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
PTCHD2	57540	broad.mit.edu	37	1	11561290	11561290	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:11561290G>A	uc001ash.3	+	2	379	c.241G>A	c.(241-243)GGC>AGC	p.G81S	PTCHD2_uc001asi.1_Missense_Mutation_p.G81S	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	81	Helical; (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCTCTTCCTGGGCTGCAGCAT	0.612													13	32	---	---	---	---	PASS
CLCNKA	1187	broad.mit.edu	37	1	16355720	16355720	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:16355720C>A	uc001axu.2	+	12	1233	c.1153C>A	c.(1153-1155)CAG>AAG	p.Q385K	CLCNKA_uc001axt.2_RNA|CLCNKA_uc001axv.2_Missense_Mutation_p.Q385K|CLCNKA_uc010obw.1_Missense_Mutation_p.Q342K|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010obx.1_Missense_Mutation_p.Q32K|CLCNKA_uc010oby.1_Missense_Mutation_p.P114Q	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	385					excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GCTCGACCCCCAGCACCTTTG	0.622													24	16	---	---	---	---	PASS
PAX7	5081	broad.mit.edu	37	1	19018313	19018313	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:19018313C>A	uc001bay.2	+	5	1250	c.652C>A	c.(652-654)CGA>AGA	p.R218R	PAX7_uc001baz.2_Silent_p.R216R|PAX7_uc010oct.1_Silent_p.R218R	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1	218	Homeobox.				anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		GCGCAAGCAGCGACGCAGTCG	0.642			T	FOXO1A	alveolar rhabdomyosarcoma								6	1	---	---	---	---	PASS
KIAA0754	643314	broad.mit.edu	37	1	39876375	39876375	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:39876375G>T	uc009vvt.1	+	1	1200	c.438G>T	c.(436-438)GAG>GAT	p.E146D	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	10											0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			AATTTGCAGAGAGGATAGAAG	0.478													5	103	---	---	---	---	PASS
PTPRF	5792	broad.mit.edu	37	1	44084851	44084851	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:44084851G>T	uc001cjr.2	+	27	4964	c.4624G>T	c.(4624-4626)GGG>TGG	p.G1542W	PTPRF_uc001cjs.2_Missense_Mutation_p.G1533W|PTPRF_uc001cju.2_Missense_Mutation_p.G931W|PTPRF_uc009vwt.2_Missense_Mutation_p.G1102W|PTPRF_uc001cjv.2_Missense_Mutation_p.G1013W|PTPRF_uc001cjw.2_Missense_Mutation_p.G768W	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1542	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCTAGACGCAGGGCCCATGGT	0.642													12	3	---	---	---	---	PASS
USP1	7398	broad.mit.edu	37	1	62916148	62916148	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:62916148G>T	uc001daj.1	+	9	2182	c.1854G>T	c.(1852-1854)ATG>ATT	p.M618I	USP1_uc001dak.1_Missense_Mutation_p.M618I|USP1_uc001dal.1_Missense_Mutation_p.M618I	NM_001017415	NP_001017415	O94782	UBP1_HUMAN	ubiquitin specific protease 1	618					DNA repair|monoubiquitinated protein deubiquitination|regulation of DNA repair|response to UV|ubiquitin-dependent protein catabolic process	nucleoplasm	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		TTGACCAAATGTGTGAAATAG	0.378													11	20	---	---	---	---	PASS
ANKRD13C	81573	broad.mit.edu	37	1	70819844	70819844	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:70819844G>A	uc001dex.3	-	1	574	c.248C>T	c.(247-249)TCC>TTC	p.S83F	ANKRD13C_uc009wbk.2_Missense_Mutation_p.S83F|ANKRD13C_uc001dey.3_Missense_Mutation_p.S83F|HHLA3_uc010oqp.1_5'Flank|HHLA3_uc001dfa.2_5'Flank|HHLA3_uc001dfb.2_5'Flank|HHLA3_uc001dfc.2_5'Flank	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	83					protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0						AGTCACGGAGGAATTGTGCAG	0.652													9	19	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152323767	152323767	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:152323767G>A	uc001ezw.3	-	3	6568	c.6495C>T	c.(6493-6495)TCC>TCT	p.S2165S	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2165	Filaggrin 10.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCTGTGTGGACTGTCCAT	0.507													36	175	---	---	---	---	PASS
MEF2D	4209	broad.mit.edu	37	1	156450735	156450735	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:156450735C>T	uc001fpc.2	-	4	677	c.287G>A	c.(286-288)TGC>TAC	p.C96Y	MEF2D_uc001fpb.2_Missense_Mutation_p.C96Y|MEF2D_uc001fpd.2_Missense_Mutation_p.C96Y|MEF2D_uc001fpe.1_Missense_Mutation_p.C96Y|MEF2D_uc009wsa.2_RNA	NM_005920	NP_005911	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	96					apoptosis|muscle organ development|nervous system development|positive regulation of transcription from RNA polymerase II promoter	nucleus	activating transcription factor binding|histone deacetylase binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGGCTGTCGCAGCCGTTGAA	0.672											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	37	31	---	---	---	---	PASS
PYHIN1	149628	broad.mit.edu	37	1	158908982	158908982	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:158908982G>A	uc001ftb.2	+	4	769	c.524G>A	c.(523-525)CGT>CAT	p.R175H	PYHIN1_uc001fta.3_Missense_Mutation_p.R175H|PYHIN1_uc001ftc.2_Missense_Mutation_p.R166H|PYHIN1_uc001ftd.2_Missense_Mutation_p.R175H|PYHIN1_uc001fte.2_Missense_Mutation_p.R166H	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1	175					cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)					GCCATGGGCCGTTCCCCACCT	0.532													12	75	---	---	---	---	PASS
FCGR3A	2214	broad.mit.edu	37	1	161518242	161518242	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:161518242G>T	uc001gat.3	-	4	425	c.288C>A	c.(286-288)CTC>CTA	p.L96L	FCGR3A_uc001gar.2_Silent_p.L132L|FCGR3A_uc001gas.2_Silent_p.L131L|FCGR3A_uc009wuh.2_Silent_p.L95L|FCGR3A_uc009wui.2_Silent_p.L96L	NM_001127595	NP_001121067	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor	96	Ig-like C2-type 1.|Extracellular (Potential).				immune response|regulation of immune response	extracellular region|integral to membrane|plasma membrane	IgG binding|receptor activity			ovary(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCGGGTCACTGAGGGTGGAGA	0.512													13	105	---	---	---	---	PASS
FCGR3B	2215	broad.mit.edu	37	1	161599599	161599599	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:161599599G>T	uc009wul.2	-	3	562	c.288C>A	c.(286-288)CTC>CTA	p.L96L		NM_000570	NP_000561	O75015	FCG3B_HUMAN	low affinity immunoglobulin gamma Fc region	96	Ig-like C2-type 1.				immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCGGGTCACTGAGGGTGGAGA	0.502													6	57	---	---	---	---	PASS
RASAL2	9462	broad.mit.edu	37	1	178425887	178425887	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:178425887G>A	uc001glr.2	+	11	1945	c.1820G>A	c.(1819-1821)CGT>CAT	p.R607H	RASAL2_uc001glq.2_Missense_Mutation_p.R748H|RASAL2_uc009wxc.2_Missense_Mutation_p.R121H	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	607					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						CCTCTCCCTCGTGTTCTTGCT	0.453													53	214	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276983	186276983	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:186276983G>T	uc001gru.3	+	7	2183	c.2132G>T	c.(2131-2133)GGG>GTG	p.G711V	PRG4_uc001grt.3_Missense_Mutation_p.G670V|PRG4_uc009wyl.2_Missense_Mutation_p.G618V|PRG4_uc009wym.2_Missense_Mutation_p.G577V|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	711	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|43; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						ACCCCTAAAGGGACTGCTCCA	0.587													7	192	---	---	---	---	PASS
FAM58B	339521	broad.mit.edu	37	1	200183203	200183203	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:200183203C>A	uc009wzi.1	+	1	548	c.512C>A	c.(511-513)GCC>GAC	p.A171D		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	171					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent		protein kinase binding				0	Prostate(682;0.19)					ACCCCCGTTGCCGTCACTGCC	0.632													8	31	---	---	---	---	PASS
PPFIA4	8497	broad.mit.edu	37	1	203025576	203025576	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:203025576C>A	uc001gyz.2	+	5	1255	c.662C>A	c.(661-663)CCC>CAC	p.P221H	PPFIA4_uc009xaj.2_Missense_Mutation_p.P852H|PPFIA4_uc010pqf.1_Missense_Mutation_p.P434H|PPFIA4_uc001gza.2_Missense_Mutation_p.P221H|PPFIA4_uc001gzb.1_5'Flank	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f	221					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						CCTTCCTCACCCAGGACGCTG	0.572													4	30	---	---	---	---	PASS
DUSP10	11221	broad.mit.edu	37	1	221913078	221913078	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:221913078C>T	uc001hmy.1	-	2	191	c.9G>A	c.(7-9)CCG>CCA	p.P3P	DUSP10_uc001hmx.1_5'Flank|DUSP10_uc001hmz.1_Intron	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a	3					inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0103)		CTAAAGGAGACGGAGGCATGA	0.483													37	27	---	---	---	---	PASS
TTC13	79573	broad.mit.edu	37	1	231047278	231047278	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:231047278G>A	uc001huf.3	-	20	2278	c.2247C>T	c.(2245-2247)TGC>TGT	p.C749C	TTC13_uc009xfi.2_Silent_p.C696C|TTC13_uc009xfj.2_RNA|TTC13_uc001hug.3_Silent_p.C695C|TTC13_uc009xfk.1_Silent_p.C638C	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	749							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		AGATTAAGTTGCAGACAGCAT	0.289													7	13	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237664052	237664052	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:237664052T>A	uc001hyl.1	+	21	2365	c.2245T>A	c.(2245-2247)TTA>ATA	p.L749I		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	749	Cytoplasmic (By similarity).|B30.2/SPRY 1.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CCAACATCTGTTAAGAACTGA	0.393													99	105	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240370373	240370373	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:240370373T>G	uc010pyd.1	+	5	2486	c.2261T>G	c.(2260-2262)GTG>GGG	p.V754G	FMN2_uc010pye.1_Missense_Mutation_p.V758G	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	754					actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GAGGGCGGGGTGCTGACACTG	0.542													6	16	---	---	---	---	PASS
OR11L1	391189	broad.mit.edu	37	1	248004842	248004842	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:248004842G>T	uc001idn.1	-	1	357	c.357C>A	c.(355-357)GCC>GCA	p.A119A		NM_001001959	NP_001001959	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AACGGTCATAGGCCATGAAGG	0.607													7	20	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11733151	11733151	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:11733151T>C	uc002rbk.1	+	11	1895	c.1595T>C	c.(1594-1596)ATG>ACG	p.M532T	GREB1_uc002rbo.1_Missense_Mutation_p.M166T	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	532						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CTCTCCGAGATGTTCCGGCTG	0.662													10	12	---	---	---	---	PASS
FAM49A	81553	broad.mit.edu	37	2	16736368	16736368	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:16736368C>G	uc010exm.1	-	10	1025	c.877G>C	c.(877-879)GAC>CAC	p.D293H	FAM49A_uc002rck.1_Missense_Mutation_p.D293H	NM_030797	NP_110424	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	293						intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			TCCACACTGTCTGGGGCCTGC	0.448													5	36	---	---	---	---	PASS
GALNT14	79623	broad.mit.edu	37	2	31165143	31165143	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:31165143G>A	uc002rnr.2	-	9	1474	c.855C>T	c.(853-855)TTC>TTT	p.F285F	GALNT14_uc002rnq.2_Silent_p.F265F|GALNT14_uc002rns.2_Silent_p.F290F|GALNT14_uc010ymr.1_Silent_p.F250F|GALNT14_uc010ezo.1_Silent_p.F252F|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	285	Lumenal (Potential).|Catalytic subdomain B.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					TGTCGATCACGAAGAGCCCTC	0.498													17	43	---	---	---	---	PASS
PROKR1	10887	broad.mit.edu	37	2	68882479	68882479	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:68882479A>T	uc010yqj.1	+	2	953	c.953A>T	c.(952-954)AAG>ATG	p.K318M	PROKR1_uc002ses.2_RNA	NM_138964	NP_620414	Q8TCW9	PKR1_HUMAN	G protein-coupled receptor 73	318	Extracellular (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1						GTGAAGGAGAAGCACTACCTC	0.557													25	40	---	---	---	---	PASS
