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
DUSP27	92235	broad.mit.edu	37	1	167097555	167097555	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr1:167097555G>T	uc001geb.1	+	5	3187	c.3187G>T	c.(3187-3189)GCC>TCC	p.A1063S		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	1063					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3						CCCAAATTGGGCCAGGTCCAG	0.552													5	34	---	---	---	---	PASS
TPO	7173	broad.mit.edu	37	2	1499889	1499889	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:1499889G>A	uc002qww.2	+	12	2226	c.2135G>A	c.(2134-2136)GGC>GAC	p.G712D	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Missense_Mutation_p.G655D|TPO_uc002qwr.2_Missense_Mutation_p.G712D|TPO_uc002qwx.2_Missense_Mutation_p.G655D|TPO_uc010yio.1_Missense_Mutation_p.G539D|TPO_uc010yip.1_Missense_Mutation_p.G712D|TPO_uc002qwy.1_Missense_Mutation_p.G52D|TPO_uc002qwz.2_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	712	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TTCCAAGTCGGCAAATTCCCC	0.562													3	49	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30987143	30987143	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:30987143T>C	uc002rnn.2	-	6	730	c.554A>G	c.(553-555)TAT>TGT	p.Y185C	CAPN13_uc002rnp.1_Missense_Mutation_p.Y185C	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	185	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GAGGAAGCCATAGTGCAGATC	0.577													9	22	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54753666	54753666	+	Silent	SNP	G	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:54753666G>A	uc002rxu.2	+	2	360	c.111G>A	c.(109-111)GCG>GCA	p.A37A	SPTBN1_uc002rxv.1_Silent_p.A37A|RPL23AP32_uc010yot.1_5'Flank	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	37	Actin-binding.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			ACAGCTCTGCGCGGCTTTTTG	0.532													16	54	---	---	---	---	PASS
HS6ST1	9394	broad.mit.edu	37	2	129075939	129075939	+	Nonsense_Mutation	SNP	T	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:129075939T>A	uc002tpt.3	-	1	233	c.199A>T	c.(199-201)AAG>TAG	p.K67*		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	67	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		AAGTAGTACTTCTTCTCGTAG	0.547													6	55	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179436669	179436669	+	Silent	SNP	A	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:179436669A>C	uc010zfg.1	-	275	66710	c.66486T>G	c.(66484-66486)GGT>GGG	p.G22162G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G15857G|TTN_uc010zfi.1_Silent_p.G15790G|TTN_uc010zfj.1_Silent_p.G15665G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23089							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTAGGTCTTCACCTGCCAGTA	0.453													11	33	---	---	---	---	PASS
NGLY1	55768	broad.mit.edu	37	3	25778887	25778887	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr3:25778887T>C	uc003cdl.2	-	6	1049	c.941A>G	c.(940-942)AAT>AGT	p.N314S	NGLY1_uc010hfg.2_Missense_Mutation_p.N314S|NGLY1_uc003cdm.2_Missense_Mutation_p.N314S|NGLY1_uc011awo.1_Missense_Mutation_p.N272S|NGLY1_uc003cdk.2_RNA	NM_018297	NP_060767	Q96IV0	NGLY1_HUMAN	N-glycanase 1 isoform 1	314					glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1						TGTAAAACAATTGGCCCACTC	0.308													8	61	---	---	---	---	PASS
SLC34A2	10568	broad.mit.edu	37	4	25678365	25678365	+	Silent	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr4:25678365C>T	uc003grr.2	+	13	2148	c.2067C>T	c.(2065-2067)GCC>GCT	p.A689A	SLC34A2_uc003grs.2_Silent_p.A688A|SLC34A2_uc010iev.2_Silent_p.A688A	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	689	Cytoplasmic (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)				AATGCACGGCCTTGTAGGGGA	0.562													12	56	---	---	---	---	PASS
