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
DBT	1629	broad.mit.edu	37	1	100706430	100706430	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr1:100706430C>T	uc001dta.3	-	1	95	c.62G>A	c.(61-63)cGc>cAc	p.R21H	DBT_uc010oug.2_5'UTR|DBT_uc021oqo.1_Missense_Mutation_p.R21H	NM_001918	NP_001909	P11182	ODB2_HUMAN	Homo sapiens dihydrolipoamide branched chain transacylase E2 (DBT), nuclear gene encoding mitochondrial protein, mRNA.	21					branched chain family amino acid catabolic process|fatty-acyl-CoA biosynthetic process	microtubule cytoskeleton|mitochondrial alpha-ketoglutarate dehydrogenase complex|mitochondrial nucleoid	acyltransferase activity|cofactor binding|dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity|protein binding			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		TTGAAAATAGCGAACACAAAT	0.313												
ANP32E	81611	broad.mit.edu	37	1	150202934	150202934	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr1:150202934A>G	uc001etw.3	-	2	669	c.299T>C	c.(298-300)aTa>aCa	p.I100T	ANP32E_uc010pbu.2_Missense_Mutation_p.I52T|ANP32E_uc010pbv.2_Intron|ANP32E_uc001etv.4_Missense_Mutation_p.I100T|ANP32E_uc010pbw.1_Missense_Mutation_p.I100T	NM_030920	NP_001129951	Q9BTT0	AN32E_HUMAN	Homo sapiens acidic (leucine-rich) nuclear phosphoprotein 32 family, member E (ANP32E), transcript variant 1, mRNA.	100						cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGATCTTTTATTTTGTTTCC	0.363												
HMCN1	83872	broad.mit.edu	37	1	186084452	186084452	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr1:186084452C>T	uc001grq.1	+	74	11696	c.11467C>T	c.(11467-11469)Ctg>Ttg	p.L3823L	MIR548F1_uc021pgf.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	Homo sapiens hemicentin 1 (HMCN1), mRNA.	3823	Ig-like C2-type 37.				response to stimulus|visual perception	basement membrane	calcium ion binding			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TCAAACTACTCTGGCTTGTGA	0.398												
SMYD2	56950	broad.mit.edu	37	1	214505455	214505455	+	Nonsense_Mutation	SNP	C	C	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr1:214505455C>A	uc021pix.1	+	9	1065	c.1032C>A	c.(1030-1032)taC>taA	p.Y344*	SMYD2_uc009xdl.1_Intron	NM_020197	NP_064582	Q9NRG4	SMYD2_HUMAN	Homo sapiens SET and MYND domain containing 2 (SMYD2), mRNA.	344					negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	cytosol|nucleus	histone methyltransferase activity (H3-K36 specific)|p53 binding|RNA polymerase II core binding|zinc ion binding			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		ACATGATGTACCAGGCCATGG	0.517											OREG0012979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
SLC39A12	221074	broad.mit.edu	37	10	18270258	18270258	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr10:18270258G>A	uc001ipo.2	+	5	1215	c.942G>A	c.(940-942)agG>agA	p.R314R	SLC39A12_uc001ipn.2_Silent_p.R314R|SLC39A12_uc001ipp.2_Silent_p.R314R|SLC39A12_uc010qck.1_Silent_p.R180R	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	Homo sapiens solute carrier family 39 (zinc transporter), member 12 (SLC39A12), transcript variant 1, mRNA.	314					zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TCTCTGCTAGGCAGCTGGTGG	0.448												
FAM196A	642938	broad.mit.edu	37	10	128973691	128973691	+	Silent	SNP	C	C	T	rs139302074	byFrequency	TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr10:128973691C>T	uc001lju.1	-	0	1010	c.969G>A	c.(967-969)tcG>tcA	p.S323S	DOCK1_uc001ljt.3_Intron|DOCK1_uc010qun.2_Intron|FAM196A_uc010quo.1_Silent_p.S323S|FAM196A_uc001ljv.1_Silent_p.S323S|FAM196A_uc009yap.1_Silent_p.S323S	NM_001039762	NP_001034851	Q6ZSG2	F196A_HUMAN	Homo sapiens family with sequence similarity 196, member A (FAM196A), mRNA.	323										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TGTGAGTCTGCGACGGCTGCT	0.642												
MRPL23	6150	broad.mit.edu	37	11	1973439	1973439	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:1973439G>C	uc001lux.3	+	3	314	c.223_splice	c.e3+1	p.G75_splice		NM_021134	NP_066957	Q16540	RM23_HUMAN	Homo sapiens mitochondrial ribosomal protein L23 (MRPL23), nuclear gene encoding mitochondrial protein, mRNA.	75					translation	mitochondrial large ribosomal subunit	nucleotide binding|RNA binding|structural constituent of ribosome			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		GGTGCAGCATGGTGAGTGCCC	0.602												