REG3G	130120	broad.mit.edu	37	2	79253251	79253251	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:79253251C>A	uc002snw.2	+	2	117	c.32C>A	c.(31-33)TCC>TAC	p.S11Y	REG3G_uc002snx.2_Missense_Mutation_p.S11Y|REG3G_uc010ffu.2_Missense_Mutation_p.S11Y	NM_198448	NP_940850	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma precursor	11					acute-phase response	extracellular region	sugar binding				0						CCCAGTGTGTCCTGGATGCTG	0.537													18	39	---	---	---	---	PASS
C2orf51	200523	broad.mit.edu	37	2	88828671	88828671	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:88828671C>A	uc002stb.1	+	4	364	c.222C>A	c.(220-222)CCC>CCA	p.P74P		NM_152670	NP_689883	Q96LM6	TSC21_HUMAN	chromosome 2 open reading frame 51	74						nucleus				skin(1)	1						TCAAAAGACCCCACATGACTG	0.557													36	54	---	---	---	---	PASS
EDAR	10913	broad.mit.edu	37	2	109539886	109539886	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:109539886G>A	uc002teq.3	-	5	811	c.380C>T	c.(379-381)CCG>CTG	p.P127L	EDAR_uc010fjn.2_Missense_Mutation_p.P127L|EDAR_uc010yws.1_Missense_Mutation_p.P127L	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	127	TNFR-Cys 3.|Extracellular (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GATGTTCCTCGGTCTGTTCTC	0.547													25	30	---	---	---	---	PASS
ACTR3	10096	broad.mit.edu	37	2	114688952	114688952	+	Silent	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:114688952A>T	uc002tkx.1	+	5	731	c.411A>T	c.(409-411)CCA>CCT	p.P137P	ACTR3_uc010yyc.1_Silent_p.P75P|ACTR3_uc010yyd.1_Silent_p.P86P	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog	137					cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						TCAATGTTCCAGGCTTGTACA	0.318													18	24	---	---	---	---	PASS
MARCO	8685	broad.mit.edu	37	2	119750717	119750717	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:119750717G>T	uc002tln.1	+	16	1402	c.1270G>T	c.(1270-1272)GTC>TTC	p.V424F	MARCO_uc010yyf.1_Missense_Mutation_p.V346F	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	424	SRCR.|Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6						CTCAGTGTCCGTCAGGATTGT	0.517													12	138	---	---	---	---	PASS
CLASP1	23332	broad.mit.edu	37	2	122227508	122227508	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:122227508C>T	uc002tnc.2	-	9	1131	c.741G>A	c.(739-741)GTG>GTA	p.V247V	CLASP1_uc010yyw.1_RNA|CLASP1_uc002tnb.2_RNA|CLASP1_uc010yyx.1_RNA|CLASP1_uc010yyy.1_RNA|CLASP1_uc010yyz.1_Silent_p.V247V|CLASP1_uc010yza.1_Silent_p.V247V|CLASP1_uc010yzb.1_RNA|CLASP1_uc010yzc.1_RNA|CLASP1_uc002tng.1_Silent_p.V247V	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1	247					axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					TGTTACCATCCACAGAATCTT	0.388													26	64	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125262047	125262047	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:125262047C>A	uc002tno.2	+	8	1602	c.1238C>A	c.(1237-1239)TCG>TAG	p.S413*	CNTNAP5_uc010flu.2_Nonsense_Mutation_p.S414*	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	413	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TCTGAGGGCTCGGGAACCCTG	0.542													4	100	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141122335	141122335	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:141122335C>A	uc002tvj.1	-	72	11998	c.11026G>T	c.(11026-11028)GCT>TCT	p.A3676S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3676	Extracellular (Potential).|LDL-receptor class A 30.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AACTCATCAGCTCTACATATA	0.393										TSP Lung(27;0.18)			24	30	---	---	---	---	PASS
KIF5C	3800	broad.mit.edu	37	2	149838057	149838057	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:149838057C>T	uc010zbu.1	+	14	1919	c.1551C>T	c.(1549-1551)GAC>GAT	p.D517D	KIF5C_uc002tws.1_RNA|KIF5C_uc002twt.2_Silent_p.D69D	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C	517					microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		AGCTGACAGACGAGCTGGCCC	0.512													7	11	---	---	---	---	PASS
ANKAR	150709	broad.mit.edu	37	2	190571740	190571740	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:190571740G>T	uc002uqw.1	+	8	1774	c.1774G>T	c.(1774-1776)GCT>TCT	p.A592S	ANKAR_uc002uqu.2_RNA	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	663	ANK 4.					integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			TTCTATCGGTGCTAACTGGAG	0.313													8	33	---	---	---	---	PASS
MSTN	2660	broad.mit.edu	37	2	190925015	190925015	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr2:190925015G>T	uc002urp.2	-	2	653	c.520C>A	c.(520-522)CTG>ATG	p.L174M		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	174					muscle organ development|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			ATGAGTCTCAGGATTTGCACA	0.398													6	78	---	---	---	---	PASS
RBM6	10180	broad.mit.edu	37	3	50012788	50012788	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:50012788G>A	uc003cyc.2	+	5	1579	c.1446G>A	c.(1444-1446)ATG>ATA	p.M482I	RBM6_uc011bdh.1_RNA|RBM6_uc010hlc.1_Missense_Mutation_p.M1I|RBM6_uc003cyd.2_5'UTR|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_RNA|RBM6_uc010hle.1_RNA|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	482	RRM.				RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		CTGATGGCATGCCTGTAAAGA	0.383													32	33	---	---	---	---	PASS
EPHA3	2042	broad.mit.edu	37	3	89456489	89456489	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:89456489C>A	uc003dqy.2	+	8	1890	c.1665C>A	c.(1663-1665)CTC>CTA	p.L555L	EPHA3_uc010hon.1_RNA	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	555	Helical; (Potential).					extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CAATTATTCTCCTCACTGTTG	0.413										TSP Lung(6;0.00050)			14	16	---	---	---	---	PASS
OR5H6	79295	broad.mit.edu	37	3	97983832	97983832	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:97983832C>A	uc003dsi.1	+	1	704	c.704C>A	c.(703-705)ACA>AAA	p.T235K		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	235	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3						ATATCTTATACAATTATCCTC	0.328													5	35	---	---	---	---	PASS
HSPBAP1	79663	broad.mit.edu	37	3	122512524	122512524	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:122512524C>G	uc003efu.1	-	1	127	c.4G>C	c.(4-6)GCA>CCA	p.A2P	DIRC2_uc003efw.3_5'Flank|DIRC2_uc010hrl.2_5'Flank|DIRC2_uc010hrm.2_5'Flank|HSPBAP1_uc003efv.1_Missense_Mutation_p.A2P	NM_024610	NP_078886	Q96EW2	HBAP1_HUMAN	Hspb associated protein 1	2						cytoplasm				ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.0531)		GAGCCTGCTGCCATGGCTACC	0.662													29	28	---	---	---	---	PASS
RUVBL1	8607	broad.mit.edu	37	3	127820473	127820473	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:127820473C>A	uc003ekh.2	-	5	636	c.532G>T	c.(532-534)GAA>TAA	p.E178*	RUVBL1_uc003eke.2_5'UTR|RUVBL1_uc003ekf.2_Nonsense_Mutation_p.E118*|RUVBL1_uc010hss.2_Nonsense_Mutation_p.E178*	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1	178					cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)		TGCAAACTTTCAAAAATGCTG	0.418													7	292	---	---	---	---	PASS
NPHP3	27031	broad.mit.edu	37	3	132400856	132400856	+	Silent	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:132400856G>C	uc003epe.1	-	27	3968	c.3891C>G	c.(3889-3891)CTC>CTG	p.L1297L	NPHP3_uc003eoz.1_Silent_p.L176L|NPHP3_uc003epd.1_Silent_p.L539L	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3	1297					maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						TTCCACCCAAGAGTGATGTTT	0.388													58	30	---	---	---	---	PASS
NMD3	51068	broad.mit.edu	37	3	160952514	160952514	+	Splice_Site	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:160952514G>T	uc003feb.1	+	6	477	c.358_splice	c.e6-1	p.V120_splice	NMD3_uc003fec.2_Splice_Site_p.V120_splice|NMD3_uc003fed.1_Splice_Site_p.V120_splice|NMD3_uc010hwh.2_5'Flank	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			TGTTTTATCAGGTGATGAATG	0.308													4	47	---	---	---	---	PASS
EPHB3	2049	broad.mit.edu	37	3	184297281	184297281	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:184297281G>T	uc003foz.2	+	10	2255	c.1818G>T	c.(1816-1818)AAG>AAT	p.K606N		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	606	Cytoplasmic (Potential).					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)			CTGGAATGAAGGTTTATATTG	0.567													7	313	---	---	---	---	PASS
WHSC2	7469	broad.mit.edu	37	4	1993339	1993339	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:1993339G>T	uc003gem.2	-	2	587	c.347C>A	c.(346-348)TCG>TAG	p.S116*	WHSC2_uc003gel.2_Nonsense_Mutation_p.S30*|WHSC2_uc003gen.2_Intron	NM_005663	NP_005654	Q9H3P2	NELFA_HUMAN	Wolf-Hirschhorn syndrome candidate 2 protein	105					multicellular organismal development|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm				skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0155)			CAGGTTAAGCGAGCCTGTGTC	0.532													4	45	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3424106	3424106	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:3424106G>A	uc003ggw.2	+	11	3746	c.2842G>A	c.(2842-2844)GAG>AAG	p.E948K	RGS12_uc003ggv.2_Missense_Mutation_p.E948K|RGS12_uc003ggy.1_Missense_Mutation_p.E346K|RGS12_uc003ggz.2_Missense_Mutation_p.E300K|RGS12_uc010icu.1_Missense_Mutation_p.E147K|RGS12_uc011bvs.1_Missense_Mutation_p.E290K|RGS12_uc003gha.2_Missense_Mutation_p.E290K|RGS12_uc010icv.2_Missense_Mutation_p.E147K|RGS12_uc003ghb.2_Missense_Mutation_p.E147K	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	948						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCCCCAGTCGGAGGCCTGCAG	0.667													6	4	---	---	---	---	PASS
LGI2	55203	broad.mit.edu	37	4	25028544	25028544	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:25028544G>A	uc003grf.2	-	3	386	c.287C>T	c.(286-288)TCA>TTA	p.S96L		NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	96	LRR 1.					extracellular region					0		Breast(46;0.173)				GATCGTGAATGAGTTAGAATT	0.383													34	18	---	---	---	---	PASS
NPFFR2	10886	broad.mit.edu	37	4	73012827	73012827	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:73012827A>C	uc003hgg.2	+	4	965	c.867A>C	c.(865-867)GAA>GAC	p.E289D	NPFFR2_uc010iig.1_Missense_Mutation_p.E71D|NPFFR2_uc003hgi.2_Missense_Mutation_p.E190D|NPFFR2_uc003hgh.2_Missense_Mutation_p.E187D|NPFFR2_uc003hgj.2_RNA	NM_004885	NP_004876	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	289	Extracellular (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			TGCAAGAAGAAAAATATTACC	0.433													25	68	---	---	---	---	PASS
THAP6	152815	broad.mit.edu	37	4	76447060	76447060	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:76447060C>T	uc003him.2	+	4	500	c.403C>T	c.(403-405)CAG>TAG	p.Q135*	THAP6_uc010iis.1_Nonsense_Mutation_p.Q94*|THAP6_uc003hin.2_Intron|THAP6_uc011cbm.1_Nonsense_Mutation_p.Q135*|THAP6_uc010iiu.1_RNA|THAP6_uc003hio.1_Intron|THAP6_uc010iiv.2_Nonsense_Mutation_p.Q135*	NM_144721	NP_653322	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	135						microtubule cytoskeleton	DNA binding|metal ion binding				0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ATTCCAATCCCAGTTCATTTT	0.348													32	15	---	---	---	---	PASS
DMP1	1758	broad.mit.edu	37	4	88583873	88583873	+	Missense_Mutation	SNP	G	A	A	rs149603030		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:88583873G>A	uc003hqv.2	+	6	1047	c.943G>A	c.(943-945)GGT>AGT	p.G315S	DMP1_uc003hqw.2_Missense_Mutation_p.G299S	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1	315					biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AGACAGCAAGGGTGACTCTCA	0.512													13	36	---	---	---	---	PASS
NFKB1	4790	broad.mit.edu	37	4	103498032	103498032	+	Splice_Site	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:103498032G>T	uc011ceq.1	+	7	872	c.405_splice	c.e7-1	p.G135_splice	NFKB1_uc011cep.1_Splice_Site_p.G136_splice|NFKB1_uc011cer.1_5'Flank	NM_003998	NP_003989	P19838	NFKB1_HUMAN	nuclear factor kappa-B, subunit 1 isoform 1						anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|breast(2)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)	TTTTTCTCCAGCTTCGCAAAC	0.383													39	18	---	---	---	---	PASS