TMEM184C	55751	broad.mit.edu	37	4	148545026	148545026	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr4:148545026T>G	uc003ila.3	+	2	734	c.165T>G	c.(163-165)TTT>TTG	p.F55L		NM_018241	NP_060711	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	55	Helical; (Potential).					integral to membrane					0						CTGGAATCTTTTTGCTGTTGA	0.308													23	66	---	---	---	---	PASS
DDX60L	91351	broad.mit.edu	37	4	169300651	169300651	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr4:169300651T>C	uc003irq.3	-	32	4447	c.4226A>G	c.(4225-4227)TAT>TGT	p.Y1409C		NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1409							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTTATTTAAATAGTCCTAAAA	0.303													11	15	---	---	---	---	PASS
FOXI1	2299	broad.mit.edu	37	5	169535492	169535492	+	Silent	SNP	G	A	A	rs55685928	byFrequency	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr5:169535492G>A	uc003mai.3	+	2	1059	c.1014G>A	c.(1012-1014)GCG>GCA	p.A338A	FOXI1_uc003maj.3_Silent_p.A243A	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	338					epidermal cell fate specification|otic placode formation|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGACTGGGCGAACCCCATGC	0.582									Pendred_syndrome				23	56	---	---	---	---	PASS
HLA-C	3107	broad.mit.edu	37	6	31238931	31238931	+	Silent	SNP	G	A	A	rs697743	byFrequency	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr6:31238931G>A	uc003nsy.2	-	3	545	c.538C>T	c.(538-540)CTG>TTG	p.L180L	HLA-C_uc011dnj.1_Silent_p.L152L|HLA-C_uc003nsx.2_Silent_p.L59L|HLA-C_uc003nsz.2_Silent_p.L180L|HLA-C_uc010jsl.2_Silent_p.L180L|HLA-C_uc003nta.2_Silent_p.L180L|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_Silent_p.L59L|HLA-B_uc003ntf.2_Silent_p.L180L	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	180	Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						TAGGCTCTCAGCTGCTCCGCC	0.682													3	25	---	---	---	---	PASS
GRM4	2914	broad.mit.edu	37	6	34004179	34004179	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr6:34004179G>A	uc003oir.3	-	8	1878	c.1708C>T	c.(1708-1710)CGC>TGC	p.R570C	GRM4_uc011dsn.1_Missense_Mutation_p.R523C|GRM4_uc010jvh.2_Missense_Mutation_p.R570C|GRM4_uc010jvi.2_Missense_Mutation_p.R262C|GRM4_uc003oio.2_Missense_Mutation_p.R262C|GRM4_uc003oip.2_RNA|GRM4_uc011dsl.1_Missense_Mutation_p.R430C|GRM4_uc003oiq.2_Missense_Mutation_p.R437C|GRM4_uc011dsm.1_Missense_Mutation_p.R401C	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	570	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	CAGCCCGTGCGGTTCTCTGTG	0.652													15	38	---	---	---	---	PASS
BEND6	221336	broad.mit.edu	37	6	56882125	56882125	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr6:56882125G>A	uc010kab.2	+	5	1226	c.640G>A	c.(640-642)GCA>ACA	p.A214T	BEND6_uc003pdi.3_Missense_Mutation_p.A116T	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6	214	BEN.										0						CCTGACAGGGGCAAAATCCTC	0.388													3	30	---	---	---	---	PASS
FZD6	8323	broad.mit.edu	37	8	104340556	104340556	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr8:104340556A>G	uc003ylh.2	+	5	1737	c.1453A>G	c.(1453-1455)ATT>GTT	p.I485V	FZD6_uc003yli.2_Missense_Mutation_p.I485V|FZD6_uc003ylj.2_Missense_Mutation_p.I485V|FZD6_uc011lhn.1_Missense_Mutation_p.I451V|FZD6_uc011lho.1_Missense_Mutation_p.I180V|FZD6_uc011lhp.1_Missense_Mutation_p.I430V	NM_003506	NP_003497	O60353	FZD6_HUMAN	frizzled 6 isoform a precursor	485	Helical; Name=7; (Potential).				angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			GATGACATTAATTGTTGGCAT	0.358													14	47	---	---	---	---	PASS
AQP7P1	375719	broad.mit.edu	37	9	67281846	67281846	+	RNA	SNP	C	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr9:67281846C>A	uc004aem.1	-	1		c.59G>T			AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_Intron|AQP7P1_uc004aep.1_Intron					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						TACAGTGGCCCGAGCCCATGG	0.532													3	60	---	---	---	---	PASS