ANO5	203859	broad.mit.edu	37	11	22239813	22239813	+	Missense_Mutation	SNP	T	T	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:22239813T>G	uc001mqi.2	+	3	477	c.160T>G	c.(160-162)Ttc>Gtc	p.F54V	ANO5_uc001mqj.2_Missense_Mutation_p.F53V	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	Homo sapiens anoctamin 5 (ANO5), transcript variant 1, mRNA.	54						chloride channel complex|endoplasmic reticulum membrane	chloride channel activity	p.L53F(1)		breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATTCAATTTGTTCCTGAGGCG	0.403												
OR5D16	390144	broad.mit.edu	37	11	55606889	55606889	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:55606889C>A	uc010rio.2	+	0	662	c.662C>A	c.(661-663)gCa>gAa	p.A221E		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	Homo sapiens olfactory receptor, family 5, subfamily D, member 16 (OR5D16), mRNA.	221					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ACATCTTATGCATTCATCATT	0.468												
OR5D16	390144	broad.mit.edu	37	11	55606937	55606937	+	Missense_Mutation	SNP	G	G	A	rs148616685		TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:55606937G>A	uc010rio.2	+	0	710	c.710G>A	c.(709-711)cGc>cAc	p.R237H		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	Homo sapiens olfactory receptor, family 5, subfamily D, member 16 (OR5D16), mRNA.	237					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				AGTGGGCACCGCAAAGTCTTC	0.488												
OR5M3	219482	broad.mit.edu	37	11	56237927	56237927	+	Missense_Mutation	SNP	G	G	A	rs147367874	byFrequency	TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:56237927G>A	uc010rjk.2	-	0	88	c.47C>T	c.(46-48)aCg>aTg	p.T16M	OR8U8_uc001nit.2_Intron	NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	Homo sapiens olfactory receptor, family 5, subfamily M, member 3 (OR5M3), mRNA.	16					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					TCGACGGCTCGTTAGCCCCAA	0.383												
ANO1	55107	broad.mit.edu	37	11	69949227	69949227	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:69949227G>A	uc001opj.3	+	2	802	c.497G>A	c.(496-498)tGc>tAc	p.C166Y	ANO1_uc001opl.2_Non-coding_Transcript|ANO1_uc001opk.1_Missense_Mutation_p.C138Y	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	Homo sapiens anoctamin 1, calcium activated chloride channel (ANO1), transcript variant 1, mRNA.	166					multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29						AACGTGCTGTGCAGAGAGGCC	0.532												
PAAF1	80227	broad.mit.edu	37	11	73627614	73627614	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:73627614G>A	uc001ouk.1	+	8	878	c.844G>A	c.(844-846)Gct>Act	p.A282T	PAAF1_uc001oul.1_Missense_Mutation_p.A265T|PAAF1_uc001oum.1_Missense_Mutation_p.A265T	NM_025155	NP_079431	Q9BRP4	PAAF1_HUMAN	Homo sapiens proteasomal ATPase-associated factor 1 (PAAF1), mRNA.	282					interspecies interaction between organisms	proteasome complex	protein binding			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					TGGCTCAGACGCTTTCAACTG	0.423												
XRRA1	143570	broad.mit.edu	37	11	74559419	74559419	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:74559419A>G	uc009yub.3	-	14	1777	c.1445T>C	c.(1444-1446)aTg>aCg	p.M482T	XRRA1_uc001ovm.2_Non-coding_Transcript|XRRA1_uc001ovn.3_Missense_Mutation_p.M105T|XRRA1_uc001ovo.3_Missense_Mutation_p.M90T|XRRA1_uc001ovp.4_Missense_Mutation_p.M207T|XRRA1_uc001ovq.4_Missense_Mutation_p.M395T|XRRA1_uc001ovr.2_Missense_Mutation_p.M105T|XRRA1_uc001ovs.1_Missense_Mutation_p.M84T	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	Homo sapiens X-ray radiation resistance associated 1 (XRRA1), mRNA.	482					response to X-ray	cytoplasm|nucleus				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						TGGCTCTAGCATATCCTTTGA	0.552												
