCDC87	55231	broad.mit.edu	37	11	66358540	66358540	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:66358540C>A	uc001oiq.3	-	1	2015	c.1947G>T	c.(1945-1947)GTG>GTT	p.V649V	CCS_uc001oir.2_5'Flank	NM_018219	NP_060689	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	649										ovary(1)|skin(1)	2						ACTCTCCTGGCACAAAGTCTG	0.542													5	56	---	---	---	---	PASS
KRTAP5-10	387273	broad.mit.edu	37	11	71276767	71276767	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:71276767C>T	uc001oqt.1	+	1	159	c.134C>T	c.(133-135)CCC>CTC	p.P45L		NM_001012710	NP_001012728	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	45						keratin filament				skin(1)	1						TGCTGTGTGCCCGTCTGCTGC	0.687													12	72	---	---	---	---	PASS
CCDC83	220047	broad.mit.edu	37	11	85610060	85610060	+	Splice_Site	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:85610060T>C	uc001pbh.1	+	7	1184	c.672_splice	c.e7+2	p.E224_splice	CCDC83_uc001pbg.1_Splice_Site_p.E224_splice|CCDC83_uc001pbi.1_Splice_Site|CCDC83_uc001pbj.1_Splice_Site_p.E125_splice	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83											skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				AAAAAAGAGGTAAGTGGAATT	0.348													5	52	---	---	---	---	PASS
MMP13	4322	broad.mit.edu	37	11	102822866	102822866	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:102822866C>A	uc001phl.2	-	5	702	c.674G>T	c.(673-675)GGC>GTC	p.G225V		NM_002427	NP_002418	P45452	MMP13_HUMAN	matrix metalloproteinase 13 preproprotein	225					collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)		TAAGGAGTGGCCGAACTCATG	0.443													10	112	---	---	---	---	PASS
VPS11	55823	broad.mit.edu	37	11	118939986	118939986	+	Silent	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:118939986C>T	uc010ryx.1	+	3	310	c.268C>T	c.(268-270)CTG>TTG	p.L90L	VPS11_uc010ryy.1_5'UTR	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	90					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		GGTGACACACCTGTACCAACT	0.512													8	71	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123909270	123909270	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:123909270T>A	uc001pzq.1	-	1	439	c.439A>T	c.(439-441)ACT>TCT	p.T147S		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		CTGAGCCAAGTGCCGGTGGCC	0.557													9	158	---	---	---	---	PASS
CCDC15	80071	broad.mit.edu	37	11	124857428	124857428	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:124857428A>G	uc001qbm.3	+	8	1565	c.1306A>G	c.(1306-1308)AAA>GAA	p.K436E		NM_025004	NP_079280	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	436						centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		TGTTCTCCCTAAAGACCAGAG	0.423													8	66	---	---	---	---	PASS
KCNJ5	3762	broad.mit.edu	37	11	128781411	128781411	+	Silent	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:128781411G>T	uc001qet.2	+	2	557	c.243G>T	c.(241-243)CTG>CTT	p.L81L	KCNJ5_uc009zck.2_Silent_p.L81L|KCNJ5_uc001qew.2_Silent_p.L81L	NM_000890	NP_000881	P48544	IRK5_HUMAN	potassium inwardly-rectifying channel J5	81	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glibenclamide(DB01016)	TCACCACCCTGGTGGACCTCA	0.552													8	84	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	131781454	131781454	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr11:131781454A>G	uc001qgp.2	+	1	743	c.79A>G	c.(79-81)ACA>GCA	p.T27A	NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Missense_Mutation_p.T27A|NTM_uc001qgq.2_Missense_Mutation_p.T27A	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1	27					cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CCTTGTACCCACAGGAGTGCC	0.627											OREG0021537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	45	---	---	---	---	PASS
PLBD1	79887	broad.mit.edu	37	12	14689564	14689564	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:14689564T>A	uc001rcc.1	-	5	800	c.639A>T	c.(637-639)AAA>AAT	p.K213N		NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	213					lipid catabolic process	extracellular region	hydrolase activity				0						GGCTGCCGTTTTTTGTGGGAG	0.448													12	76	---	---	---	---	PASS
KIAA0528	9847	broad.mit.edu	37	12	22678621	22678621	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:22678621T>C	uc001rfq.2	-	5	596	c.368A>G	c.(367-369)AAT>AGT	p.N123S	KIAA0528_uc010sir.1_5'UTR|KIAA0528_uc010sis.1_Missense_Mutation_p.N123S|KIAA0528_uc010sit.1_Missense_Mutation_p.N123S|KIAA0528_uc010siu.1_Missense_Mutation_p.N123S|KIAA0528_uc001rfr.2_Missense_Mutation_p.N123S|KIAA0528_uc009ziy.1_Missense_Mutation_p.N123S	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	123							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						GACAACTACATTGATTTCCCC	0.284													14	134	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40748141	40748141	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:40748141A>G	uc001rmg.3	+	45	6738	c.6617A>G	c.(6616-6618)CAT>CGT	p.H2206R	LRRK2_uc009zjw.2_Missense_Mutation_p.H1044R|LRRK2_uc001rmi.2_Missense_Mutation_p.H1039R	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2206					activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GCCTTGGTGCATCTTCCTGTT	0.393													9	48	---	---	---	---	PASS
NELL2	4753	broad.mit.edu	37	12	45168619	45168619	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:45168619T>C	uc001rog.2	-	9	1500	c.905A>G	c.(904-906)CAG>CGG	p.Q302R	NELL2_uc001rof.3_Missense_Mutation_p.Q301R|NELL2_uc001roh.2_Missense_Mutation_p.Q302R|NELL2_uc009zkd.2_Missense_Mutation_p.Q301R|NELL2_uc010skz.1_Missense_Mutation_p.Q352R|NELL2_uc010sla.1_Missense_Mutation_p.Q325R|NELL2_uc001roi.1_Missense_Mutation_p.Q302R|NELL2_uc010slb.1_Missense_Mutation_p.Q301R|NELL2_uc001roj.2_Missense_Mutation_p.Q302R	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	302	VWFC 1.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		AGTTTCACACTGGATGGTTCC	0.358											OREG0021741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	34	---	---	---	---	PASS