NEIL3	55247	broad.mit.edu	37	4	178243682	178243682	+	Missense_Mutation	SNP	G	T	T	rs34112288	byFrequency	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:178243682G>T	uc003iut.2	+	2	343	c.226G>T	c.(226-228)GTG>TTG	p.V76L	NEIL3_uc010irs.2_Intron	NM_018248	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3	76					base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TTACAGTGGCGTGGAAACTTT	0.393								BER_DNA_glycosylases					12	62	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13737392	13737392	+	Silent	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:13737392T>C	uc003jfd.2	-	66	11466	c.11424A>G	c.(11422-11424)CAA>CAG	p.Q3808Q	DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3808	Potential.				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CTGAGTTAATTTGAACTTCTG	0.413									Kartagener_syndrome				17	70	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33662055	33662055	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:33662055G>C	uc003jia.1	-	6	1169	c.1006C>G	c.(1006-1008)CCT>GCT	p.P336A	ADAMTS12_uc010iuq.1_Missense_Mutation_p.P336A	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	336	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TGATGAACAGGATTGAGGTCA	0.493										HNSCC(64;0.19)			14	72	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36049132	36049132	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:36049132C>A	uc003jjz.1	-	4	795	c.702G>T	c.(700-702)AGG>AGT	p.R234S	UGT3A2_uc011cos.1_Missense_Mutation_p.R200S|UGT3A2_uc011cot.1_Intron	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	234	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACAAAACTGGCCTAGAGCCTT	0.418													101	34	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37169396	37169396	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:37169396C>A	uc011cpa.1	-	34	6961	c.6730G>T	c.(6730-6732)GGA>TGA	p.G2244*	C5orf42_uc011coy.1_Nonsense_Mutation_p.G744*|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Nonsense_Mutation_p.G1319*|C5orf42_uc003jkr.1_Nonsense_Mutation_p.G277*	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	2244										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GGAATACTTCCTGTATGTAAG	0.448													6	139	---	---	---	---	PASS
MAN2A1	4124	broad.mit.edu	37	5	109181611	109181611	+	Missense_Mutation	SNP	G	T	T	rs142363192		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:109181611G>T	uc003kou.1	+	18	3709	c.2746G>T	c.(2746-2748)GTC>TTC	p.V916F		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	916	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)		TCAAGCAAATGTCTATCCCAT	0.378													37	21	---	---	---	---	PASS
FTMT	94033	broad.mit.edu	37	5	121188071	121188071	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:121188071G>C	uc003kss.2	+	1	422	c.413G>C	c.(412-414)GGC>GCC	p.G138A		NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial precursor	138	Ferritin-like diiron.				cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CAGCGAGGAGGCCGGATCCGC	0.582													25	5	---	---	---	---	PASS
SEPT8	23176	broad.mit.edu	37	5	132099577	132099577	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:132099577G>A	uc003kxr.2	-	4	593	c.355C>T	c.(355-357)CCC>TCC	p.P119S	SEPT8_uc003kxs.1_Missense_Mutation_p.P119S|SEPT8_uc003kxu.2_Missense_Mutation_p.P119S|SEPT8_uc011cxi.1_Missense_Mutation_p.P117S|SEPT8_uc003kxv.2_Missense_Mutation_p.P117S|SEPT8_uc003kxt.2_Missense_Mutation_p.P59S	NM_001098811	NP_001092281	Q92599	SEPT8_HUMAN	septin 8 isoform a	119					cell cycle	septin complex	GTP binding|protein binding			ovary(2)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCAACTATGGGCCTGTAACTA	0.587											OREG0003468	type=REGULATORY REGION|Gene=LOC540614|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	10	70	---	---	---	---	PASS
HAVCR1	26762	broad.mit.edu	37	5	156482444	156482444	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:156482444T>G	uc010jij.1	-	3	332	c.147A>C	c.(145-147)AGA>AGC	p.R49S	HAVCR1_uc011ddl.1_5'Flank|HAVCR1_uc003lwi.2_Missense_Mutation_p.R49S|HAVCR1_uc011ddm.1_Missense_Mutation_p.R49S	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	49	Extracellular (Potential).|Ig-like V-type.				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AACATGAGCCTCTATTCCAGC	0.502													11	9	---	---	---	---	PASS
KCNMB1	3779	broad.mit.edu	37	5	169810700	169810700	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr5:169810700G>T	uc003maq.1	-	3	689	c.289C>A	c.(289-291)CGG>AGG	p.R97R	KCNIP1_uc003map.2_Intron|KCNMB1_uc003mar.2_Silent_p.R97R	NM_004137	NP_004128	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated	97	Extracellular (Potential).				platelet activation|synaptic transmission		calcium-activated potassium channel activity|potassium channel regulator activity			ovary(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)		TTCTGGTCCCGAGTGTCCTCC	0.582													3	30	---	---	---	---	PASS
OR12D3	81797	broad.mit.edu	37	6	29342547	29342547	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:29342547T>C	uc003nme.2	-	1	522	c.518A>G	c.(517-519)AAT>AGT	p.N173S		NM_030959	NP_112221	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D,	173	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)	3						GAAGAAGTGATTGAGTTTCTG	0.463													19	36	---	---	---	---	PASS
BRD2	6046	broad.mit.edu	37	6	32947734	32947734	+	Silent	SNP	A	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:32947734A>G	uc003ocn.3	+	11	3672	c.1971A>G	c.(1969-1971)TTA>TTG	p.L657L	BRD2_uc003ocq.3_Silent_p.L657L|BRD2_uc003ocp.3_Silent_p.L537L|BRD2_uc010juh.2_Silent_p.L692L	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	657	ET.				spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5						TCAACAAATTACCTGGGGAGA	0.502													13	19	---	---	---	---	PASS
UNC5CL	222643	broad.mit.edu	37	6	41002666	41002666	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:41002666C>A	uc003opi.2	-	2	237	c.148G>T	c.(148-150)GAG>TAG	p.E50*	UNC5CL_uc010jxe.1_Nonsense_Mutation_p.E50*	NM_173561	NP_775832	Q8IV45	UN5CL_HUMAN	unc-5 homolog C-like	50	Cytoplasmic (Potential).				signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACTGGTTCCTCTTGACCATTC	0.597													4	42	---	---	---	---	PASS
RMND1	55005	broad.mit.edu	37	6	151766462	151766462	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:151766462G>T	uc003qoi.2	-	2	665	c.485C>A	c.(484-486)CCA>CAA	p.P162Q	RMND1_uc011eeq.1_5'Flank|RMND1_uc003qoj.2_Missense_Mutation_p.P162Q|RMND1_uc011eer.1_Missense_Mutation_p.P162Q	NM_017909	NP_060379	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog	162											0		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		AGACAGAACTGGAAGGTTGGT	0.502													4	35	---	---	---	---	PASS
TIAM2	26230	broad.mit.edu	37	6	155578117	155578117	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:155578117C>A	uc003qqb.2	+	29	6241	c.4968C>A	c.(4966-4968)CAC>CAA	p.H1656Q	TIAM2_uc003qqe.2_Missense_Mutation_p.H1656Q|TIAM2_uc010kjj.2_Missense_Mutation_p.H1218Q|TIAM2_uc003qqf.2_Missense_Mutation_p.H1032Q|TIAM2_uc011efl.1_Missense_Mutation_p.H1000Q|TIAM2_uc003qqg.2_Missense_Mutation_p.H968Q|TIAM2_uc003qqh.2_Missense_Mutation_p.H581Q|uc003qqi.1_5'Flank	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1656					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGATCCGTCACCAGTCCCTTG	0.507													15	19	---	---	---	---	PASS
NOX3	50508	broad.mit.edu	37	6	155750148	155750148	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:155750148G>A	uc003qqm.2	-	9	1028	c.925C>T	c.(925-927)CAC>TAC	p.H309Y		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	309	Extracellular (Potential).|FAD-binding FR-type.						electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		TTTTTCATGTGAAGTTCCAGG	0.493													5	115	---	---	---	---	PASS
TULP4	56995	broad.mit.edu	37	6	158900915	158900915	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr6:158900915A>T	uc003qrf.2	+	7	2516	c.1159A>T	c.(1159-1161)AGC>TGC	p.S387C	TULP4_uc011efo.1_Missense_Mutation_p.S387C|TULP4_uc003qrg.2_Missense_Mutation_p.S387C	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	387	SOCS box.				intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GGCCATCGCCAGCACCTTGCG	0.627													19	18	---	---	---	---	PASS
POM121L12	285877	broad.mit.edu	37	7	53104165	53104165	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:53104165C>T	uc003tpz.2	+	1	817	c.801C>T	c.(799-801)TTC>TTT	p.F267F		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	267											0						TCTGGGACTTCTGGGAGGCGA	0.642													18	219	---	---	---	---	PASS
MRPS17	51373	broad.mit.edu	37	7	56020981	56020981	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:56020981C>A	uc003trd.2	+	2	123	c.93C>A	c.(91-93)ACC>ACA	p.T31T	MRPS17_uc003trb.2_Silent_p.T126T	NM_015969	NP_057053	Q9Y2R5	RT17_HUMAN	mitochondrial ribosomal protein S17 precursor	31					translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TGAGAGTGACCAGGCTTGTTC	0.458													7	447	---	---	---	---	PASS
SEMA3C	10512	broad.mit.edu	37	7	80439994	80439994	+	Silent	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:80439994G>C	uc003uhj.2	-	6	1033	c.471C>G	c.(469-471)TCC>TCG	p.S157S	SEMA3C_uc011kgw.1_Silent_p.S175S|SEMA3C_uc011kgx.1_Silent_p.S9S	NM_006379	NP_006370	Q99985	SEM3C_HUMAN	semaphorin 3C precursor	157	Sema.				immune response|response to drug	membrane	receptor activity			ovary(1)	1						ATTCACACTTGGAGTCAATCA	0.358													26	41	---	---	---	---	PASS
UFSP1	402682	broad.mit.edu	37	7	100486765	100486765	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:100486765A>T	uc003uxc.3	-	1	575	c.128T>A	c.(127-129)CTG>CAG	p.L43Q	uc010lhm.1_5'Flank	NM_001015072	NP_001015072	Q6NVU6	UFSP1_HUMAN	inactive Ufm1-specific protease 1	43											0	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTCCCCGTGCAGCCCCACTCC	0.701													12	26	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113558921	113558921	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:113558921C>A	uc010ljy.1	-	1	162	c.131G>T	c.(130-132)CGA>CTA	p.R44L		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	44					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						ATCAGAACCTCGTCTACTTGG	0.378													4	96	---	---	---	---	PASS
GCC1	79571	broad.mit.edu	37	7	127222187	127222187	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:127222187G>A	uc003vma.2	-	2	2627	c.2209C>T	c.(2209-2211)CTG>TTG	p.L737L		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	737	Potential.|GRIP.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2						TGGCGGCCCAGGGAGTCAGGT	0.532													18	68	---	---	---	---	PASS
MKRN1	23608	broad.mit.edu	37	7	140156495	140156495	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:140156495G>A	uc003vvt.2	-	5	1168	c.943C>T	c.(943-945)CGC>TGC	p.R315C	MKRN1_uc003vvs.2_Missense_Mutation_p.R251C|MKRN1_uc011krd.1_Missense_Mutation_p.R49C|MKRN1_uc003vvv.3_Missense_Mutation_p.R315C|MKRN1_uc003vvu.3_Missense_Mutation_p.R251C	NM_013446	NP_038474	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1 isoform 1	315	RING-type.						ligase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.00956)					CTCCACTTGCGAATGCACTTG	0.488													13	40	---	---	---	---	PASS
USP17L2	377630	broad.mit.edu	37	8	11995031	11995031	+	Silent	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:11995031G>C	uc003wvc.1	-	1	1239	c.1239C>G	c.(1237-1239)CCC>CCG	p.P413P	FAM66D_uc011kxp.1_Intron|FAM66D_uc011kxo.1_Intron	NM_201402	NP_958804	Q6R6M4	U17L2_HUMAN	deubiquitinating enzyme 3	413					apoptosis|cell cycle|G2/M transition checkpoint|mitotic cell cycle G1/S transition checkpoint|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)	3						CCTGGAGGCAGGGGTGGTCTC	0.567													39	68	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55539267	55539267	+	Missense_Mutation	SNP	C	T	T	rs112323560		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:55539267C>T	uc003xsd.1	+	4	2973	c.2825C>T	c.(2824-2826)ACG>ATG	p.T942M	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	942					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AGAAATGAAACGAGTGTGGTA	0.303													12	34	---	---	---	---	PASS