TLE4	7091	broad.mit.edu	37	9	82320809	82320809	+	Silent	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr9:82320809C>T	uc004ald.2	+	10	1563	c.714C>T	c.(712-714)AGC>AGT	p.S238S	TLE4_uc004alc.2_Silent_p.S245S|TLE4_uc010mpr.2_Silent_p.S124S|TLE4_uc004ale.2_5'UTR|TLE4_uc011lsq.1_Silent_p.S213S|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Silent_p.S184S	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	Error:Variant_position_missing_in_O60756_after_alignment										lung(2)|ovary(1)|breast(1)|skin(1)	5						TGCAGGACAGCGATGGTGAGA	0.398													6	129	---	---	---	---	PASS
SLK	9748	broad.mit.edu	37	10	105761232	105761232	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr10:105761232C>A	uc001kxo.1	+	8	929	c.895C>A	c.(895-897)CCC>ACC	p.P299T	SLK_uc001kxp.1_Missense_Mutation_p.P299T	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2	299					apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TTCCAACAAACCCATCCGAGA	0.274													7	32	---	---	---	---	PASS
KRTAP5-9	3846	broad.mit.edu	37	11	71259904	71259904	+	Silent	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr11:71259904C>T	uc001oqs.1	+	1	439	c.201C>T	c.(199-201)GGC>GGT	p.G67G		NM_005553	NP_005544	P26371	KRA59_HUMAN	keratin associated protein 5-9	67	8 X 4 AA repeats of C-C-X-P.				epidermis development	keratin filament					0						CCTGTGGGGGCTCCAAGGGAG	0.627													8	159	---	---	---	---	PASS
APLP2	334	broad.mit.edu	37	11	129979414	129979414	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr11:129979414C>A	uc010sby.1	+	2	353	c.196C>A	c.(196-198)CAG>AAG	p.Q66K	APLP2_uc001qfp.2_Missense_Mutation_p.Q66K|APLP2_uc001qfq.2_Missense_Mutation_p.Q66K|APLP2_uc010sbz.1_Intron|APLP2_uc001qfr.2_Intron|APLP2_uc001qfs.2_Missense_Mutation_p.Q66K|APLP2_uc001qfv.2_Missense_Mutation_p.Q13K	NM_001642	NP_001633	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	66	Extracellular (Potential).				G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)		TGTGAACATTCAGACTGGGAA	0.458													3	46	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53342968	53342968	+	Missense_Mutation	SNP	C	T	T	rs76301931	by1000genomes	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr12:53342968C>T	uc001sbe.2	+	2	80	c.11C>T	c.(10-12)ACC>ATC	p.T4I	KRT18_uc009zmn.1_Missense_Mutation_p.T4I|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_Missense_Mutation_p.T4I|KRT18_uc009zmo.2_Missense_Mutation_p.T4I|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	4	Head.				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						ATGAGCTTCACCACTCGCTCC	0.672													6	130	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53343005	53343005	+	Silent	SNP	G	A	A	rs80354424	by1000genomes	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr12:53343005G>A	uc001sbe.2	+	2	117	c.48G>A	c.(46-48)CTG>CTA	p.L16L	KRT18_uc009zmn.1_Silent_p.L16L|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_Silent_p.L16L|KRT18_uc009zmo.2_Silent_p.L16L|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	16	Head.				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						ACCGGTCCCTGGGCTCTGTCC	0.677													6	116	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53343007	53343007	+	Missense_Mutation	SNP	G	A	A	rs79476176	by1000genomes	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr12:53343007G>A	uc001sbe.2	+	2	119	c.50G>A	c.(49-51)GGC>GAC	p.G17D	KRT18_uc009zmn.1_Missense_Mutation_p.G17D|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_Missense_Mutation_p.G17D|KRT18_uc009zmo.2_Missense_Mutation_p.G17D|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	17	Head.				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						CGGTCCCTGGGCTCTGTCCAG	0.677													6	117	---	---	---	---	PASS
BBS10	79738	broad.mit.edu	37	12	76740951	76740951	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr12:76740951C>T	uc001syd.1	-	2	898	c.814G>A	c.(814-816)GGA>AGA	p.G272R		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	272					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2						AACTCTGATCCAGAAGTGGAA	0.373									Bardet-Biedl_syndrome				12	26	---	---	---	---	PASS