PDE1B	5153	broad.mit.edu	37	12	54966472	54966472	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:54966472G>T	uc001sgd.1	+	7	848	c.682G>T	c.(682-684)GCA>TCA	p.A228S	PDE1B_uc010soz.1_Missense_Mutation_p.A91S|PDE1B_uc010spa.1_Missense_Mutation_p.A187S|PDE1B_uc001sgf.2_Missense_Mutation_p.A91S|PDE1B_uc001sge.2_Missense_Mutation_p.A208S|PDE1B_uc009znq.2_Missense_Mutation_p.A24S	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	228	Catalytic (By similarity).				activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						CCAGATCCACGCAGCCGATGT	0.512													22	274	---	---	---	---	PASS
GRIP1	23426	broad.mit.edu	37	12	66765701	66765701	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:66765701T>C	uc001stk.2	-	22	2870	c.2629A>G	c.(2629-2631)ATC>GTC	p.I877V	GRIP1_uc010sta.1_Missense_Mutation_p.I821V|GRIP1_uc001stj.2_Missense_Mutation_p.I644V|GRIP1_uc001stl.1_Missense_Mutation_p.I754V|GRIP1_uc001stm.2_Missense_Mutation_p.I862V	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	929					androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CCCGACATGATTGTTGCCTGT	0.517													4	46	---	---	---	---	PASS
KCNC2	3747	broad.mit.edu	37	12	75444382	75444382	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:75444382G>A	uc001sxg.1	-	3	1947	c.1403C>T	c.(1402-1404)CCA>CTA	p.P468L	KCNC2_uc009zry.2_Missense_Mutation_p.P468L|KCNC2_uc001sxe.2_Missense_Mutation_p.P468L|KCNC2_uc001sxf.2_Missense_Mutation_p.P468L|KCNC2_uc010stw.1_Missense_Mutation_p.P468L	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	468	Helical; Name=Segment S6; (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6						GACAGGCACTGGCATGGCTAT	0.498													4	40	---	---	---	---	PASS
PLXNC1	10154	broad.mit.edu	37	12	94641745	94641745	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr12:94641745C>G	uc001tdc.2	+	13	2704	c.2455C>G	c.(2455-2457)CGC>GGC	p.R819G		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	819	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						TTCAAAAGTGCGCACGAATGT	0.463													5	79	---	---	---	---	PASS
MTMR6	9107	broad.mit.edu	37	13	25823431	25823431	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr13:25823431A>G	uc001uqf.3	-	14	2124	c.1805T>C	c.(1804-1806)TTT>TCT	p.F602S	MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	602						cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		TGATTTAGAAAACTCTTCTGC	0.413													4	66	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109644761	109644761	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr13:109644761G>T	uc001vqt.1	+	21	2467	c.2341G>T	c.(2341-2343)GGT>TGT	p.G781C	MYO16_uc010agk.1_Missense_Mutation_p.G803C|MYO16_uc001vqu.1_Missense_Mutation_p.G581C|MYO16_uc010tjh.1_Missense_Mutation_p.G293C	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	781	Myosin head-like 1.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GGACATTTTTGGTTTTGAAGA	0.313													11	43	---	---	---	---	PASS
OR4K1	79544	broad.mit.edu	37	14	20403871	20403871	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:20403871G>C	uc001vwj.1	+	1	46	c.46G>C	c.(46-48)GGA>CGA	p.G16R		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	16	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		TGTACTTTTGGGACTCTCTAA	0.343													20	211	---	---	---	---	PASS
PCK2	5106	broad.mit.edu	37	14	24573040	24573040	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:24573040C>T	uc001wlt.2	+	10	1922	c.1790C>T	c.(1789-1791)TCC>TTC	p.S597F	NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_Intron|PCK2_uc010tnw.1_Missense_Mutation_p.S463F|PCK2_uc010tnx.1_Missense_Mutation_p.S463F|PCK2_uc001wlu.3_Missense_Mutation_p.S431F	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase	597					gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)		CAGCTGTTCTCCCTCCCCAAG	0.577													8	50	---	---	---	---	PASS
POLE2	5427	broad.mit.edu	37	14	50130032	50130032	+	Splice_Site	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:50130032C>G	uc001wwu.2	-	10	769	c.755_splice	c.e10+1	p.R252_splice	SDCCAG1_uc010anj.1_Intron|POLE2_uc010ann.2_Splice_Site|POLE2_uc001wwv.2_Splice_Site|POLE2_uc010ano.2_Splice_Site	NM_002692	NP_002683	P56282	DPOE2_HUMAN	DNA-directed DNA polymerase epsilon 2						DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity			ovary(1)|skin(1)	2	all_epithelial(31;0.0021)|Breast(41;0.0124)					CATTTTAATACCTAGTAGTAC	0.378													6	40	---	---	---	---	PASS
SLC39A9	55334	broad.mit.edu	37	14	69922539	69922539	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:69922539G>T	uc001xle.2	+	6	1329	c.649G>T	c.(649-651)GCA>TCA	p.A217S	SLC39A9_uc010aqx.2_Missense_Mutation_p.A194S|SLC39A9_uc001xlf.3_Missense_Mutation_p.A217S|SLC39A9_uc001xlg.3_RNA	NM_018375	NP_060845	Q9NUM3	S39A9_HUMAN	solute carrier family 39 (zinc transporter),	217	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		CTTTGCATTGGCAGCACCAGT	0.438													4	87	---	---	---	---	PASS
NEK9	91754	broad.mit.edu	37	14	75558095	75558095	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:75558095G>A	uc001xrl.2	-	19	2474	c.2320C>T	c.(2320-2322)CCA>TCA	p.P774S	NEK9_uc001xrj.2_5'UTR|NEK9_uc001xrk.2_Missense_Mutation_p.P274S	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	774	Pro/Ser/Thr-rich.|Interaction with NEK6.				cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)		CCTCCACTTGGGTCAGGAGTT	0.567													5	44	---	---	---	---	PASS
C14orf143	90141	broad.mit.edu	37	14	90263621	90263621	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:90263621T>C	uc001xxt.2	-	6	543	c.458A>G	c.(457-459)GAA>GGA	p.E153G	C14orf143_uc001xxs.2_Missense_Mutation_p.E129G	NM_145231	NP_660274	Q9BUY7	EFC11_HUMAN	hypothetical protein LOC90141	153	EF-hand 3.						calcium ion binding				0		all_cancers(154;0.136)		Epithelial(152;0.194)		CAGGGCATATTCAAAGTCTCT	0.398													5	46	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96783592	96783592	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:96783592G>T	uc001yfi.2	-	20	3465	c.3100C>A	c.(3100-3102)CGT>AGT	p.R1034S		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1034										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)		CTGCGAGAACGATAGTTGGGA	0.358													6	48	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106208314	106208314	+	RNA	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr14:106208314A>T	uc010tyt.1	-	3627		c.58900T>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Missense_Mutation_p.W62R|uc001ysf.2_Missense_Mutation_p.W62R					Parts of antibodies, mostly variable regions.												0						CCATTCAGCCAGTCCTGGTGC	0.592													6	166	---	---	---	---	PASS