HNF4G	3174	broad.mit.edu	37	8	76470903	76470903	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:76470903C>A	uc003yaq.2	+	8	1013	c.743C>A	c.(742-744)CCA>CAA	p.P248Q	HNF4G_uc003yar.2_Missense_Mutation_p.P285Q	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	248					endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			TTTTTTGATCCAGGTTGGTTT	0.303													5	145	---	---	---	---	PASS
PSKH2	85481	broad.mit.edu	37	8	87060971	87060971	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:87060971G>T	uc011lfy.1	-	3	878	c.878C>A	c.(877-879)GCG>GAG	p.A293E		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	293	Protein kinase.						ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)			AAAGTCCTTCGCCAAGTGGGA	0.413													9	30	---	---	---	---	PASS
MATN2	4147	broad.mit.edu	37	8	98943719	98943719	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:98943719G>A	uc003yic.2	+	3	912	c.681G>A	c.(679-681)ACG>ACA	p.T227T	MATN2_uc003yib.1_Silent_p.T227T|MATN2_uc010mbh.1_Silent_p.T227T|MATN2_uc003yid.2_Silent_p.T227T|MATN2_uc003yie.1_Silent_p.T227T|MATN2_uc010mbi.1_Silent_p.T101T	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	227	VWFA 1.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AGATTGAGACGCTGACCTCCG	0.443													17	45	---	---	---	---	PASS
MATN2	4147	broad.mit.edu	37	8	98943720	98943720	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:98943720C>A	uc003yic.2	+	3	913	c.682C>A	c.(682-684)CTG>ATG	p.L228M	MATN2_uc003yib.1_Missense_Mutation_p.L228M|MATN2_uc010mbh.1_Missense_Mutation_p.L228M|MATN2_uc003yid.2_Missense_Mutation_p.L228M|MATN2_uc003yie.1_Missense_Mutation_p.L228M|MATN2_uc010mbi.1_Missense_Mutation_p.L102M	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	228	VWFA 1.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GATTGAGACGCTGACCTCCGT	0.443													17	45	---	---	---	---	PASS
KCNS2	3788	broad.mit.edu	37	8	99441494	99441494	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:99441494C>A	uc003yin.2	+	2	1637	c.1287C>A	c.(1285-1287)AGC>AGA	p.S429R		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	429	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			CCATGCGCAGCTGTGACTTTG	0.488													15	124	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100789166	100789166	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:100789166C>A	uc003yiv.2	+	41	7597	c.7486C>A	c.(7486-7488)CTT>ATT	p.L2496I	VPS13B_uc003yiw.2_Missense_Mutation_p.L2471I	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	2496					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTGTCATCACCTTGACCAACT	0.408													5	97	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103309124	103309124	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:103309124C>A	uc003ykr.1	-	28	3695	c.3662G>T	c.(3661-3663)TGC>TTC	p.C1221F	UBR5_uc003yks.1_Missense_Mutation_p.C1221F	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1221	UBR-type.				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TACTCACTTGCAATCATGACC	0.328													10	15	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110478882	110478882	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:110478882G>A	uc003yne.2	+	50	8593	c.8489G>A	c.(8488-8490)AGC>AAC	p.S2830N		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2830	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GCTGAGTGGAGCATTGGGTTC	0.468										HNSCC(38;0.096)			4	12	---	---	---	---	PASS
KLHL38	340359	broad.mit.edu	37	8	124663821	124663821	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:124663821A>T	uc003yqs.1	-	1	1370	c.1346T>A	c.(1345-1347)ATC>AAC	p.I449N		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	449	Kelch 4.										0						ATTTACCTGGATAAGGCGCAC	0.507													21	102	---	---	---	---	PASS
SLURP1	57152	broad.mit.edu	37	8	143823221	143823221	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:143823221C>A	uc003ywy.2	-	2	204	c.178G>T	c.(178-180)GAG>TAG	p.E60*		NM_020427	NP_065160	P55000	SLUR1_HUMAN	ARS component B precursor	60	UPAR/Ly6.				cell activation|cell adhesion	extracellular space	cytokine activity				0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGGCCTCACCTGCCTCCACC	0.662													6	22	---	---	---	---	PASS
SCRIB	23513	broad.mit.edu	37	8	144886281	144886281	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr8:144886281C>T	uc003yzp.1	-	22	3062	c.3055G>A	c.(3055-3057)GTC>ATC	p.V1019I	SCRIB_uc003yzn.1_5'UTR|SCRIB_uc003yzo.1_Missense_Mutation_p.V1019I	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	1019	Interaction with ARHGEF7.|PDZ 3.				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)			GAGCCTCCGACAATACTAAGC	0.617													9	7	---	---	---	---	PASS
KIAA2026	158358	broad.mit.edu	37	9	5988539	5988539	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:5988539C>A	uc003zjq.3	-	2	816	c.600G>T	c.(598-600)TTG>TTT	p.L200F		NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	200										ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TCTTTTCTCTCAAGTGCCTTG	0.428													4	37	---	---	---	---	PASS
CDKN2A	1029	broad.mit.edu	37	9	21971120	21971120	+	Nonsense_Mutation	SNP	G	A	A	rs121913388		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:21971120G>A	uc003zpk.2	-	2	450	c.238C>T	c.(238-240)CGA>TGA	p.R80*	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Missense_Mutation_p.P135L	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	80	ANK 3.		R -> P (in CMM2; loss of CDK4 binding).|R -> L (in a head and neck tumor).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.R80*(88)|p.?(13)|p.R80Q(2)|p.P135L(2)|p.T79fs*37(1)|p.L65fs*38(1)|p.R80fs*66(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)|p.R80?(1)|p.R80L(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TGCACGGGTCGGGTGAGAGTG	0.726	R80*(MEWO_SKIN)|R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)	17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			11	1	---	---	---	---	PASS
DNAI1	27019	broad.mit.edu	37	9	34493264	34493264	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:34493264A>G	uc003zum.2	+	9	947	c.754A>G	c.(754-756)ACC>GCC	p.T252A		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	252					cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GAAGGCAAAGACCCCAGTGGC	0.463									Kartagener_syndrome				5	79	---	---	---	---	PASS
OR13C4	138804	broad.mit.edu	37	9	107289409	107289409	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:107289409A>C	uc011lvn.1	-	1	82	c.82T>G	c.(82-84)TTT>GTT	p.F28V		NM_001001919	NP_001001919	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C,	28	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						ATCAGAGCAAAGAAAATGATC	0.413													33	57	---	---	---	---	PASS
C5	727	broad.mit.edu	37	9	123780009	123780009	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:123780009T>C	uc004bkv.2	-	13	1658	c.1628A>G	c.(1627-1629)TAT>TGT	p.Y543C	C5_uc010mvm.1_Missense_Mutation_p.Y543C|C5_uc010mvn.1_Missense_Mutation_p.Y543C	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein	543					activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	GACGATGTAATAGACCAGAAG	0.408													25	59	---	---	---	---	PASS
FUT7	2529	broad.mit.edu	37	9	139925444	139925444	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:139925444G>T	uc004ckq.2	-	2	1596	c.747C>A	c.(745-747)GGC>GGA	p.G249G	ABCA2_uc011mel.1_5'Flank|ABCA2_uc011mem.1_5'Flank|ABCA2_uc004ckl.1_5'Flank|ABCA2_uc004ckm.1_5'Flank|C9orf139_uc004ckp.1_Intron	NM_004479	NP_004470	Q11130	FUT7_HUMAN	fucosyltransferase 7	249	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CTGGCACAGTGCCAGCCACCA	0.622													41	63	---	---	---	---	PASS
AKR1E2	83592	broad.mit.edu	37	10	4884670	4884670	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:4884670C>A	uc001ihi.2	+	8	926	c.811C>A	c.(811-813)CCA>ACA	p.P271T	AKR1E2_uc001ihl.1_RNA|AKR1E2_uc010qam.1_Missense_Mutation_p.P175T|AKR1E2_uc001ihh.1_Missense_Mutation_p.P214T|AKR1E2_uc009xhw.2_Missense_Mutation_p.P173T|AKR1E2_uc001ihj.2_RNA|AKR1E2_uc001ihk.2_Missense_Mutation_p.P214T	NM_001040177	NP_001035267	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	271	NADP (By similarity).					cytoplasm	1,5-anhydro-D-fructose reductase activity				0						ATCTATCACCCCAAGTCACAT	0.333													33	71	---	---	---	---	PASS
MRC1	4360	broad.mit.edu	37	10	17949583	17949583	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:17949583C>A	uc001ipk.2	+	28	4050	c.3947C>A	c.(3946-3948)TCC>TAC	p.S1316Y		NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor	1316	Extracellular (Potential).|C-type lectin 8.				receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						AGTCCGGTCTCCTTTGTCAAC	0.403													9	48	---	---	---	---	PASS
ERCC6	2074	broad.mit.edu	37	10	50691393	50691393	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:50691393T>A	uc001jhs.3	-	9	2145	c.1991A>T	c.(1990-1992)CAG>CTG	p.Q664L	ERCC6_uc010qgr.1_Missense_Mutation_p.Q34L|ERCC6_uc001jhr.3_Missense_Mutation_p.Q64L	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	664	Helicase ATP-binding.				base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16						AGGTCATACCTGTTTGCAAGC	0.378								Direct_reversal_of_damage|NER					26	11	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108536394	108536394	+	Silent	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:108536394T>C	uc001kym.2	-	4	791	c.783A>G	c.(781-783)GAA>GAG	p.E261E	SORCS1_uc001kyl.2_Silent_p.E261E|SORCS1_uc009xxs.2_Silent_p.E261E|SORCS1_uc001kyn.1_Silent_p.E261E|SORCS1_uc001kyo.2_Silent_p.E261E	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	261	Lumenal (Potential).|BNR 2.					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AAGTTGCCCCTTCATCTGAGC	0.403													26	18	---	---	---	---	PASS
C10orf84	63877	broad.mit.edu	37	10	120095118	120095118	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:120095118C>T	uc001ldo.2	-	4	537	c.270G>A	c.(268-270)CAG>CAA	p.Q90Q	C10orf84_uc010qss.1_Silent_p.Q90Q	NM_022063	NP_071346	Q9H8W3	F204A_HUMAN	hypothetical protein LOC63877	90											0		Colorectal(252;0.101)		all cancers(201;0.0244)		TTGTGCTTTTCTGTTCAGAAT	0.313													13	6	---	---	---	---	PASS
C10orf137	26098	broad.mit.edu	37	10	127429673	127429673	+	Silent	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:127429673T>C	uc001liq.1	+	17	2567	c.2274T>C	c.(2272-2274)AAT>AAC	p.N758N	C10orf137_uc001lin.2_Silent_p.N724N|C10orf137_uc001lio.1_Silent_p.N724N|C10orf137_uc001lip.1_Silent_p.N462N|C10orf137_uc001lir.2_Silent_p.N252N|C10orf137_uc001lis.1_Silent_p.N84N	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	758					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TGGCCCAGAATGCAAATAATA	0.438													42	24	---	---	---	---	PASS
GPR123	84435	broad.mit.edu	37	10	134898363	134898363	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr10:134898363C>A	uc001llw.2	+	8	1425	c.1425C>A	c.(1423-1425)CTC>CTA	p.L475L				Q86SQ6	GP123_HUMAN	RecName: Full=Probable G-protein coupled receptor 123;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		AGCTGAGCCTCCCTGAGGAGG	0.647													4	27	---	---	---	---	PASS
LRRC56	115399	broad.mit.edu	37	11	551689	551689	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:551689G>T	uc010qvz.1	+	10	1340	c.835G>T	c.(835-837)GAG>TAG	p.E279*		NM_198075	NP_932341	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	279										skin(1)	1		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACTTGACCCCGAGCTGTCCCT	0.687													3	16	---	---	---	---	PASS
DEAF1	10522	broad.mit.edu	37	11	686886	686886	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:686886G>A	uc001lqq.1	-	5	1469	c.776C>T	c.(775-777)GCG>GTG	p.A259V	DEAF1_uc009ycf.1_RNA	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	259	SAND.				embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		GGGTCGGCCCGCGTAGCGAAT	0.607													9	13	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093575	1093575	+	Silent	SNP	G	C	C	rs114864285	by1000genomes	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:1093575G>C	uc001lsx.1	+	31	12507	c.12480G>C	c.(12478-12480)ACG>ACC	p.T4160T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4160						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccacaactacGGTGACCGCAA	0.308													3	14	---	---	---	---	PASS