ADAMTS8	11095	broad.mit.edu	37	11	130281492	130281492	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr11:130281492C>T	uc001qgg.4	-	5	1928	c.1570G>A	c.(1570-1572)Gtg>Atg	p.V524M	ADAMTS8_uc001qgf.3_Missense_Mutation_p.V5M	NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 8 (ADAMTS8), mRNA.	524	Disintegrin.				negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding	p.V553M(1)|p.V524M(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	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;0.039)|Lung(977;0.213)		CCATCTGCCACGGGCTGCAAC	0.577												
KRT4	3851	broad.mit.edu	37	12	53208029	53208029	+	Silent	SNP	G	G	A	rs143824965	by1000genomes	TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:53208029G>A	uc001saz.3	-	0	36	c.36C>T	c.(34-36)aaC>aaT	p.N12N		NM_002272	NP_002263	B4DRS2	B4DRS2_HUMAN	Homo sapiens keratin 4 (KRT4), mRNA.	0						keratin filament	structural molecule activity			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						TCCCGCACCCGTTGAGCATGT	0.542												
MYO1A	4640	broad.mit.edu	37	12	57432332	57432332	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:57432332G>A	uc001smw.4	-	16	1864	c.1624C>T	c.(1624-1626)Ctc>Ttc	p.L542F	MYO1A_uc010sqz.2_Missense_Mutation_p.L380F|MYO1A_uc009zpd.3_Missense_Mutation_p.L542F	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	Homo sapiens myosin IA (MYO1A), transcript variant 2, mRNA.	542	Myosin head-like.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						GACCGAAGGAGGGGGTGCTGG	0.537												
C12orf66	144577	broad.mit.edu	37	12	64588399	64588399	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:64588399G>A	uc001srw.4	-	2	620	c.561C>T	c.(559-561)ttC>ttT	p.F187F		NM_152440	NP_689653	Q96MD2	CL066_HUMAN	Homo sapiens chromosome 12 open reading frame 66 (C12orf66), mRNA.	187										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						CTTCCAGCTGGAAACTGCTTT	0.478												
KSR2	283455	broad.mit.edu	37	12	118016952	118016952	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:118016952G>A	uc001two.2	-	6	1265	c.1210C>T	c.(1210-1212)Ctt>Ttt	p.L404F		NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	Homo sapiens kinase suppressor of ras 2 (KSR2), mRNA.	433					intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity	p.L465F(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGCCAAAAAGCATCCCTTTC	0.478												
CCDC60	160777	broad.mit.edu	37	12	119866567	119866567	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:119866567G>A	uc001txe.3	+	2	635	c.170_splice	c.e2+1	p.R57_splice	AF086288_uc001txf.3_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	Homo sapiens coiled-coil domain containing 60 (CCDC60), mRNA.	57										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ATACGAAGCCGGTGAGTGAGC	0.502												
GPR133	283383	broad.mit.edu	37	12	131487816	131487816	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr12:131487816G>T	uc010tbm.2	+	10	1768	c.1209G>T	c.(1207-1209)caG>caT	p.Q403H	GPR133_uc001uit.4_Missense_Mutation_p.Q371H	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	Homo sapiens G protein-coupled receptor 133 (GPR133), mRNA.	371					neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GCACGCCCCAGGTCACCGTGG	0.617												
DCLK1	9201	broad.mit.edu	37	13	36428681	36428681	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr13:36428681C>T	uc001uvf.3	-	5	1273	c.990G>A	c.(988-990)tcG>tcA	p.S330S	MAB21L1_uc001uvc.3_Intron|DCLK1_uc001uve.4_Silent_p.S23S|DCLK1_uc010teh.2_Silent_p.S23S|DCLK1_uc010abk.3_Silent_p.S23S|DCLK1_uc001uvh.4_Silent_p.S23S	NM_004734	NP_004725	O15075	DCLK1_HUMAN	Homo sapiens doublecortin-like kinase 1 (DCLK1), transcript variant 1, mRNA.	330	Pro/Ser-rich.				cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity	p.S330S(3)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ATGGGCTTGGCGACTTGCCTG	0.493												