SNORD116-1	100033413	broad.mit.edu	37	15	25296707	25296707	+	RNA	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr15:25296707G>C	uc001yxg.2	+	1		c.85G>C				NR_003316				Homo sapiens small nucleolar RNA, C/D box 116-1 (SNORD116-1), non-coding RNA.												0						ATTCTCATCGGAACTGAGGTC	0.478													11	68	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28492038	28492038	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr15:28492038C>G	uc001zbj.2	-	22	3347	c.3241G>C	c.(3241-3243)GAG>CAG	p.E1081Q		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1081					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CCCATTAGCTCTGGACCTTGA	0.428													3	38	---	---	---	---	PASS
ACSM2B	348158	broad.mit.edu	37	16	20563569	20563569	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:20563569C>A	uc002dhj.3	-	7	1001	c.791G>T	c.(790-792)GGT>GTT	p.G264V	ACSM2B_uc002dhk.3_Missense_Mutation_p.G264V|ACSM2B_uc010bwf.1_Missense_Mutation_p.G264V	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	264					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5						CAGTATCCAACCTGTGTCTGA	0.433													12	128	---	---	---	---	PASS
SCNN1G	6340	broad.mit.edu	37	16	23197812	23197812	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:23197812C>T	uc002dlm.1	+	2	359	c.220C>T	c.(220-222)CTC>TTC	p.L74F		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	74	Helical; (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GTGCGCCCTCCTCGTCTTCTC	0.582													3	49	---	---	---	---	PASS
ITGAX	3687	broad.mit.edu	37	16	31382999	31382999	+	Missense_Mutation	SNP	G	A	A	rs146647978	byFrequency	TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:31382999G>A	uc002ebu.1	+	17	2121	c.2054G>A	c.(2053-2055)CGC>CAC	p.R685H	ITGAX_uc002ebt.2_Missense_Mutation_p.R685H	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	685	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						GACCCTGGCCGCCTGAGTCCC	0.607													4	45	---	---	---	---	PASS
NOD2	64127	broad.mit.edu	37	16	50756589	50756589	+	Missense_Mutation	SNP	G	T	T	rs104895453		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:50756589G>T	uc002egm.1	+	8	2876	c.2771G>T	c.(2770-2772)GGT>GTT	p.G924V	NOD2_uc010cbl.1_Missense_Mutation_p.G674V|NOD2_uc010cbm.1_Missense_Mutation_p.G674V|NOD2_uc010cbn.1_RNA|NOD2_uc010cbo.1_RNA|NOD2_uc010cbp.1_RNA|NOD2_uc010cbq.1_Missense_Mutation_p.G62V|NOD2_uc010cbr.1_RNA|NOD2_uc010vgq.1_5'UTR	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	924			G -> D (associated with Crohn disease).		activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)				GAAGCCTTGGGTGATCACCAG	0.557													26	231	---	---	---	---	PASS
RPGRIP1L	23322	broad.mit.edu	37	16	53730170	53730170	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:53730170T>C	uc002ehp.2	-	3	187	c.123A>G	c.(121-123)GCA>GCG	p.A41A	RPGRIP1L_uc002eho.3_Silent_p.A41A|RPGRIP1L_uc010vgy.1_Silent_p.A41A|RPGRIP1L_uc010cbx.2_Silent_p.A41A|RPGRIP1L_uc010vgz.1_Silent_p.A41A|RPGRIP1L_uc002ehq.1_Silent_p.A41A|RPGRIP1L_uc010cby.1_Silent_p.A41A	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	41					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)				CACGTGACACTGCCTGGCGAG	0.403													8	141	---	---	---	---	PASS
CPNE7	27132	broad.mit.edu	37	16	89650453	89650453	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr16:89650453C>A	uc002fnp.2	+	6	805	c.675C>A	c.(673-675)ATC>ATA	p.I225I	CPNE7_uc002fnq.2_Silent_p.I150I	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	225					lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		CCGAGGACATCTCGGGGAACA	0.706													4	39	---	---	---	---	PASS
OR1D2	4991	broad.mit.edu	37	17	2996153	2996153	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:2996153G>A	uc010vrb.1	-	1	138	c.138C>T	c.(136-138)ATC>ATT	p.I46I		NM_002548	NP_002539	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D,	46	Helical; Name=1; (Potential).				cellular component movement|chemotaxis|protein import into nucleus, translocation|sensory perception of smell|single fertilization	integral to plasma membrane	olfactory receptor activity			ovary(1)	1						TGATGGCCAGGATGATGAGCA	0.547													8	63	---	---	---	---	PASS
NEURL4	84461	broad.mit.edu	37	17	7230235	7230235	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:7230235G>A	uc002gga.1	-	4	894	c.887C>T	c.(886-888)CCG>CTG	p.P296L	NEURL4_uc002ggb.1_Missense_Mutation_p.P296L|NEURL4_uc002ggc.1_5'Flank	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	296							protein binding			upper_aerodigestive_tract(1)|ovary(1)	2						TTCCCCTGCCGGTGGGGAGCT	0.562													3	36	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10450814	10450814	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:10450814C>G	uc010coi.2	-	4	454	c.326G>C	c.(325-327)CGT>CCT	p.R109P	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.R109P|MYH2_uc010coj.2_Missense_Mutation_p.R109P	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	109	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GGCTGCATAACGTTCTTTGAG	0.483													13	97	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11642197	11642197	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:11642197G>T	uc002gne.2	+	29	5883	c.5815G>T	c.(5815-5817)GTA>TTA	p.V1939L	DNAH9_uc010coo.2_Missense_Mutation_p.V1233L	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1939	AAA 1 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GGTTCACCAGGTAAAAAGCAT	0.448													5	51	---	---	---	---	PASS