XPO4	64328	broad.mit.edu	37	13	21436893	21436893	+	Silent	SNP	G	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr13:21436893G>T	uc001unq.3	-	3	316	c.280C>A	c.(280-282)CGA>AGA	p.R94R	XPO4_uc010tcr.1_Silent_p.R20R	NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	94					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		AGGAATGTTCGCAGAGACTCG	0.433													9	257	---	---	---	---	PASS
SLC7A1	6541	broad.mit.edu	37	13	30107118	30107118	+	Silent	SNP	A	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr13:30107118A>C	uc001uso.2	-	4	759	c.372T>G	c.(370-372)GGT>GGG	p.G124G		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	124	Extracellular (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)	CGCTTGAAGTACCTGCCACAA	0.547													8	21	---	---	---	---	PASS
RPS6KA5	9252	broad.mit.edu	37	14	91360831	91360831	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr14:91360831T>G	uc001xys.2	-	13	1785	c.1570A>C	c.(1570-1572)ATC>CTC	p.I524L	RPS6KA5_uc010twi.1_Missense_Mutation_p.I445L|RPS6KA5_uc001xyt.2_Missense_Mutation_p.I524L	NM_004755	NP_004746	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, polypeptide 5	524	Protein kinase 2.				axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		TTCCTCATGATGTAGCTGGCT	0.448													25	54	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106552556	106552556	+	RNA	SNP	C	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr14:106552556C>A	uc010tyt.1	-	1447		c.30279G>T								Parts of antibodies, mostly variable regions.												0						TACCAAGCCTCCCCCAGACTC	0.557													17	66	---	---	---	---	PASS
MORF4L1	10933	broad.mit.edu	37	15	79177371	79177371	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:79177371T>C	uc002bel.2	+	4	406	c.218T>C	c.(217-219)CTT>CCT	p.L73P	MORF4L1_uc010bli.1_Intron|MORF4L1_uc010blj.1_Intron|MORF4L1_uc002bem.2_Intron|MORF4L1_uc010une.1_Intron	NM_206839	NP_996670	Q9UBU8	MO4L1_HUMAN	MORF-related gene 15 isoform 2	73					double-strand break repair via homologous recombination|histone deacetylation|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Sin3 complex	protein N-terminus binding				0						ATTGTAGCCCTTTTTCCTGTT	0.443													3	93	---	---	---	---	PASS
AP3B2	8120	broad.mit.edu	37	15	83346500	83346500	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:83346500C>A	uc010uoh.1	-	12	1478	c.1301G>T	c.(1300-1302)GGA>GTA	p.G434V	AP3B2_uc010uoi.1_Missense_Mutation_p.G434V|AP3B2_uc010uoj.1_Missense_Mutation_p.G402V|AP3B2_uc010uog.1_Missense_Mutation_p.G70V	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	434					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)			TGCACAGCGTCCAATGGCCTG	0.537													4	14	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	91027480	91027480	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr15:91027480C>G	uc002bpl.1	+	30	3918	c.3817C>G	c.(3817-3819)CCA>GCA	p.P1273A		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1273	C1.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTGTGATGTCCCAGAGCTTCA	0.423													33	121	---	---	---	---	PASS
BCAR1	9564	broad.mit.edu	37	16	75269477	75269477	+	Silent	SNP	A	C	C	rs61729595	by1000genomes	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr16:75269477A>C	uc002fdv.2	-	5	1443	c.1320T>G	c.(1318-1320)TCT>TCG	p.S440S	BCAR1_uc002fdt.2_5'UTR|BCAR1_uc002fdu.2_Silent_p.S230S|BCAR1_uc010cgu.2_Silent_p.S429S|BCAR1_uc010vna.1_Silent_p.S438S|BCAR1_uc010vnb.1_Silent_p.S486S|BCAR1_uc002fdw.2_Silent_p.S440S|BCAR1_uc010vnc.1_Silent_p.S292S|BCAR1_uc010vnd.1_Silent_p.S458S|BCAR1_uc002fdx.2_Silent_p.S458S	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	440	Ser-rich.				actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)		AGGAGGACGCAGACTGGCTGC	0.701													9	4	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274150	39274150	+	Missense_Mutation	SNP	T	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:39274150T>A	uc002hvz.2	-	1	457	c.418A>T	c.