CCKBR	887	broad.mit.edu	37	11	6291936	6291936	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:6291936C>T	uc001mcp.2	+	4	907	c.714C>T	c.(712-714)TAC>TAT	p.Y238Y	CCKBR_uc001mcq.2_Silent_p.Y166Y|CCKBR_uc001mcr.2_Silent_p.Y238Y|CCKBR_uc001mcs.2_Silent_p.Y238Y|CCKBR_uc001mct.1_5'Flank	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	238	Helical; Name=5; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CCGTGGCCTACGGGCTTATCT	0.582													9	31	---	---	---	---	PASS
OR2AG1	144125	broad.mit.edu	37	11	6806970	6806970	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:6806970G>A	uc001mer.1	+	1	702	c.702G>A	c.(700-702)AGG>AGA	p.R234R		NM_001004489	NP_001004489	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATGAGGGGAGGAAGAAAGCCC	0.498													27	19	---	---	---	---	PASS
NRIP3	56675	broad.mit.edu	37	11	9005648	9005648	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:9005648G>C	uc001mhg.2	-	5	700	c.586C>G	c.(586-588)CTT>GTT	p.L196V	NRIP3_uc010rbu.1_3'UTR	NM_020645	NP_065696	Q9NQ35	NRIP3_HUMAN	nuclear receptor interacting protein 3	196					proteolysis		aspartic-type endopeptidase activity				0				Epithelial(150;4.77e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0241)		TGTAGACCAAGGGACAAGTTT	0.388													58	43	---	---	---	---	PASS
ABCC8	6833	broad.mit.edu	37	11	17428178	17428178	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:17428178G>T	uc001mnc.2	-	26	3446	c.3320C>A	c.(3319-3321)GCC>GAC	p.A1107D		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	1107	Cytoplasmic (By similarity).|ABC transmembrane type-1 2.				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	CCTCATGGGGGCTAGGATGAT	0.413													9	4	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	20005751	20005751	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:20005751C>T	uc010rdm.1	+	12	3156	c.2795C>T	c.(2794-2796)ACC>ATC	p.T932I	NAV2_uc001mpp.2_Missense_Mutation_p.T845I|NAV2_uc001mpr.3_Missense_Mutation_p.T909I	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	932						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						GTACGGGAGACCCTGCAACGA	0.572													27	14	---	---	---	---	PASS
SLC5A12	159963	broad.mit.edu	37	11	26725099	26725099	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:26725099T>A	uc001mra.2	-	6	1113	c.800A>T	c.(799-801)AAA>ATA	p.K267I	SLC5A12_uc001mrb.2_RNA|SLC5A12_uc001mrc.3_Missense_Mutation_p.K267I	NM_178498	NP_848593	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/glucose	267	Cytoplasmic (Potential).				sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)|skin(1)	2						CTTTTCTGTTTTGCAAGAGAT	0.358													38	22	---	---	---	---	PASS
OR5M8	219484	broad.mit.edu	37	11	56258265	56258265	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:56258265C>A	uc001nix.1	-	1	582	c.582G>T	c.(580-582)AAG>AAT	p.K194N		NM_001005282	NP_001005282	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M,	194	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	Esophageal squamous(21;0.00352)					TTGACAACTCCTTGTTGTAGG	0.418													20	82	---	---	---	---	PASS
OR9G9	504191	broad.mit.edu	37	11	56468292	56468292	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:56468292G>T	uc010rjn.1	+	1	429	c.429G>T	c.(427-429)CTG>CTT	p.L143L		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	143	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GTGCATTGCTGGTAGCAGTCT	0.468													6	162	---	---	---	---	PASS
OR9G9	504191	broad.mit.edu	37	11	56468738	56468738	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:56468738G>A	uc010rjn.1	+	1	875	c.875G>A	c.(874-876)AGG>AAG	p.R292K		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	292	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TACAGCCTAAGGAATAAGGAT	0.393													9	89	---	---	---	---	PASS
TCN1	6947	broad.mit.edu	37	11	59622223	59622223	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:59622223T>A	uc001noj.2	-	7	1121	c.1023A>T	c.(1021-1023)AGA>AGT	p.R341S		NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor	341					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(2)	2		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTCATTGATTCTCACAGAGT	0.408													13	54	---	---	---	---	PASS
GANAB	23193	broad.mit.edu	37	11	62397403	62397403	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:62397403C>T	uc001nub.2	-	14	1653	c.1620G>A	c.(1618-1620)TGG>TGA	p.W540*	GANAB_uc001ntz.2_5'Flank|GANAB_uc001nua.2_Nonsense_Mutation_p.W562*|GANAB_uc001nuc.2_Nonsense_Mutation_p.W443*|GANAB_uc010rma.1_Nonsense_Mutation_p.W448*|GANAB_uc010rmb.1_Nonsense_Mutation_p.W426*	NM_198334	NP_938148	Q14697	GANAB_HUMAN	neutral alpha-glucosidase AB isoform 2	540					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5						TCATGTCATTCCAGACAAAGA	0.532													20	64	---	---	---	---	PASS
RAB30	27314	broad.mit.edu	37	11	82708291	82708291	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:82708291G>A	uc001ozu.2	-	3	329	c.68C>T	c.(67-69)ACG>ATG	p.T23M	RAB30_uc009yve.2_Missense_Mutation_p.T21M|RAB30_uc010rst.1_Missense_Mutation_p.T21M|RAB30_uc001ozv.2_Missense_Mutation_p.T21M|RAB30_uc009yvg.1_Missense_Mutation_p.T21M	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family	23	GTP (By similarity).				protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						GACGAGGCACGTCTTCCCCAC	0.408													8	44	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85447586	85447586	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:85447586A>T	uc010rth.1	-	5	817	c.541T>A	c.(541-543)TCA>ACA	p.S181T	SYTL2_uc010rtg.1_Missense_Mutation_p.S182T|SYTL2_uc010rti.1_Missense_Mutation_p.S181T|SYTL2_uc010rtj.1_Missense_Mutation_p.S133T|SYTL2_uc001pbf.3_Missense_Mutation_p.S181T|SYTL2_uc010rtf.1_Missense_Mutation_p.S39T	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	181					intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CCATTTTTTGACTGTTCATTT	0.323													6	22	---	---	---	---	PASS
SIK3	23387	broad.mit.edu	37	11	116729359	116729359	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:116729359T>C	uc001ppy.2	-	20	2540	c.2504A>G	c.(2503-2505)CAT>CGT	p.H835R	SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|SIK3_uc001ppw.2_Intron|SIK3_uc001ppx.2_Intron|SIK3_uc001pqb.2_Missense_Mutation_p.H138R	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK	835	Gln-rich.					cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						CGAAAACAGATGGGGGTGTAA	0.547													52	59	---	---	---	---	PASS
TNFRSF1A	7132	broad.mit.edu	37	12	6440025	6440025	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:6440025C>T	uc001qnu.2	-	6	900	c.619G>A	c.(619-621)GAC>AAC	p.D207N	TNFRSF1A_uc001qnt.2_Missense_Mutation_p.D99N|TNFRSF1A_uc010sey.1_5'UTR|TNFRSF1A_uc010sez.1_Missense_Mutation_p.D99N|TNFRSF1A_uc009zek.2_Missense_Mutation_p.D164N	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	207	Extracellular (Potential).				apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3						TCACCTGAGTCCTCAGTGCCC	0.453													12	57	---	---	---	---	PASS
TNFRSF1A	7132	broad.mit.edu	37	12	6440077	6440077	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:6440077C>A	uc001qnu.2	-	6	848	c.567G>T	c.(565-567)CTG>CTT	p.L189L	TNFRSF1A_uc001qnt.2_Silent_p.L81L|TNFRSF1A_uc010sey.1_5'UTR|TNFRSF1A_uc010sez.1_Silent_p.L81L|TNFRSF1A_uc009zek.2_Silent_p.L146L	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	189	TNFR-Cys 4.|Extracellular (Potential).				apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3						TCGTGCACTCCAGGCTTTTCT	0.512													4	45	---	---	---	---	PASS
KIAA1467	57613	broad.mit.edu	37	12	13208823	13208823	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:13208823C>G	uc001rbi.2	+	2	399	c.376C>G	c.(376-378)CCC>GCC	p.P126A	KIAA1467_uc009zhx.1_RNA	NM_020853	NP_065904	A2RU67	K1467_HUMAN	hypothetical protein LOC57613	126						integral to membrane				central_nervous_system(2)|skin(1)	3		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		TTTCCTGATCCCCTGTCCTCC	0.577													13	33	---	---	---	---	PASS
RASSF8	11228	broad.mit.edu	37	12	26220541	26220541	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:26220541C>T	uc001rgx.2	+	4	1254	c.1033C>T	c.(1033-1035)CGG>TGG	p.R345W	RASSF8_uc001rgy.2_Missense_Mutation_p.R345W|RASSF8_uc001rgz.2_Missense_Mutation_p.R345W|RASSF8_uc009zjd.1_Missense_Mutation_p.R345W|RASSF8_uc009zje.1_Missense_Mutation_p.R345W	NM_007211	NP_009142	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family	345					signal transduction						0	Colorectal(261;0.0847)					TAAGGAGTTGCGGCAAGTCAA	0.438													16	24	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53345369	53345369	+	Silent	SNP	C	T	T	rs145578755		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:53345369C>T	uc001sbe.2	+	5	831	c.762C>T	c.(760-762)GCC>GCT	p.A254A	KRT18_uc009zmn.1_Silent_p.A254A|KRT18_uc001sbf.1_Silent_p.A81A|KRT18_uc001sbg.2_Silent_p.A254A|KRT18_uc009zmo.2_Silent_p.A254A|KRT8_uc009zml.1_5'Flank|KRT8_uc009zmm.1_5'Flank	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	254	Interaction with DNAJB6.|Coil 2.|Rod.|Necessary for interaction with PNN.				anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity			skin(1)	1						ACATCCGGGCCCAATATGACG	0.587													10	22	---	---	---	---	PASS
CALCOCO1	57658	broad.mit.edu	37	12	54115366	54115366	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:54115366C>T	uc001sef.2	-	6	787	c.643G>A	c.(643-645)GAG>AAG	p.E215K	CALCOCO1_uc010som.1_Missense_Mutation_p.E182K|CALCOCO1_uc010son.1_Missense_Mutation_p.E92K|CALCOCO1_uc001seh.2_Missense_Mutation_p.E215K|CALCOCO1_uc009znd.2_Missense_Mutation_p.E215K|CALCOCO1_uc001seg.2_Missense_Mutation_p.E92K|CALCOCO1_uc010soo.1_Missense_Mutation_p.E208K	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	215					steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1						ATGTCCCTCTCTTCTGTGATC	0.532													6	292	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56717636	56717636	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:56717636C>T	uc001skx.2	-	14	2512	c.2139G>A	c.(2137-2139)CAG>CAA	p.Q713Q	PAN2_uc001skw.2_5'UTR|PAN2_uc001skz.2_Silent_p.Q712Q|PAN2_uc001sky.2_Silent_p.Q709Q	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	713					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						CCTGTGTATTCTGGTCCAGGC	0.512													6	37	---	---	---	---	PASS
GAS2L3	283431	broad.mit.edu	37	12	101005798	101005798	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:101005798G>A	uc001thu.2	+	6	550	c.324G>A	c.(322-324)GTG>GTA	p.V108V	GAS2L3_uc009zty.2_Silent_p.V108V|GAS2L3_uc001thv.2_Silent_p.V4V	NM_174942	NP_777602	Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	108	CH.				cell cycle arrest					skin(1)	1						TGAGAAAAGTGCCCTGTAAGA	0.353													31	20	---	---	---	---	PASS
PEBP1	5037	broad.mit.edu	37	12	118575878	118575878	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:118575878G>T	uc001twu.1	+	2	315	c.170G>T	c.(169-171)GGT>GTT	p.G57V	PEBP1_uc010szc.1_Missense_Mutation_p.G57V	NM_002567	NP_002558	P30086	PEBP1_HUMAN	prostatic binding protein	57							ATP binding|phosphatidylethanolamine binding|serine-type endopeptidase inhibitor activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCGTGGGATGGTCTTGATTCA	0.438								Direct_reversal_of_damage					3	21	---	---	---	---	PASS
TAOK3	51347	broad.mit.edu	37	12	118693369	118693369	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr12:118693369G>C	uc001twx.2	-	3	299	c.4C>G	c.(4-6)CGT>GGT	p.R2G	TAOK3_uc001twy.3_Missense_Mutation_p.R2G	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	2					MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACCCCTTTACGCATGATGGCC	0.398													39	102	---	---	---	---	PASS
SLC7A1	6541	broad.mit.edu	37	13	30104821	30104821	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr13:30104821C>A	uc001uso.2	-	5	945	c.558G>T	c.(556-558)TCG>TCT	p.S186S		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	186	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	TGACCATGGCCGACTCTTTCA	0.433													47	18	---	---	---	---	PASS