TTLL6	284076	broad.mit.edu	37	17	46847213	46847213	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:46847213G>T	uc010wlo.1	-	15	2322	c.2287C>A	c.(2287-2289)CTA>ATA	p.L763I	TTLL6_uc002iob.2_Missense_Mutation_p.L456I|TTLL6_uc010dbi.2_Intron|TTLL6_uc002ioc.2_Missense_Mutation_p.L516I|TTLL6_uc002iod.2_Intron	NM_001130918	NP_001124390	Q8N841	TTLL6_HUMAN	tubulin tyrosine ligase-like family, member 6	715						cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0						TCACTCTTTAGCAAAGTCCAG	0.463													4	48	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51900915	51900915	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr17:51900915G>A	uc002iua.2	+	1	677	c.521G>A	c.(520-522)CGC>CAC	p.R174H	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	174	Potential.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						CGAGCTAGACGCGCCCTCGAT	0.547													7	64	---	---	---	---	PASS
WDR7	23335	broad.mit.edu	37	18	54605772	54605772	+	Missense_Mutation	SNP	A	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr18:54605772A>C	uc002lgk.1	+	24	4051	c.3840A>C	c.(3838-3840)AGA>AGC	p.R1280S	WDR7_uc002lgl.1_Missense_Mutation_p.R1247S	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	1280										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		AGGTACACAGACATACGGCTC	0.348													5	41	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55317699	55317699	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr18:55317699T>A	uc002lgw.2	-	26	3431	c.3431A>T	c.(3430-3432)TAC>TTC	p.Y1144F	uc002lgu.1_Intron|uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	1144	Helical; (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				TAACCAAATGTATGGCTGTCT	0.413									Byler_disease				3	32	---	---	---	---	PASS
ZCCHC2	54877	broad.mit.edu	37	18	60241357	60241357	+	Silent	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr18:60241357C>G	uc002lip.3	+	13	2043	c.2043C>G	c.(2041-2043)GTC>GTG	p.V681V	ZCCHC2_uc002lio.2_RNA|ZCCHC2_uc002liq.2_Silent_p.V151V	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	681					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2						ACGGTTCTGTCAACCAGACTG	0.398													4	76	---	---	---	---	PASS
TMPRSS9	360200	broad.mit.edu	37	19	2413785	2413785	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:2413785G>A	uc010xgx.1	+	9	1240	c.1240G>A	c.(1240-1242)GAA>AAA	p.E414K	TMPRSS9_uc002lvv.1_Missense_Mutation_p.E448K	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	414	Extracellular (Potential).|Peptidase S1 1.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				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)		CGGGTGTGCGGAAGCCCGGCG	0.647													6	57	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9060192	9060192	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:9060192G>C	uc002mkp.2	-	3	27458	c.27254C>G	c.(27253-27255)TCT>TGT	p.S9085C		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	9087	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						AGCCCCAGGAGAACCTGTTTG	0.468													3	67	---	---	---	---	PASS
ZNF560	147741	broad.mit.edu	37	19	9577721	9577721	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:9577721C>A	uc002mlp.1	-	10	2112	c.1902G>T	c.(1900-1902)GGG>GGT	p.G634G	ZNF560_uc010dwr.1_Silent_p.G528G	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	634	C2H2-type 11; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						CAAAGGCTTTCCCACAGTCCT	0.378													6	92	---	---	---	---	PASS
ZNF563	147837	broad.mit.edu	37	19	12429653	12429653	+	Nonsense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:12429653T>A	uc002mtp.2	-	4	1424	c.1186A>T	c.(1186-1188)AAG>TAG	p.K396*		NM_145276	NP_660319	Q8TA94	ZN563_HUMAN	zinc finger protein 563	396	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CCACATATCTTGCATTTATGA	0.428													10	146	---	---	---	---	PASS
CD97	976	broad.mit.edu	37	19	14517527	14517527	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:14517527T>C	uc002myl.2	+	16	2187	c.2064T>C	c.(2062-2064)TTT>TTC	p.F688F	CD97_uc002mym.2_Silent_p.F639F|CD97_uc002myn.2_Silent_p.F595F	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor	688	Extracellular (Potential).				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)|breast(1)	4						GGTTGGACTTTGAGCAGGGCT	0.622											OREG0025312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	117	---	---	---	---	PASS
CILP2	148113	broad.mit.edu	37	19	19654982	19654982	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:19654982G>T	uc002nmv.3	+	8	1713	c.1628G>T	c.(1627-1629)CGA>CTA	p.R543L	CILP2_uc002nmw.3_Missense_Mutation_p.R549L	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	543						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1						TTTGATCCTCGAGGTGCCGGC	0.607													3	44	---	---	---	---	PASS
RASGRP4	115727	broad.mit.edu	37	19	38911761	38911761	+	Silent	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:38911761G>C	uc002oir.2	-	3	502	c.288C>G	c.(286-288)GCC>GCG	p.A96A	RASGRP4_uc010efz.1_5'Flank|RASGRP4_uc010ega.1_5'Flank|RASGRP4_uc010xua.1_Silent_p.A96A|RASGRP4_uc010xub.1_Silent_p.A96A|RASGRP4_uc010xuc.1_Silent_p.A96A|RASGRP4_uc010xud.1_Silent_p.A96A|RASGRP4_uc010xue.1_Silent_p.A96A|RASGRP4_uc010egb.2_Silent_p.A96A	NM_170604	NP_733749	Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4 isoform a	96	N-terminal Ras-GEF.				activation of phospholipase C activity|cell growth|cell proliferation|myeloid cell differentiation|positive regulation of Ras protein signal transduction|regulation of G-protein coupled receptor protein signaling pathway|response to extracellular stimulus|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|membrane fraction|plasma membrane|soluble fraction	diacylglycerol binding|GTP-dependent protein binding|metal ion binding|Ras guanyl-nucleotide exchange factor activity			pancreas(1)|lung(1)|skin(1)	3	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CAGCCAGGTCGGCGGACGGCA	0.632													11	49	---	---	---	---	PASS
ZNF230	7773	broad.mit.edu	37	19	44515309	44515309	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:44515309A>G	uc002oyb.1	+	5	1369	c.1118A>G	c.(1117-1119)TAC>TGC	p.Y373C		NM_006300	NP_006291	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	373	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				GGGAAGGGCTACATTAGTAAG	0.458													10	45	---	---	---	---	PASS