(418-420)AGC>TGC	p.S140C		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	140	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ctggagatgctgcagctgggg	0.129													3	39	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274157	39274157	+	Silent	SNP	G	A	A	rs145503152		TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:39274157G>A	uc002hvz.2	-	1	450	c.411C>T	c.(409-411)CCC>CCT	p.P137P		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	137	23.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			tgctgcagctggggtggcagc	0.109													7	38	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274205	39274205	+	Silent	SNP	T	C	C	rs80322614		TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:39274205T>C	uc002hvz.2	-	1	402	c.363A>G	c.(361-363)AGA>AGG	p.R121R		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	121	20.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcactggggtctgcagcagc	0.095													4	58	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274206	39274206	+	Missense_Mutation	SNP	C	T	T	rs79388709		TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:39274206C>T	uc002hvz.2	-	1	401	c.362G>A	c.(361-363)AGA>AAA	p.R121K		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	121	20.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcactggggtctgcagcagct	0.100													4	58	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234300	45234300	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:45234300G>T	uc002ild.3	-	7	948	c.821C>A	c.(820-822)GCT>GAT	p.A274D	CDC27_uc002ile.3_Missense_Mutation_p.A274D|CDC27_uc002ilf.3_Missense_Mutation_p.A274D|CDC27_uc010wkp.1_Missense_Mutation_p.A213D|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	274					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TGGACTAAGAGCTGCTGGTCC	0.363													4	47	---	---	---	---	PASS
CHAF1A	10036	broad.mit.edu	37	19	4442949	4442949	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr19:4442949C>T	uc002mal.2	+	15	2898	c.2798C>T	c.(2797-2799)TCC>TTC	p.S933F		NM_005483	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	933	Binds to p60.				cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAGCCGCTTCCGGAGCTGGG	0.672								Chromatin_Structure					5	18	---	---	---	---	PASS
C20orf194	25943	broad.mit.edu	37	20	3236652	3236652	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:3236652C>G	uc002wii.2	-	34	3312	c.3261G>C	c.(3259-3261)CAG>CAC	p.Q1087H	C20orf194_uc002wij.3_Missense_Mutation_p.Q826H|C20orf194_uc002wik.2_Missense_Mutation_p.Q761H	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943	1087											0						TGGAAACCACCTGCTTAGCTG	0.597													8	27	---	---	---	---	PASS
C20orf12	55184	broad.mit.edu	37	20	18446022	18446022	+	Splice_Site	SNP	C	A	A	rs74875927	byFrequency	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:18446022C>A	uc010zsa.1	-	2	191	c.-18_splice	c.e2-1		C20orf12_uc002wqr.3_RNA|C20orf12_uc002wqs.3_Splice_Site|C20orf12_uc002wqq.3_Splice_Site|C20orf12_uc002wqu.1_RNA|C20orf12_uc010gct.1_Splice_Site|POLR3F_uc002wqv.2_5'Flank|POLR3F_uc002wqw.2_5'Flank|POLR3F_uc002wqx.2_5'Flank	NM_001099407	NP_001092877	Q9NVP4	CT012_HUMAN	hypothetical protein LOC55184							intracellular	zinc ion binding			ovary(1)	1		Myeloproliferative disorder(85;0.0122)				ctctctctctctctATATATA	0.318													6	3	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40735499	40735499	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:40735499T>G	uc002xkg.2	-	24	3501	c.3317A>C	c.(3316-3318)AAT>ACT	p.N1106T	PTPRT_uc010ggj.2_Missense_Mutation_p.N1125T|PTPRT_uc010ggi.2_Missense_Mutation_p.N309T	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1106	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).		N -> I (in a colorectal cancer; reduced phosphatase activity).		homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CACCCCTTCATTCTCGGCCAT	0.562													4	103	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	47989844	47989844	+	Silent	SNP	A	C	C			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr20:47989844A>C	uc002xur.1	-	2	2417	c.2253T>G	c.