TBC1D4	9882	broad.mit.edu	37	13	76055559	76055559	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr13:76055559C>T	uc001vjl.1	-	1	692	c.345G>A	c.(343-345)GCG>GCA	p.A115A	TBC1D4_uc010aer.2_Silent_p.A115A|TBC1D4_uc010aes.2_Silent_p.A115A	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	115	PID 1.					cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		AGATGAATACCGCCGGGTTGG	0.662													31	7	---	---	---	---	PASS
RBM26	64062	broad.mit.edu	37	13	79946001	79946001	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr13:79946001G>C	uc001vkz.2	-	4	406	c.392C>G	c.(391-393)TCA>TGA	p.S131*	RBM26_uc001vky.2_Nonsense_Mutation_p.S131*|RBM26_uc001vla.2_Nonsense_Mutation_p.S131*|RBM26_uc001vkx.2_5'Flank|RBM26_uc001vlb.1_5'Flank	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	131					mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		TCGGGAGCTTGACTGGGGAGG	0.368													9	28	---	---	---	---	PASS
NOVA1	4857	broad.mit.edu	37	14	26917694	26917694	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:26917694A>T	uc001wpy.2	-	5	1313	c.995T>A	c.(994-996)TTA>TAA	p.L332*	NOVA1_uc001wpz.2_Nonsense_Mutation_p.L308*|NOVA1_uc001wqa.2_Nonsense_Mutation_p.L210*	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1	335	Ala-rich.				locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		ACCTAAACCTAAAGTGTTGAG	0.299													17	16	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44974483	44974483	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:44974483C>A	uc001wvn.2	-	1	2017	c.1708G>T	c.(1708-1710)GAA>TAA	p.E570*		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	570	Ala-rich.					cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		GGGGCCTCTTCTATAGAAACT	0.517													17	37	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975345	44975345	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:44975345C>G	uc001wvn.2	-	1	1155	c.846G>C	c.(844-846)GAG>GAC	p.E282D		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	282						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		CAGGTCTGGGCTCCGCTTTAG	0.473													19	29	---	---	---	---	PASS
EXOC5	10640	broad.mit.edu	37	14	57700535	57700535	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:57700535C>T	uc001xct.2	-	9	1032	c.781G>A	c.(781-783)GTT>ATT	p.V261I	EXOC5_uc001xcs.2_5'Flank|EXOC5_uc010trg.1_Missense_Mutation_p.V206I|EXOC5_uc010trh.1_Missense_Mutation_p.V196I	NM_006544	NP_006535	O00471	EXOC5_HUMAN	SEC10 protein	261					exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm				ovary(2)|breast(1)	3						ATATCTCCAACTTGTTTGTTC	0.308													12	37	---	---	---	---	PASS
ARID4A	5926	broad.mit.edu	37	14	58813807	58813807	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:58813807T>G	uc001xdp.2	+	14	1398	c.1144T>G	c.(1144-1146)TCC>GCC	p.S382A	ARID4A_uc001xdo.2_Missense_Mutation_p.S382A|ARID4A_uc001xdq.2_Missense_Mutation_p.S382A|ARID4A_uc010apg.1_Missense_Mutation_p.S60A	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	382	ARID.				negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6						TTCAGCTGCTTCCTACAATGT	0.279													9	17	---	---	---	---	PASS
JDP2	122953	broad.mit.edu	37	14	75904629	75904629	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:75904629G>A	uc010asj.2	+	2	73	c.6G>A	c.(4-6)ATG>ATA	p.M2I	JDP2_uc010tvb.1_Missense_Mutation_p.M2I|JDP2_uc010tvc.1_Missense_Mutation_p.M2I|JDP2_uc001xrq.2_Missense_Mutation_p.M13I	NM_001135047	NP_001128519	Q8WYK2	JDP2_HUMAN	Jun dimerization protein 2 isoform a	2						nucleus	sequence-specific DNA binding				0				BRCA - Breast invasive adenocarcinoma(234;0.0296)		CTGCTATGATGCCTGGGCAGA	0.667													8	6	---	---	---	---	PASS
TMED8	283578	broad.mit.edu	37	14	77810117	77810117	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:77810117T>A	uc001xto.1	-	4	377	c.377A>T	c.(376-378)CAG>CTG	p.Q126L	TMED8_uc010ast.1_RNA|TMED8_uc001xtn.1_5'Flank	NM_213601	NP_998766	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain	126					transport	integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ATGTTCAGACTGGATCATAAC	0.448													41	79	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94088266	94088266	+	Nonsense_Mutation	SNP	G	T	T	rs78490074	byFrequency	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr14:94088266G>T	uc001ybv.1	+	28	4305	c.4222G>T	c.(4222-4224)GAG>TAG	p.E1408*	KIAA1409_uc001ybs.1_Nonsense_Mutation_p.E1386*	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1563						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TGAAATCCCCGAGAACCCAGC	0.512													4	98	---	---	---	---	PASS
TRPM1	4308	broad.mit.edu	37	15	31354881	31354881	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:31354881C>G	uc001zfm.2	-	8	1052	c.924G>C	c.(922-924)GAG>GAC	p.E308D	TRPM1_uc010azy.2_Missense_Mutation_p.E215D|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	308	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CTAGAAGCTGCTCCCTGAGGG	0.343													8	23	---	---	---	---	PASS
DUOXA2	405753	broad.mit.edu	37	15	45408422	45408422	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:45408422C>A	uc001zuo.2	+	3	586	c.306C>A	c.(304-306)CTC>CTA	p.L102L	DUOX2_uc010bea.2_5'Flank|DUOX2_uc001zun.2_5'Flank|DUOXA2_uc010beb.2_RNA	NM_207581	NP_997464	Q1HG44	DOXA2_HUMAN	dual oxidase activator 2	102	Extracellular (Potential).				protein transport	endoplasmic reticulum membrane|integral to membrane					0		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		TCCGTCTGCTCGTGGGCCTGG	0.567													5	155	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52561963	52561963	+	Silent	SNP	G	T	T	rs142061334	by1000genomes	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:52561963G>T	uc010bff.2	-	8	1064	c.927C>A	c.(925-927)ACC>ACA	p.T309T	MYO5C_uc010uga.1_RNA|MYO5C_uc010ugb.1_RNA|MYO5C_uc010ugc.1_Intron	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	309	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		GAAGCGTGAAGGTCTTTTGAG	0.323													5	98	---	---	---	---	PASS
CSNK1G1	53944	broad.mit.edu	37	15	64495336	64495336	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:64495336C>G	uc002anf.2	-	10	1532	c.1052G>C	c.(1051-1053)CGA>CCA	p.R351P	CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Missense_Mutation_p.R351P|CSNK1G1_uc002anh.1_Missense_Mutation_p.R351P|CSNK1G1_uc002anj.2_Missense_Mutation_p.R333P	NM_022048	NP_071331	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	351					Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0						GTGGCTTTCTCGAGTTATTGC	0.453													9	19	---	---	---	---	PASS
PARP6	56965	broad.mit.edu	37	15	72542428	72542428	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:72542428G>A	uc002auc.2	-	18	1883	c.1424C>T	c.(1423-1425)TCC>TTC	p.S475F	PARP6_uc002aua.2_Missense_Mutation_p.S321F|PARP6_uc002aub.2_RNA|PARP6_uc002aud.3_RNA|PARP6_uc002auf.1_Missense_Mutation_p.S476F	NM_020214	NP_064599	Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	475	PARP catalytic.						NAD+ ADP-ribosyltransferase activity				0						CTCAATGTGGGACCCACTGTA	0.507													7	41	---	---	---	---	PASS
KIAA1024	23251	broad.mit.edu	37	15	79749056	79749056	+	Silent	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr15:79749056C>G	uc002bew.1	+	2	642	c.567C>G	c.(565-567)GCC>GCG	p.A189A	KIAA1024_uc010unk.1_Silent_p.A189A	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251	189						integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4						AAAACCGCGCCGCTTCCCTGG	0.572													14	32	---	---	---	---	PASS
TMC7	79905	broad.mit.edu	37	16	19041589	19041589	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr16:19041589T>C	uc002dfq.2	+	6	885	c.755T>C	c.(754-756)ATT>ACT	p.I252T	TMC7_uc010vao.1_Missense_Mutation_p.I252T|TMC7_uc002dfp.2_Missense_Mutation_p.I252T|TMC7_uc010vap.1_Missense_Mutation_p.I142T	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a	252	Extracellular (Potential).					integral to membrane				skin(2)|ovary(1)	3						CATTACACCATTGATGGGGTG	0.483													44	27	---	---	---	---	PASS
TMEM159	57146	broad.mit.edu	37	16	21181808	21181808	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr16:21181808G>A	uc002dif.3	+	3	508	c.147G>A	c.(145-147)CCG>CCA	p.P49P	TMEM159_uc002dig.3_RNA|TMEM159_uc010vbf.1_Silent_p.P73P|TMEM159_uc002dih.3_Silent_p.P49P	NM_020422	NP_065155	Q96B96	TM159_HUMAN	transmembrane protein 159	49						integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0972)		ACAGCCATCCGTTTCTGGCCT	0.537													55	19	---	---	---	---	PASS
USP6	9098	broad.mit.edu	37	17	5039221	5039221	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:5039221C>T	uc002gau.1	+	17	2892	c.662C>T	c.(661-663)CCA>CTA	p.P221L	USP6_uc002gav.1_Missense_Mutation_p.P221L|USP6_uc010ckz.1_5'UTR|uc002gba.2_5'Flank|uc002gbb.2_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	221	Rab-GAP TBC.				protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						CACTCCCTGCCAGGTAGGTGA	0.622			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								17	25	---	---	---	---	PASS
ATP1B2	482	broad.mit.edu	37	17	7557573	7557573	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:7557573C>T	uc002gif.1	+	4	1133	c.550C>T	c.(550-552)CGG>TGG	p.R184W		NM_001678	NP_001669	P14415	AT1B2_HUMAN	Na+/K+ -ATPase beta 2 subunit	184	Extracellular (Potential).				ATP biosynthetic process|blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|sodium:potassium-exchanging ATPase activity	p.0?(2)|p.?(1)		central_nervous_system(1)|pancreas(1)	2		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)		CAAGATGAACCGGGTATCTAT	0.557													37	123	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577022	7577022	+	Nonsense_Mutation	SNP	G	A	A	rs121913344		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:7577022G>A	uc002gim.2	-	8	1110	c.916C>T	c.(916-918)CGA>TGA	p.R306*	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Nonsense_Mutation_p.R306*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.R174*|TP53_uc010cng.1_Nonsense_Mutation_p.R174*|TP53_uc002gii.1_Nonsense_Mutation_p.R174*|TP53_uc010cnh.1_Nonsense_Mutation_p.R306*|TP53_uc010cni.1_Nonsense_Mutation_p.R306*|TP53_uc002gij.2_Nonsense_Mutation_p.R306*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	306	Bipartite nuclear localization signal.|Interaction with HIPK1 (By similarity).|Interaction with CARM1.		R -> Q (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R306*(99)|p.0?(7)|p.?(3)|p.R306R(2)|p.R306fs*39(2)|p.K305fs*1(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TGCTTACCTCGCTTAGTGCTC	0.562	R306*(MFE296_ENDOMETRIUM)|R306*(HCC1937_BREAST)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			39	60	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577138	7577138	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:7577138C>G	uc002gim.2	-	8	994	c.800G>C	c.(799-801)CGG>CCG	p.R267P	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R267P|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R135P|TP53_uc010cng.1_Missense_Mutation_p.R135P|TP53_uc002gii.1_Missense_Mutation_p.R135P|TP53_uc010cnh.1_Missense_Mutation_p.R267P|TP53_uc010cni.1_Missense_Mutation_p.R267P|TP53_uc002gij.2_Missense_Mutation_p.R267P	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	267	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> H (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R267W(20)|p.R267P(13)|p.0?(7)|p.R267Q(7)|p.R267R(5)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.R267fs*78(1)|p.N268fs*77(1)|p.L265_K305del41(1)|p.R267G(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.R267L(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		AAAGCTGTTCCGTCCCAGTAG	0.527		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			5	18	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578177	7578177	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:7578177C>T	uc002gim.2	-	6	866	c.672G>A	c.(670-672)GAG>GAA	p.E224E	TP53_uc002gig.1_Silent_p.E224E|TP53_uc002gih.2_Silent_p.E224E|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Silent_p.E92E|TP53_uc010cng.1_Silent_p.E92E|TP53_uc002gii.1_Silent_p.E92E|TP53_uc010cnh.1_Silent_p.E224E|TP53_uc010cni.1_Silent_p.E224E|TP53_uc002gij.2_Silent_p.E224E|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Silent_p.E131E|TP53_uc002gio.2_Silent_p.E92E|TP53_uc010vug.1_Silent_p.E185E	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	224	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.E224D(11)|p.0?(7)|p.E224E(6)|p.E224K(5)|p.E224*(4)|p.?(3)|p.E224G(2)|p.E224fs*4(1)|p.E224fs*5(1)|p.V218_E224delVPYEPPE(1)|p.E224fs*23(1)|p.V225fs*24(1)|p.E224fs*24(1)|p.E224_V225insXX(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CAAACCAGACCTCAGGCGGCT	0.522		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			11	20	---	---	---	---	PASS