SIGLEC12	89858	broad.mit.edu	37	19	52001375	52001375	+	Silent	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:52001375A>T	uc002pwx.1	-	5	1358	c.1302T>A	c.(1300-1302)CCT>CCA	p.P434P	SIGLEC12_uc002pww.1_Silent_p.P316P|SIGLEC12_uc010eoy.1_Silent_p.P161P	NM_053003	NP_443729	Q96PQ1	SIG12_HUMAN	sialic acid binding immunoglobulin-like	434	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|skin(2)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CATGCACTCGAGGCAGCTCCA	0.607													3	25	---	---	---	---	PASS
LENG8	114823	broad.mit.edu	37	19	54963896	54963896	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:54963896A>G	uc002qfv.1	+	4	424	c.280A>G	c.(280-282)AAC>GAC	p.N94D	LENG8_uc002qfw.2_Missense_Mutation_p.N94D			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;	94	Tyr-rich.						protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCAGCAGTACAACTATGCCTA	0.418													9	59	---	---	---	---	PASS
ZNF584	201514	broad.mit.edu	37	19	58926981	58926981	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr19:58926981G>T	uc002qsp.2	+	3	712	c.260G>T	c.(259-261)AGC>ATC	p.S87I	ZNF584_uc010yia.1_RNA|ZNF584_uc002qsr.2_Missense_Mutation_p.S42I|ZNF584_uc010yib.1_Missense_Mutation_p.S79I	NM_173548	NP_775819	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	87	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		ACTCCAGTCAGCAGAGCAGAA	0.552													3	38	---	---	---	---	PASS
TRIB3	57761	broad.mit.edu	37	20	368895	368895	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr20:368895C>T	uc002wdm.2	+	2	747	c.241C>T	c.(241-243)CGG>TGG	p.R81W	TRIB3_uc002wdn.2_Missense_Mutation_p.R108W	NM_021158	NP_066981	Q96RU7	TRIB3_HUMAN	tribbles 3	81	Protein kinase.				apoptosis|cellular lipid metabolic process|insulin receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fatty acid biosynthetic process|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein binding|positive regulation of ubiquitin-protein ligase activity|regulation of glucose transport|regulation of MAP kinase activity|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	ATP binding|protein kinase activity|protein kinase binding|protein kinase inhibitor activity|transcription corepressor activity|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			central_nervous_system(2)	2		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		GGAGGGCGGGCGGGCCTACCA	0.667													4	55	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20592039	20592039	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr20:20592039T>C	uc002wrz.2	-	14	1863	c.1720A>G	c.(1720-1722)ACA>GCA	p.T574A	RALGAPA2_uc010gcx.2_Missense_Mutation_p.T278A|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	574					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						ACAGCTTCTGTTATCCTGAGT	0.378													20	178	---	---	---	---	PASS
CTSZ	1522	broad.mit.edu	37	20	57581519	57581519	+	Silent	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr20:57581519C>T	uc002yai.2	-	2	291	c.165G>A	c.(163-165)GAG>GAA	p.E55E	CTSZ_uc002yaj.3_Silent_p.E55E	NM_001336	NP_001327	Q9UBR2	CATZ_HUMAN	cathepsin Z preproprotein	55					proteolysis	endoplasmic reticulum|extracellular space|lysosome	cysteine-type endopeptidase activity			kidney(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)			GGGACAGGTACTCATGAGGCC	0.637													3	38	---	---	---	---	PASS
KRTAP22-1	337979	broad.mit.edu	37	21	31973550	31973550	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr21:31973550G>T	uc011add.1	+	1	111	c.111G>T	c.(109-111)TGG>TGT	p.W37C	KRTAP6-2_uc011adc.1_5'Flank	NM_181620	NP_853651	Q3MIV0	KR221_HUMAN	keratin associated protein 22-1	37						intermediate filament					0						ACTGCCCATGGTGTTATGAAA	0.478													12	139	---	---	---	---	PASS
KRTAP10-6	386674	broad.mit.edu	37	21	46011355	46011355	+	Silent	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr21:46011355C>T	uc002zfm.2	-	1	1032	c.1011G>A	c.(1009-1011)ACG>ACA	p.T337T	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6	337	29.|29 X 5 AA repeats of C-C-X(3).					keratin filament					0						CACAGGAGGCCGTGCGGCAGC	0.672													5	48	---	---	---	---	PASS
RAC2	5880	broad.mit.edu	37	22	37627422	37627422	+	Silent	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr22:37627422T>C	uc003arc.2	-	5	414	c.297A>G	c.(295-297)CCA>CCG	p.P99P		NM_002872	NP_002863	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2	99					axon guidance|platelet activation|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|protein binding			breast(2)|central_nervous_system(1)|skin(1)	4						GCCGCACTTCTGGGAACCACT	0.622													6	35	---	---	---	---	PASS
CACNA1I	8911	broad.mit.edu	37	22	39966962	39966962	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr22:39966962C>T	uc003ayc.2	+	1	205	c.205C>T	c.(205-207)CGG>TGG	p.R69W	CACNA1I_uc003ayd.2_Missense_Mutation_p.R69W	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	69	Cytoplasmic (Potential).|I.				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	CACCAGCCCCCGGAACTGGTG	0.637													7	61	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40283671	40283671	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr22:40283671C>T	uc003ayg.2	-	2	333	c.82G>A	c.(82-84)GAC>AAC	p.D28N		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	28	ENTH.									ovary(2)|skin(1)	3	Melanoma(58;0.0749)					CCCCAAGGGTCGTTAGAAGTT	0.393													11	73	---	---	---	---	PASS
WBP2NL	164684	broad.mit.edu	37	22	42423062	42423062	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chr22:42423062G>A	uc011ape.1	+	7	823	c.807G>A	c.(805-807)CCG>CCA	p.P269P	WBP2NL_uc003bbt.2_Silent_p.P269P|WBP2NL_uc011apk.1_Silent_p.P141P|WBP2NL_uc003bbu.2_RNA|WBP2NL_uc003bbv.1_RNA	NM_152613	NP_689826	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	269	Gly-rich.				egg activation|male pronucleus assembly|meiosis	perinuclear theca	WW domain binding			ovary(2)	2						ATGAAGGCCCGCCTGCGGGAT	0.592													13	107	---	---	---	---	PASS
ARSH	347527	broad.mit.edu	37	X	2951310	2951310	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:2951310C>A	uc011mhj.1	+	9	1573	c.1573C>A	c.(1573-1575)CCA>ACA	p.P525T		NM_001011719	NP_001011719	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	525						integral to membrane	arylsulfatase activity|metal ion binding			lung(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AACACCTGTCCCACAGCAGTT	0.498													5	24	---	---	---	---	PASS