(2251-2253)GGT>GGG	p.G751G	KCNB1_uc002xus.1_Silent_p.G751G	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	751	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACTGGTGGACACCCGCCTCAA	0.572													13	165	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	C	C	rs142470496	byFrequency	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr22:29091840T>C	uc003adu.1	-	11	1189	c.1117A>G	c.(1117-1119)AAG>GAG	p.K373E	CHEK2_uc003ads.1_Missense_Mutation_p.K152E|CHEK2_uc010gvh.1_Missense_Mutation_p.K282E|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.K416E|CHEK2_uc003adv.1_Missense_Mutation_p.K344E|CHEK2_uc003adw.1_Missense_Mutation_p.K373E|CHEK2_uc003adx.1_Missense_Mutation_p.K152E|CHEK2_uc003ady.1_Missense_Mutation_p.K373E|CHEK2_uc003adz.1_Missense_Mutation_p.K177E	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	373	Protein kinase.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(2)		central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				3	68	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	A	A	rs146546850	byFrequency	TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr22:29091841G>A	uc003adu.1	-	11	1188	c.1116C>T	c.(1114-1116)TCC>TCT	p.S372S	CHEK2_uc003ads.1_Silent_p.S151S|CHEK2_uc010gvh.1_Silent_p.S281S|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Silent_p.S415S|CHEK2_uc003adv.1_Silent_p.S343S|CHEK2_uc003adw.1_Silent_p.S372S|CHEK2_uc003adx.1_Silent_p.S151S|CHEK2_uc003ady.1_Silent_p.S372S|CHEK2_uc003adz.1_Silent_p.S176S	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	372	Protein kinase.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.S372S(1)		central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				3	67	---	---	---	---	PASS
NLGN4Y	22829	broad.mit.edu	37	Y	16952767	16952767	+	Silent	SNP	C	T	T			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chrY:16952767C>T	uc004ftg.2	+	6	2328	c.2076C>T	c.(2074-2076)GCC>GCT	p.A692A	NLGN4Y_uc004fte.2_Silent_p.A524A|NLGN4Y_uc011nas.1_Silent_p.A712A|NLGN4Y_uc004ftf.2_Silent_p.A385A|NLGN4Y_uc004fth.2_Silent_p.A692A	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked isoform 1	692	Helical; (Potential).				brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|integral to plasma membrane|synapse	neurexin binding|receptor activity				0						ACATCTTAGCCTTTGCGGCGC	0.502													3	71	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196681466	196681467	+	Frame_Shift_Ins	INS	-	A	A			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr2:196681466_196681467insA	uc002utj.3	-	51	9747_9748	c.9646_9647insT	c.(9646-9648)TCTfs	p.S3216fs		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3216					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						ATCAGCAAGAGAAAAAAATAGG	0.411													96	12	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100349724	100349724	+	Frame_Shift_Del	DEL	G	-	-			TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr7:100349724delG	uc003uwj.2	+	14	2161	c.1996delG	c.(1996-1998)GAGfs	p.E666fs	ZAN_uc003uwk.2_Frame_Shift_Del_p.E666fs|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	666	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CACCCCCACTGAGGAGACCAC	0.537													34	15	---	---	---	---	
CD68	968	broad.mit.edu	37	17	7483262	7483263	+	Frame_Shift_Del	DEL	CA	-	-	rs143998725		TCGA-G9-6364-01A-21D-1786-08	TCGA-G9-6364-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	f4a3d716-cd83-4012-91ec-ff5e45784c98	a820bb95-2a8f-46cf-b111-46f108dc789a	g.chr17:7483262_7483263delCA	uc002ghv.2	+	2	375_376	c.184_185delCA	c.(184-186)CACfs	p.H62fs	CD68_uc002ghu.2_Frame_Shift_Del_p.H35fs	NM_001251	NP_001242	P34810	CD68_HUMAN	CD68 antigen isoform A	62	Mucin-like.|Extracellular (Potential).					endosome membrane|integral to membrane|lysosomal membrane|membrane fraction|plasma membrane					0						Aaccaccactcacaggacaacc	0.317													24	14	---	---	---	---	