GLP2R	9340	broad.mit.edu	37	17	9792887	9792887	+	Silent	SNP	T	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:9792887T>G	uc002gmd.1	+	13	1527	c.1527T>G	c.(1525-1527)GGT>GGG	p.G509G		NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor	509	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				lung(2)|ovary(1)	3					Glucagon recombinant(DB00040)	CCATGCGAGGTCTTGGGGAGC	0.627													18	31	---	---	---	---	PASS
MYH4	4622	broad.mit.edu	37	17	10359023	10359023	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:10359023C>A	uc002gmn.2	-	19	2193	c.2082G>T	c.(2080-2082)CTG>CTT	p.L694L	uc002gml.1_Intron	NM_017533	NP_060003	Q9Y623	MYH4_HUMAN	myosin, heavy polypeptide 4, skeletal muscle	694	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(10)|skin(2)|central_nervous_system(1)	13						TCAGCTGATGCAGGACAAGCT	0.488													17	44	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10400644	10400644	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:10400644G>T	uc002gmo.2	-	32	4585	c.4491C>A	c.(4489-4491)GAC>GAA	p.D1497E	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1497	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						TTTCAAGTTGGTCTAAAGATT	0.338													11	37	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11532901	11532901	+	Silent	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:11532901G>C	uc002gne.2	+	7	1586	c.1518G>C	c.(1516-1518)ACG>ACC	p.T506T		NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	506	Potential.|Stem (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)		TCCAAAGCACGGTAGGGTTGG	0.512													13	49	---	---	---	---	PASS
SUPT6H	6830	broad.mit.edu	37	17	27011913	27011913	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:27011913C>A	uc002hby.2	+	19	2511	c.2421C>A	c.(2419-2421)GAC>GAA	p.D807E	SUPT6H_uc010crt.2_Missense_Mutation_p.D807E	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	807					chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)					AAGTGACAGACTTCCTTCGAC	0.478													4	62	---	---	---	---	PASS
DDX52	11056	broad.mit.edu	37	17	35993348	35993348	+	Silent	SNP	G	A	A	rs145856014	byFrequency	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:35993348G>A	uc002hoi.1	-	3	425	c.387C>T	c.(385-387)TCC>TCT	p.S129S	DDX52_uc002hoh.1_Silent_p.S21S|DDX52_uc002hoj.1_Silent_p.S37S	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a	129						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				CCAACTTTCCGGAAGTTAGTT	0.358													31	67	---	---	---	---	PASS
GSDMB	55876	broad.mit.edu	37	17	38073399	38073399	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:38073399G>T	uc010cwj.2	-	1	176	c.171C>A	c.(169-171)ACC>ACA	p.T57T	GSDMB_uc010cwk.2_RNA|GSDMB_uc010cwl.2_RNA|GSDMB_uc010cwm.2_RNA|GSDMB_uc002htg.2_Silent_p.T57T|GSDMB_uc002hth.2_Silent_p.T57T|GSDMB_uc010wem.1_Silent_p.T57T	NM_001042471	NP_001035936	Q8TAX9	GSDMB_HUMAN	gasdermin B isoform 1	57						cytoplasm				breast(1)|pancreas(1)	2						TGTCCATCAGGGTGAGGCCTG	0.517													8	174	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56670914	56670914	+	Splice_Site	SNP	A	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:56670914A>G	uc010dcz.1	-	15	2712	c.2594_splice	c.e15+1	p.S865_splice	TEX14_uc002iwr.1_Splice_Site_p.S859_splice|TEX14_uc002iws.1_Splice_Site_p.S859_splice|TEX14_uc010dda.1_Splice_Site_p.S639_splice	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATGTTGACCCACCTACTGGTA	0.423													14	31	---	---	---	---	PASS
KCNJ16	3773	broad.mit.edu	37	17	68128628	68128628	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:68128628T>C	uc002jin.2	+	5	886	c.400T>C	c.(400-402)TAT>CAT	p.Y134H	KCNJ16_uc002jio.2_Missense_Mutation_p.Y134H|KCNJ16_uc002jip.2_Missense_Mutation_p.Y134H|KCNJ16_uc002jiq.2_Missense_Mutation_p.Y166H	NM_018658	NP_061128	Q9NPI9	IRK16_HUMAN	potassium inwardly-rectifying channel J16	134	Selectivity filter (By similarity).				synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Breast(10;2.96e-09)					CACCATAGGATATGGTTATCG	0.438													7	62	---	---	---	---	PASS
MGAT5B	146664	broad.mit.edu	37	17	74899417	74899417	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:74899417C>T	uc002jti.2	+	4	614	c.511C>T	c.(511-513)CCC>TCC	p.P171S	MGAT5B_uc002jth.2_Missense_Mutation_p.P160S	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2	160	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						GTGTGAGGCACCCAGTGACCC	0.647													12	45	---	---	---	---	PASS
SGSH	6448	broad.mit.edu	37	17	78184602	78184602	+	Silent	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:78184602G>T	uc002jxz.3	-	8	1245	c.1158C>A	c.(1156-1158)CTC>CTA	p.L386L	SGSH_uc002jya.3_Silent_p.L183L|SGSH_uc002jxy.2_3'UTR	NM_000199	NP_000190	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase precursor	386			L -> R (in MPS3A).		proteoglycan metabolic process	lysosome	metal ion binding|N-sulfoglucosamine sulfohydrolase activity|sulfuric ester hydrolase activity			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GGTTGTGCACGAGGCGGAAGT	0.627													4	90	---	---	---	---	PASS
C17orf70	80233	broad.mit.edu	37	17	79514423	79514423	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:79514423G>C	uc002kaq.2	-	5	1740	c.1685C>G	c.(1684-1686)GCC>GGC	p.A562G	C17orf70_uc002kao.1_Missense_Mutation_p.A211G|C17orf70_uc010wuq.1_RNA|C17orf70_uc002kap.2_Missense_Mutation_p.A411G	NM_001109760	NP_001103230	Q0VG06	FP100_HUMAN	Fanconi anemia core complex 100 kDa subunit	562					DNA repair	cytoplasm|intermediate filament cytoskeleton|nucleoplasm	DNA binding			ovary(1)|skin(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GTAGGTGATGGCGGAGCAGGC	0.682													35	33	---	---	---	---	PASS
WDR45L	56270	broad.mit.edu	37	17	80575270	80575270	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr17:80575270G>A	uc002kfq.2	-	8	903	c.708C>T	c.(706-708)ATC>ATT	p.I236I	WDR45L_uc002kfr.2_RNA	NM_019613	NP_062559	Q5MNZ6	WIPI3_HUMAN	WDR45-like	236	WD 2.				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0952)	all_cancers(8;0.101)|all_epithelial(8;0.198)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.0835)			GATTGAAGTTGATGCTGCAGA	0.502													12	30	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21427528	21427528	+	Silent	SNP	A	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr18:21427528A>G	uc002kuq.2	+	32	4118	c.4032A>G	c.(4030-4032)TCA>TCG	p.S1344S	LAMA3_uc002kur.2_Silent_p.S1344S	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1344	Laminin EGF-like 10.|Domain III B.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGACACACTCATTCAGCTTCC	0.657													24	4	---	---	---	---	PASS
MC4R	4160	broad.mit.edu	37	18	58038736	58038736	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr18:58038736G>T	uc002lie.1	-	1	1266	c.847C>A	c.(847-849)CAC>AAC	p.H283N		NM_005912	NP_005903	P32245	MC4R_HUMAN	melanocortin 4 receptor	283	Helical; Name=7; (Potential).				feeding behavior|G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of bone resorption|positive regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|ubiquitin protein ligase binding			lung(1)	1		Colorectal(73;0.0946)				AAGTTAAAGTGAGACATGAAG	0.413													5	73	---	---	---	---	PASS
AP3D1	8943	broad.mit.edu	37	19	2137779	2137779	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:2137779A>T	uc002luz.2	-	3	443	c.220T>A	c.(220-222)TGG>AGG	p.W74R	AP3D1_uc002luy.2_Missense_Mutation_p.W74R|AP3D1_uc002lva.2_Missense_Mutation_p.W74R	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	74					eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		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)		AAGGCGGCCCAGCTGATGTCG	0.522													109	26	---	---	---	---	PASS
XAB2	56949	broad.mit.edu	37	19	7685168	7685168	+	Silent	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:7685168C>T	uc002mgx.2	-	16	2285	c.2259G>A	c.(2257-2259)ACG>ACA	p.T753T		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	753				SAT -> IP (in Ref. 2; AAF86951).	transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4						CACCGGTGCCCGTGGCACTGC	0.637								Direct_reversal_of_damage|NER					4	18	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9077425	9077425	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:9077425C>A	uc002mkp.2	-	3	10225	c.10021G>T	c.(10021-10023)GGA>TGA	p.G3341*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3342	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						AATTCCATTCCAGTTGTCTTT	0.498													5	167	---	---	---	---	PASS
ASNA1	439	broad.mit.edu	37	19	12856427	12856427	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:12856427G>T	uc002muv.2	+	4	477	c.463G>T	c.(463-465)GTG>TTG	p.V155L	ASNA1_uc002muw.2_Missense_Mutation_p.V154L	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	155					response to arsenic-containing substance	endoplasmic reticulum|nucleolus|soluble fraction	arsenite-transporting ATPase activity|ATP binding|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)	CCTCAGGCTGGTGAAGGGCAT	0.667													38	14	---	---	---	---	PASS
C19orf46	163183	broad.mit.edu	37	19	36494565	36494565	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:36494565C>G	uc002ocq.1	-	7	1070	c.981G>C	c.(979-981)AAG>AAC	p.K327N	C19orf46_uc002ocr.1_Missense_Mutation_p.E268Q|C19orf46_uc002ocs.1_Missense_Mutation_p.K214N|C19orf46_uc010een.1_Missense_Mutation_p.K242N	NM_001039876	NP_001034965	Q8N205	SYNE4_HUMAN	hypothetical protein LOC163183	327	Cytoplasmic (Potential).				establishment of epithelial cell apical/basal polarity	integral to nuclear outer membrane	actin binding			ovary(1)	1	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ATGCTTGCCTCTTCTTGTCCT	0.433													4	22	---	---	---	---	PASS
ZNF568	374900	broad.mit.edu	37	19	37440987	37440987	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:37440987G>C	uc002ofc.2	+	7	1447	c.932G>C	c.(931-933)TGT>TCT	p.C311S	ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Missense_Mutation_p.C235S|ZNF568_uc010efe.2_Missense_Mutation_p.C235S|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	311	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTAAGGATTGTTGGAAAGCC	0.383													11	31	---	---	---	---	PASS
MAP4K1	11184	broad.mit.edu	37	19	39108208	39108208	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:39108208C>T	uc002oix.1	-	2	265	c.157G>A	c.(157-159)GAT>AAT	p.D53N	MAP4K1_uc002oiy.1_Missense_Mutation_p.D53N|EIF3K_uc010xuh.1_5'Flank|EIF3K_uc002oiz.1_5'Flank|EIF3K_uc010xui.1_5'Flank	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase	53	Protein kinase.				activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCCTCCTCACCAGGCTCCATC	0.602													10	26	---	---	---	---	PASS
CEACAM6	4680	broad.mit.edu	37	19	42265295	42265295	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:42265295G>C	uc002orm.2	+	3	712	c.563G>C	c.(562-564)AGT>ACT	p.S188T		NM_002483	NP_002474	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion	188	Ig-like C2-type 1.				cell-cell signaling|signal transduction	anchored to membrane|integral to plasma membrane				ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		CTCCCGGTCAGTCCCAGGCTG	0.537													87	204	---	---	---	---	PASS
ZNF230	7773	broad.mit.edu	37	19	44515453	44515453	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr19:44515453A>G	uc002oyb.1	+	5	1513	c.1262A>G	c.(1261-1263)AAA>AGA	p.K421R		NM_006300	NP_006291	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	421	C2H2-type 10; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				AAACCCTTCAAATGTGAGGAT	0.438													47	21	---	---	---	---	PASS