WWC3	55841	broad.mit.edu	37	X	10085324	10085324	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:10085324C>A	uc004csx.3	+	11	1423	c.1225C>A	c.(1225-1227)CAG>AAG	p.Q409K	WWC3_uc010nds.2_Missense_Mutation_p.Q73K|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	409	Ser-rich.									ovary(4)	4						TGAGGGCAGCCAGCTTCTACG	0.657													6	89	---	---	---	---	PASS
WWC3	55841	broad.mit.edu	37	X	10085325	10085325	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:10085325A>G	uc004csx.3	+	11	1424	c.1226A>G	c.(1225-1227)CAG>CGG	p.Q409R	WWC3_uc010nds.2_Missense_Mutation_p.Q73R|WWC3_uc010ndt.2_RNA	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	409	Ser-rich.									ovary(4)	4						GAGGGCAGCCAGCTTCTACGC	0.657													6	88	---	---	---	---	PASS
TLR8	51311	broad.mit.edu	37	X	12939468	12939468	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:12939468A>G	uc004cve.2	+	2	2377	c.2309A>G	c.(2308-2310)CAC>CGC	p.H770R	TLR8_uc004cvd.2_Missense_Mutation_p.H788R	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	770	Extracellular (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7						TTGGAACTACACGGAAACCCC	0.403													14	75	---	---	---	---	PASS
CDKL5	6792	broad.mit.edu	37	X	18631345	18631345	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:18631345G>A	uc004cym.2	+	15	2479	c.2226G>A	c.(2224-2226)GAG>GAA	p.E742E	CDKL5_uc004cyn.2_Silent_p.E742E	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	742				Missing (in Ref. 4; CAA61445).	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)					TACCATCAGAGAGCAGTTCTG	0.368													12	96	---	---	---	---	PASS
PDHA1	5160	broad.mit.edu	37	X	19368197	19368197	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:19368197T>C	uc004czg.3	+	3	405	c.260T>C	c.(259-261)ATT>ACT	p.I87T	PDHA1_uc004czh.3_Missense_Mutation_p.I122T|PDHA1_uc011mjc.1_Missense_Mutation_p.I84T|PDHA1_uc011mjd.1_Missense_Mutation_p.I84T|PDHA1_uc010nfk.2_Missense_Mutation_p.I84T	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor	87					glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	CAGAAAATTATTCGTGGTTTC	0.443													12	113	---	---	---	---	PASS
FTHL17	53940	broad.mit.edu	37	X	31090069	31090069	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:31090069A>G	uc004dcl.1	-	1	105	c.2T>C	c.(1-3)ATG>ACG	p.M1T		NM_031894	NP_114100	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	1					cellular iron ion homeostasis|iron ion transport		ferric iron binding|oxidoreductase activity				0						GGCGGTGGCCATGGCGGGCAG	0.647													4	33	---	---	---	---	PASS
CYBB	1536	broad.mit.edu	37	X	37670075	37670075	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:37670075G>T	uc004ddr.2	+	13	1679	c.1618G>T	c.(1618-1620)GAA>TAA	p.E540*	CYBB_uc011mkf.1_Nonsense_Mutation_p.E508*|CYBB_uc011mkg.1_Nonsense_Mutation_p.E273*	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	540	Cytoplasmic (Potential).				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						CTGTGGACCTGAAGCCTTGGC	0.423													4	55	---	---	---	---	PASS
BCOR	54880	broad.mit.edu	37	X	39933922	39933922	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:39933922G>A	uc004den.3	-	4	969	c.677C>T	c.(676-678)TCC>TTC	p.S226F	BCOR_uc004dep.3_Missense_Mutation_p.S226F|BCOR_uc004deo.3_Missense_Mutation_p.S226F|BCOR_uc004dem.3_Missense_Mutation_p.S226F|BCOR_uc004deq.3_Missense_Mutation_p.S226F	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	226					heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4						CAAGCTGTAGGACTGCTGAGG	0.557													6	56	---	---	---	---	PASS
PFKFB1	5207	broad.mit.edu	37	X	54975507	54975507	+	Splice_Site	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:54975507C>A	uc004dty.1	-	9	1064	c.993_splice	c.e9+1	p.A331_splice	PFKFB1_uc010nkd.1_Intron|PFKFB1_uc011mol.1_Splice_Site_p.A266_splice	NM_002625	NP_002616	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,						energy reserve metabolic process|fructose 2,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|intracellular protein kinase cascade	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(1)	1						ATGCATCTCACCGCATCAATC	0.562													6	44	---	---	---	---	PASS
PAGE5	90737	broad.mit.edu	37	X	55249059	55249059	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:55249059G>C	uc004duj.2	+	4	498	c.256G>C	c.(256-258)GAT>CAT	p.D86H	PAGE5_uc004duk.2_Missense_Mutation_p.D66H	NM_130467	NP_569734	Q96GU1	GGEE1_HUMAN	P antigen family, member 5 isoform 1	86											0						TTAAGGGACTGATGTGGAAGC	0.398													10	100	---	---	---	---	PASS
MAGEH1	28986	broad.mit.edu	37	X	55479403	55479403	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:55479403C>G	uc004dum.2	+	1	866	c.596C>G	c.(595-597)TCG>TGG	p.S199W		NM_014061	NP_054780	Q9H213	MAGH1_HUMAN	melanoma antigen, family H, 1 protein	199					apoptosis					ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4						GACTGGGATTCGGACGATGAT	0.493													14	56	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70674030	70674030	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:70674030T>A	uc004dzu.3	+	33	4812	c.4761T>A	c.(4759-4761)AGT>AGA	p.S1587R	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.S1608R|TAF1_uc004dzv.3_Missense_Mutation_p.S761R|TAF1_uc010nld.1_RNA|TAF1_uc010nle.1_RNA|TAF1_uc010nlf.1_Missense_Mutation_p.S12R|TAF1_uc004dzx.2_RNA|TAF1_uc004dzy.2_RNA|TAF1_uc004dzw.1_RNA	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	1587	Interaction with ASF1A and ASF1B.|Bromo 2.|Protein kinase 2.			PESQYTK -> YMCTTCR (in Ref. 6; CAD87528).	G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				GACCTGAGAGTCAGTATACTA	0.373													4	37	---	---	---	---	PASS
ATP7A	538	broad.mit.edu	37	X	77254002	77254002	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:77254002C>A	uc004ecx.3	+	5	1524	c.1364C>A	c.(1363-1365)GCT>GAT	p.A455D	ATP7A_uc004ecw.2_Missense_Mutation_p.A455D	NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	455	Cytoplasmic (Potential).				ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						GTAGTAATAGCTCAGCCTTCA	0.393													11	98	---	---	---	---	PASS