TGM6	343641	broad.mit.edu	37	20	2384287	2384287	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr20:2384287C>A	uc002wfy.1	+	9	1215	c.1154C>A	c.(1153-1155)GCT>GAT	p.A385D	TGM6_uc010gal.1_Missense_Mutation_p.A385D	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	385					cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)	GTGCACCTGGCTCACGATGGC	0.622													31	45	---	---	---	---	PASS
SALL4	57167	broad.mit.edu	37	20	50406807	50406807	+	Missense_Mutation	SNP	C	T	T	rs41274696	byFrequency	TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr20:50406807C>T	uc002xwh.3	-	2	2316	c.2215G>A	c.(2215-2217)GCC>ACC	p.A739T	SALL4_uc010gii.2_Intron|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	739					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						TTAAAAGGGGCAGGACCCACT	0.592													7	20	---	---	---	---	PASS
OGFR	11054	broad.mit.edu	37	20	61444873	61444873	+	Nonsense_Mutation	SNP	G	T	T	rs141833389		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr20:61444873G>T	uc002ydj.2	+	7	1941	c.1906G>T	c.(1906-1908)GAG>TAG	p.E636*	OGFR_uc002ydk.2_Nonsense_Mutation_p.E619*|OGFR_uc002ydl.2_Nonsense_Mutation_p.E584*|uc011aam.1_Silent_p.R4R	NM_007346	NP_031372	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	636	6.|7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				regulation of cell growth	cytoplasm|membrane|nucleus	opioid receptor activity				0	Breast(26;3.65e-08)					CGAGCCAGCCGAGAGCCCATC	0.731													6	6	---	---	---	---	PASS
KRTAP6-2	337967	broad.mit.edu	37	21	31971186	31971186	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr21:31971186C>A	uc011adc.1	-	1	8	c.8G>T	c.(7-9)GGC>GTC	p.G3V	KRTAP22-1_uc011add.1_5'Flank	NM_181604	NP_853635	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	3						intermediate filament					0						GTAGTAGCTGCCGCACATCGT	0.493													21	31	---	---	---	---	PASS
GAL3ST1	9514	broad.mit.edu	37	22	30951444	30951444	+	Silent	SNP	G	A	A	rs35962480		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:30951444G>A	uc003aig.1	-	4	908	c.768C>T	c.(766-768)GAC>GAT	p.D256D	GAL3ST1_uc003aih.1_Silent_p.D256D|GAL3ST1_uc003aii.1_Silent_p.D256D|GAL3ST1_uc010gvz.1_Silent_p.D256D	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	256	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0						CCAGCGACTCGTCGAAGTACT	0.642													6	135	---	---	---	---	PASS
GAL3ST1	9514	broad.mit.edu	37	22	30951744	30951744	+	Silent	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:30951744G>A	uc003aig.1	-	4	608	c.468C>T	c.(466-468)AAC>AAT	p.N156N	GAL3ST1_uc003aih.1_Silent_p.N156N|GAL3ST1_uc003aii.1_Silent_p.N156N|GAL3ST1_uc010gvz.1_Silent_p.N156N	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	156	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0						TGAAGATGGCGTTGGTCGGCA	0.657													31	51	---	---	---	---	PASS
LIMK2	3985	broad.mit.edu	37	22	31674411	31674411	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:31674411G>T	uc003akh.2	+	16	2046	c.1901G>T	c.(1900-1902)CGG>CTG	p.R634L	LIMK2_uc003aki.2_Missense_Mutation_p.R388L|LIMK2_uc003akk.2_Missense_Mutation_p.R613L|LIMK2_uc011aln.1_Missense_Mutation_p.R551L	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a	634						mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2						GGCCTGACCCGGGACTCACCT	0.662													59	83	---	---	---	---	PASS
CDC42EP1	11135	broad.mit.edu	37	22	37964144	37964144	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:37964144C>T	uc003asz.3	+	3	896	c.493C>T	c.(493-495)CGC>TGC	p.R165C		NM_152243	NP_689449	Q00587	BORG5_HUMAN	CDC42 effector protein 1	165					positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|endomembrane system|Golgi apparatus|plasma membrane	protein binding				0	Melanoma(58;0.0574)					CACCATCTCCCGCCTGCCCCG	0.632													53	80	---	---	---	---	PASS
APOBEC3A	200315	broad.mit.edu	37	22	39357613	39357613	+	Silent	SNP	C	T	T	rs141631289		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:39357613C>T	uc003awn.2	+	3	566	c.396C>T	c.(394-396)TAC>TAT	p.Y132Y	APOBEC3A_uc011aob.1_Silent_p.Y114Y|APOBEC3A_uc011aoc.1_Silent_p.Y132Y	NM_145699	NP_663745	P31941	ABC3A_HUMAN	phorbolin 1	132					cellular response to xenobiotic stimulus|defense response to virus|DNA cytosine deamination|DNA demethylation|innate immune response|negative regulation of transposition|negative regulation of viral genome replication	cytoplasm|nucleus	cytidine deaminase activity|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)					TCTATGATTACGACCCCCTAT	0.572													8	107	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41349630	41349630	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:41349630G>A	uc003azk.2	+	2	168	c.150G>A	c.(148-150)ATG>ATA	p.M50I	XPNPEP3_uc011aoy.1_RNA	NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1	50					DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						ACCACATTATGGATCTTTGTA	0.458													18	71	---	---	---	---	PASS
TCF20	6942	broad.mit.edu	37	22	42608247	42608247	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr22:42608247C>T	uc003bcj.1	-	1	3199	c.3065G>A	c.(3064-3066)CGG>CAG	p.R1022Q	TCF20_uc003bck.1_Missense_Mutation_p.R1022Q|TCF20_uc003bnt.2_Missense_Mutation_p.R1022Q	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1022					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						GCCTCTGCTCCGCCCAGGAGA	0.547													14	37	---	---	---	---	PASS
CXorf22	170063	broad.mit.edu	37	X	35974179	35974179	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:35974179A>C	uc004ddj.2	+	8	1335	c.1276A>C	c.(1276-1278)ATG>CTG	p.M426L	CXorf22_uc010ngv.2_RNA	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	426										large_intestine(1)|lung(1)|ovary(1)	3						ACCTTGTTTCATGGGTGAACG	0.363													18	19	---	---	---	---	PASS
LAS1L	81887	broad.mit.edu	37	X	64749609	64749609	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:64749609T>C	uc004dwa.1	-	5	736	c.664A>G	c.(664-666)ATC>GTC	p.I222V	LAS1L_uc004dwc.1_Missense_Mutation_p.I222V|LAS1L_uc004dwd.1_Missense_Mutation_p.I180V	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like	222						MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4						TGTTCTGTGATGTCATCAACA	0.488													46	11	---	---	---	---	PASS
NOX1	27035	broad.mit.edu	37	X	100117753	100117753	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:100117753C>T	uc004egj.2	-	5	600	c.394G>A	c.(394-396)GCC>ACC	p.A132T	uc010nnf.2_Intron|NOX1_uc004egl.3_Missense_Mutation_p.A132T|NOX1_uc010nne.2_Missense_Mutation_p.A95T	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1 isoform long	132	Extracellular (Potential).|Ferric oxidoreductase.				angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1						CCATCTGTGGCCTGTCGGCTT	0.463													56	70	---	---	---	---	PASS
COL4A5	1287	broad.mit.edu	37	X	107834432	107834432	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:107834432C>T	uc004enz.1	+	20	1512	c.1310C>T	c.(1309-1311)CCT>CTT	p.P437L	COL4A5_uc011mso.1_Missense_Mutation_p.P437L|COL4A5_uc004eob.1_Missense_Mutation_p.P45L	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	437	Triple-helical region.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						CCAGGGCCTCCTGGCCCTGCT	0.468									Alport_syndrome_with_Diffuse_Leiomyomatosis				33	10	---	---	---	---	PASS
AKAP14	158798	broad.mit.edu	37	X	119048814	119048814	+	Silent	SNP	C	A	A			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:119048814C>A	uc004ese.2	+	5	552	c.414C>A	c.(412-414)ACC>ACA	p.T138T	AKAP14_uc004esf.2_Intron	NM_178813	NP_848928	Q86UN6	AKA28_HUMAN	A kinase (PRKA) anchor protein 14 isoform a	138						cytoplasm					0						CCTACTTCACCATGAAGGTCT	0.388													6	123	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	157918376	157918376	+	RNA	DEL	G	-	-	rs3832020		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr1:157918376delG	uc001frl.1	+	4		c.556delG								Homo sapiens cDNA FLJ32876 fis, clone TESTI2004073.																		CCTGCCAGAAGCACCATACAG	0.453											OREG0013904	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	107182708	107182708	+	RNA	DEL	C	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:107182708delC	uc003dwj.2	+	3		c.1436delC								Homo sapiens cDNA clone IMAGE:5312582.																		AGCAAAACAGCCAAGCCTTTT	0.358													4	2	---	---	---	---	
VWA5B2	90113	broad.mit.edu	37	3	183955104	183955105	+	Frame_Shift_Ins	INS	-	C	C			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr3:183955104_183955105insC	uc011bra.1	+	11	1624_1625	c.1624_1625insC	c.(1624-1626)ACCfs	p.T542fs	VWA5B2_uc011brb.1_Frame_Shift_Ins_p.T323fs|VWA5B2_uc003fnd.2_Frame_Shift_Ins_p.T262fs	NM_138345	NP_612354	B9EGN7	B9EGN7_HUMAN	von Willebrand factor A domain containing 5B2	542											0						GGCACTGCTGACCCCCCGGGAG	0.629													7	25	---	---	---	---	
GAK	2580	broad.mit.edu	37	4	898493	898495	+	In_Frame_Del	DEL	AGA	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr4:898493_898495delAGA	uc003gbm.3	-	5	654_656	c.455_457delTCT	c.(454-459)TTCTAC>TAC	p.F152del	GAK_uc003gbn.3_In_Frame_Del_p.F73del|GAK_uc010ibk.1_Intron|GAK_uc003gbo.2_RNA|GAK_uc003gbl.3_In_Frame_Del_p.F16del	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	152	Protein kinase.				cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		CACGTCTGGTAGAAGATCTTCAG	0.552													11	16	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1538685	1538687	+	In_Frame_Del	DEL	TGA	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr7:1538685_1538687delTGA	uc003skn.2	-	8	1162_1164	c.1061_1063delTCA	c.(1060-1065)CTCACC>CCC	p.354_355LT>P	INTS1_uc003skq.2_In_Frame_Del_p.354_355LT>P	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	354_355					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CAGGTGGAGGTGAGGAGCCGCAG	0.567													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68412348	68412348	+	RNA	DEL	A	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:68412348delA	uc004aew.1	+	2		c.510delA			uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		GAGGGCAAAGAAACGTGGAAT	0.552													8	5	---	---	---	---	
LAMC3	10319	broad.mit.edu	37	9	133961063	133961065	+	In_Frame_Del	DEL	AAG	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr9:133961063_133961065delAAG	uc004caa.1	+	25	4281_4283	c.4183_4185delAAG	c.(4183-4185)AAGdel	p.K1397del	LAMC3_uc010mze.1_In_Frame_Del_p.K85del	NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	1397	Domain II and I.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CTCCAGTGCCAAGAAGAAGGGCA	0.616													25	15	---	---	---	---	
ADAMTS15	170689	broad.mit.edu	37	11	130331416	130331416	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr11:130331416delG	uc010scd.1	+	2	990	c.990delG	c.(988-990)CTGfs	p.L330fs		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	330	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		GTGACACCCTGGGCATGGCTG	0.597													28	44	---	---	---	---	
FAM38A	9780	broad.mit.edu	37	16	88800396	88800398	+	In_Frame_Del	DEL	CTG	-	-	rs62639697		TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chr16:88800396_88800398delCTG	uc010vpb.1	-	17	2248_2250	c.2245_2247delCAG	c.(2245-2247)CAGdel	p.Q749del	FAM38A_uc002flr.3_In_Frame_Del_p.Q317del|FAM38A_uc010cib.2_In_Frame_Del_p.Q286del|uc010vpc.1_Intron	NM_001142864	NP_001136336	Q92508	PIEZ1_HUMAN	family with sequence similarity 38, member A	749						endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0						cctcctcctcctgctgctgctgc	0.458													0	7	---	---	---	---	
ARAF	369	broad.mit.edu	37	X	47424714	47424714	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2792-01A-01D-0983-08	TCGA-66-2792-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	b704a17a-9ee9-4555-b2bb-250ac1ec5bed	55e476a9-f8cb-4765-965d-c98e43c6742d	g.chrX:47424714delC	uc011mlq.1	+	6	655	c.522delC	c.(520-522)CGCfs	p.R174fs	ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.R40fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.R174fs|ARAF_uc004dic.1_5'UTR	NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	174					intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(2)|ovary(1)|skin(1)	7					Adenosine triphosphate(DB00171)	CCTCGAACCGCCCCCTGAATG	0.572													4	8	---	---	---	---	