PGK1	5230	broad.mit.edu	37	X	77359903	77359903	+	Splice_Site	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:77359903G>T	uc004ecz.3	+	1	237	c.65_splice	c.e1+1	p.R22_splice	PGK1_uc010nlz.2_Splice_Site|PGK1_uc011mqq.1_5'Flank	NM_000291	NP_000282	P00558	PGK1_HUMAN	phosphoglycerate kinase 1						gluconeogenesis|glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			upper_aerodigestive_tract(1)|ovary(1)	2						TCGTTATGAGGTAATTCTGCA	0.507													4	24	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91133650	91133650	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:91133650C>A	uc004efk.1	+	2	3256	c.2411C>A	c.(2410-2412)TCC>TAC	p.S804Y	PCDH11X_uc004efl.1_Missense_Mutation_p.S804Y|PCDH11X_uc004efo.1_Missense_Mutation_p.S804Y|PCDH11X_uc010nmv.1_Missense_Mutation_p.S804Y|PCDH11X_uc004efm.1_Missense_Mutation_p.S804Y|PCDH11X_uc004efn.1_Missense_Mutation_p.S804Y|PCDH11X_uc004efh.1_Missense_Mutation_p.S804Y|PCDH11X_uc004efj.1_Missense_Mutation_p.S804Y	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	804	Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						GCTGATGTATCCTCACCAACT	0.453													9	69	---	---	---	---	PASS
DIAPH2	1730	broad.mit.edu	37	X	95993591	95993591	+	Nonsense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:95993591C>T	uc004efu.3	+	3	568	c.172C>T	c.(172-174)CGA>TGA	p.R58*	DIAPH2_uc004eft.3_Nonsense_Mutation_p.R58*|DIAPH2_uc004efs.2_Nonsense_Mutation_p.R58*	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156	58					cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4						GCAGCGTGACCGAATTACAAG	0.333													3	48	---	---	---	---	PASS
SRPX2	27286	broad.mit.edu	37	X	99920283	99920283	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:99920283G>T	uc004egb.2	+	6	1056	c.576G>T	c.(574-576)AAG>AAT	p.K192N		NM_014467	NP_055282	O60687	SRPX2_HUMAN	sushi-repeat-containing protein, X-linked 2	192	HYR.				angiogenesis|cell motility|cell-cell adhesion|positive regulation of cell migration involved in sprouting angiogenesis|regulation of phosphorylation	cytoplasm|extracellular region	receptor binding			ovary(2)	2						CACGTGAGAAGATGGCAGAGC	0.527													3	13	---	---	---	---	PASS
SERPINA7	6906	broad.mit.edu	37	X	105280989	105280989	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:105280989C>A	uc004eme.1	-	1	77	c.61G>T	c.(61-63)GCA>TCA	p.A21S	SERPINA7_uc010npd.2_Missense_Mutation_p.A21S|SERPINA7_uc010npe.1_Missense_Mutation_p.A21S	NM_000354	NP_000345	P05543	THBG_HUMAN	serine (or cysteine) proteinase inhibitor, clade	21					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity				0					Levothyroxine(DB00451)|Liothyronine(DB00279)	TCAGGTGATGCACAGTGGATT	0.418													16	88	---	---	---	---	PASS
TBC1D8B	54885	broad.mit.edu	37	X	106108822	106108822	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:106108822C>T	uc004emo.2	+	15	2551	c.2386C>T	c.(2386-2388)CTT>TTT	p.L796F	MORC4_uc004emp.3_Intron	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	796						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						GAAATTGAGCCTTCAAGAATT	0.289													7	61	---	---	---	---	PASS
PRPS1	5631	broad.mit.edu	37	X	106890869	106890869	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:106890869C>A	uc004ene.3	+	6	943	c.738C>A	c.(736-738)GCC>GCA	p.A246A	PRPS1_uc010npg.2_Silent_p.A213A|PRPS1_uc011msj.1_Silent_p.A42A	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	246					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						GAGTTTATGCCATCTTGACTC	0.453													8	107	---	---	---	---	PASS
PRPS1	5631	broad.mit.edu	37	X	106890870	106890870	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:106890870A>T	uc004ene.3	+	6	944	c.739A>T	c.(739-741)ATC>TTC	p.I247F	PRPS1_uc010npg.2_Missense_Mutation_p.I214F|PRPS1_uc011msj.1_Missense_Mutation_p.I43F	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	247					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						AGTTTATGCCATCTTGACTCA	0.448													8	107	---	---	---	---	PASS
RGAG1	57529	broad.mit.edu	37	X	109696544	109696544	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:109696544C>A	uc004eor.1	+	3	2945	c.2699C>A	c.(2698-2700)CCA>CAA	p.P900Q	RGAG1_uc011msr.1_Missense_Mutation_p.P900Q	NM_020769	NP_065820	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	900										lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4						GTGTCCTCACCACTAGTAAGA	0.537													10	114	---	---	---	---	PASS
GLUD2	2747	broad.mit.edu	37	X	120181847	120181847	+	Silent	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:120181847C>A	uc004eto.2	+	1	386	c.309C>A	c.(307-309)CGC>CGA	p.R103R		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	103					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)	ACCGGGTGCGCGGCATCCTGC	0.637													4	47	---	---	---	---	PASS
SH2D1A	4068	broad.mit.edu	37	X	123499665	123499665	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:123499665G>T	uc004euf.3	+	2	537	c.192G>T	c.(190-192)TGG>TGT	p.W64C	SH2D1A_uc004euh.3_Missense_Mutation_p.W64C|SH2D1A_uc004eug.3_RNA|SH2D1A_uc010nqw.2_Intron|SH2D1A_uc004eui.3_Intron|SH2D1A_uc010nqx.2_Intron	NM_002351	NP_002342	O60880	SH21A_HUMAN	SH2 domain protein 1A isoform 1	64	SH2.				cell-cell signaling|cellular defense response	cytoplasm	SH3/SH2 adaptor activity				0						CAGGTTCTTGGAGTGCTGAGG	0.348									X-linked_Lymphoproliferative_syndrome				16	129	---	---	---	---	PASS
AIFM1	9131	broad.mit.edu	37	X	129270690	129270690	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:129270690C>T	uc004evg.2	-	11	1270	c.1092G>A	c.(1090-1092)ATG>ATA	p.M364I	AIFM1_uc011mur.1_Missense_Mutation_p.M12I|AIFM1_uc011mus.1_3'UTR|AIFM1_uc004evh.2_Missense_Mutation_p.M360I|AIFM1_uc004evi.2_Missense_Mutation_p.M77I|AIFM1_uc004evk.2_RNA	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	364	FAD-dependent oxidoreductase (By similarity).				activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5						TAGCATTGGGCATCACCTTAA	0.488													4	44	---	---	---	---	PASS
DDX26B	203522	broad.mit.edu	37	X	134681116	134681116	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:134681116T>C	uc004eyw.3	+	6	1031	c.668T>C	c.(667-669)CTA>CCA	p.L223P		NM_182540	NP_872346	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	223	VWFA.										0	Acute lymphoblastic leukemia(192;6.56e-05)					TTAGAATCTCTAGTTCAAAAA	0.333													20	180	---	---	---	---	PASS
MAP7D3	79649	broad.mit.edu	37	X	135313040	135313040	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:135313040G>T	uc004ezt.2	-	9	1590	c.1499C>A	c.(1498-1500)TCT>TAT	p.S500Y	MAP7D3_uc004ezs.2_Missense_Mutation_p.S464Y|MAP7D3_uc011mwc.1_Missense_Mutation_p.S482Y|MAP7D3_uc010nsa.1_Missense_Mutation_p.S458Y	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	500						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)					ATTTTCAGGAGATGATGACCA	0.408													9	77	---	---	---	---	PASS
ZIC3	7547	broad.mit.edu	37	X	136649363	136649363	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:136649363G>A	uc004fak.2	+	1	1018	c.513G>A	c.(511-513)GGG>GGA	p.G171G		NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3	171					cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					AGGGCGCTGGGCACCCGTCGC	0.697													7	55	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140994572	140994572	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:140994572G>A	uc004fbt.2	+	4	1668	c.1382G>A	c.(1381-1383)AGT>AAT	p.S461N	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	461							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					CTTTTCCAGAGTTCCCCTGAG	0.488										HNSCC(15;0.026)			20	176	---	---	---	---	PASS
SLITRK4	139065	broad.mit.edu	37	X	142717525	142717525	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:142717525C>A	uc004fbx.2	-	2	1776	c.1400G>T	c.(1399-1401)GGC>GTC	p.G467V	SLITRK4_uc004fby.2_Missense_Mutation_p.G467V	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	467	Extracellular (Potential).|LRR 10.					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					GTCAAAGGTGCCTGCTGAGAT	0.388													10	80	---	---	---	---	PASS
SLITRK2	84631	broad.mit.edu	37	X	144905921	144905921	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:144905921T>A	uc004fcd.2	+	5	2968	c.1978T>A	c.(1978-1980)TTA>ATA	p.L660I	SLITRK2_uc010nsp.2_Missense_Mutation_p.L660I|SLITRK2_uc010nso.2_Missense_Mutation_p.L660I|SLITRK2_uc011mwq.1_Missense_Mutation_p.L660I|SLITRK2_uc011mwr.1_Missense_Mutation_p.L660I|SLITRK2_uc011mws.1_Missense_Mutation_p.L660I|SLITRK2_uc004fcg.2_Missense_Mutation_p.L660I|SLITRK2_uc011mwt.1_Missense_Mutation_p.L660I	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	660	Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					TACCAACAACTTAGACGTAAG	0.458													11	74	---	---	---	---	PASS
AFF2	2334	broad.mit.edu	37	X	148035201	148035201	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:148035201G>T	uc004fcp.2	+	10	1968	c.1489G>T	c.(1489-1491)GAT>TAT	p.D497Y	AFF2_uc004fcq.2_Missense_Mutation_p.D487Y|AFF2_uc004fcr.2_Missense_Mutation_p.D458Y|AFF2_uc011mxb.1_Missense_Mutation_p.D462Y|AFF2_uc004fcs.2_Missense_Mutation_p.D464Y|AFF2_uc011mxc.1_Missense_Mutation_p.D138Y	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	497					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					CTCTGAGTCGGATTCAGACAC	0.587													11	97	---	---	---	---	PASS
MAGEA6	4105	broad.mit.edu	37	X	151869553	151869553	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:151869553C>A	uc004ffq.1	+	3	437	c.243C>A	c.(241-243)AGC>AGA	p.S81R	MAGEA6_uc004ffr.1_Missense_Mutation_p.S81R|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	81							protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					CTCTCTGGAGCCAATCCTATG	0.602													8	42	---	---	---	---	PASS
MAGEA12	4111	broad.mit.edu	37	X	151900645	151900645	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:151900645C>G	uc010ntp.2	-	3	510	c.156G>C	c.(154-156)GAG>GAC	p.E52D	MAGEA12_uc004fgb.2_Intron|MAGEA12_uc004fgc.2_Missense_Mutation_p.E52D|CSAG1_uc004fge.2_5'Flank|CSAG1_uc004fgf.2_5'Flank|CSAG1_uc004fgd.2_5'Flank	NM_005367	NP_005358	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	52										skin(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					CAGCAGGCACCTCCCGCAGGG	0.612													6	72	---	---	---	---	PASS
FAM50A	9130	broad.mit.edu	37	X	153678436	153678436	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:153678436G>T	uc004fll.3	+	11	987	c.889G>T	c.(889-891)GAG>TAG	p.E297*		NM_004699	NP_004690	Q14320	FA50A_HUMAN	XAP-5 protein	297					spermatogenesis	nucleus				ovary(1)	1	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGCCACTGTGGAGAAGGATGA	0.612													8	89	---	---	---	---	PASS
F8	2157	broad.mit.edu	37	X	154182256	154182256	+	Missense_Mutation	SNP	T	A	A	rs137852427		TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:154182256T>A	uc004fmt.2	-	12	1985	c.1814A>T	c.(1813-1815)TAC>TTC	p.Y605F		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	605	F5/8 type A 2.|Plastocyanin-like 4.		Y -> H (in HEMA).|Y -> S (in HEMA; severe).		acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTCTGTGAGGTACCAGCTTCG	0.423													19	161	---	---	---	---	PASS
FUNDC2	65991	broad.mit.edu	37	X	154261815	154261815	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:154261815G>T	uc004fmw.2	+	2	421	c.271G>T	c.(271-273)GGT>TGT	p.G91C		NM_023934	NP_076423	Q9BWH2	FUND2_HUMAN	FUN14 domain containing 2	91						mitochondrion					0	all_cancers(53;3.51e-17)|all_epithelial(53;5.13e-11)|all_lung(58;3.84e-07)|Lung NSC(58;1.2e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GTTCATTGGAGGTGTCACTGG	0.453													9	75	---	---	---	---	PASS
SPRY3	10251	broad.mit.edu	37	X	155003644	155003644	+	Silent	SNP	G	A	A			TCGA-34-5234-01A-01D-1632-08	TCGA-34-5234-10A-01D-1632-08									Somatic	Phase_I	Capture				Illumina GAIIx	7b19ae84-2cab-47e7-87df-46c497da17e0	be106855-927a-4cdd-b779-214d377fb068	g.chrX:155003644G>A	uc004fnq.1	+	2	565	c.111G>A	c.(109-111)CAG>CAA	p.Q37Q	SPRY3_uc010nvl.1_Silent_p.Q37Q	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	37					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCTGTAAACAGGCCCTCTCCA	0.532													12	95	---	---	---	---	PASS