GRK1	6011	broad.mit.edu	37	13	114321752	114321752	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr13:114321752C>T	uc010tkf.2	+	0	156	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_002929	NP_002920	Q15835	RK_HUMAN	Homo sapiens G protein-coupled receptor kinase 1 (GRK1), mRNA.	17	N-terminal.				regulation of G-protein coupled receptor protein signaling pathway|rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway	membrane	ATP binding|G-protein coupled receptor kinase activity|rhodopsin kinase activity|signal transducer activity			ovary(2)	2	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.234)			CCTTCATCGCCGCCCGAGGCA	0.647												
SCFD1	23256	broad.mit.edu	37	14	31139520	31139520	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:31139520C>G	uc001wqm.1	+	10	938	c.914C>G	c.(913-915)gCt>gGt	p.A305G	SCFD1_uc001wqn.1_Missense_Mutation_p.A238G|SCFD1_uc010tpg.1_Missense_Mutation_p.A246G|SCFD1_uc010tph.1_Missense_Mutation_p.A120G|SCFD1_uc010amf.1_Missense_Mutation_p.A120G|SCFD1_uc010tpi.1_Missense_Mutation_p.A213G|SCFD1_uc010amd.1_Missense_Mutation_p.A137G	NM_016106	NP_057190	Q8WVM8	SCFD1_HUMAN	Homo sapiens sec1 family domain containing 1 (SCFD1), transcript variant 1, mRNA.	305					post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		AACTCTCCAGCTGGTGCTAGA	0.328												
FANCM	57697	broad.mit.edu	37	14	45665510	45665510	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:45665510G>A	uc001wwd.4	+	20	5575	c.5476G>A	c.(5476-5478)Gaa>Aaa	p.E1826K	FANCM_uc010anf.3_Missense_Mutation_p.E1800K|FANCM_uc001wwe.4_Missense_Mutation_p.E1362K|FANCM_uc010ang.3_Missense_Mutation_p.E1075K	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Homo sapiens Fanconi anemia, complementation group M (FANCM), mRNA.	1826	Interaction with FAAP24 and EME1.				DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AGGTGGTCATGAAATCACTTC	0.418								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia			
ESR2	2100	broad.mit.edu	37	14	64727172	64727172	+	Missense_Mutation	SNP	A	A	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:64727172A>T	uc001xha.1	-	4	1415	c.947T>A	c.(946-948)aTt>aAt	p.I316N	ESR2_uc001xgy.2_Missense_Mutation_p.I316N|ESR2_uc001xgu.3_Missense_Mutation_p.I316N|ESR2_uc001xgv.3_Missense_Mutation_p.I316N|ESR2_uc001xgw.3_Non-coding_Transcript|ESR2_uc001xgx.3_Missense_Mutation_p.I316N|ESR2_uc010aqb.1_Non-coding_Transcript|ESR2_uc010aqc.1_Missense_Mutation_p.I316N|ESR2_uc001xgz.2_Missense_Mutation_p.I316N|ESR2_uc010aqd.1_Non-coding_Transcript	NM_001437	NP_001428	Q92731	ESR2_HUMAN	Homo sapiens estrogen receptor 2 (ER beta) (ESR2), transcript variant a, mRNA.	316	Steroid-binding.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CCTACCGGGAATCTTCTTGGC	0.532												
SERPINA6	866	broad.mit.edu	37	14	94780400	94780400	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:94780400C>T	uc001ycv.3	-	1	690	c.586G>A	c.(586-588)Gtc>Atc	p.V196I	SERPINA6_uc010auv.3_Non-coding_Transcript	NM_001756	NP_001747	P08185	CBG_HUMAN	Homo sapiens serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6 (SERPINA6), mRNA.	196					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TTGACCAGGACGAGGATGGCT	0.502												
AHNAK2	113146	broad.mit.edu	37	14	105410846	105410846	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:105410846A>G	uc010axc.1	-	6	11062	c.10942T>C	c.(10942-10944)Ttc>Ctc	p.F3648L	AHNAK2_uc021sen.1_5'Flank|AHNAK2_uc021seo.1_Intron|AHNAK2_uc001ypx.2_Missense_Mutation_p.F3548L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	Homo sapiens AHNAK nucleoprotein 2 (AHNAK2), mRNA.	3648						nucleus				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GATACCCTGAATGACGGCATC	0.592												
AHNAK2	113146	broad.mit.edu	37	14	105417866	105417866	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr14:105417866C>T	uc010axc.1	-	6	4042	c.3922G>A	c.(3922-3924)Gca>Aca	p.A1308T	AHNAK2_uc021seo.1_Intron|AHNAK2_uc001ypx.2_Missense_Mutation_p.A1208T	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	Homo sapiens AHNAK nucleoprotein 2 (AHNAK2), mRNA.	1308						nucleus				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCCAGCTGTGCGCCATCCAAC	0.597												
DUOX2	50506	broad.mit.edu	37	15	45392270	45392270	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr15:45392270G>A	uc001zun.3	-	23	3365	c.3162C>T	c.(3160-3162)ggC>ggT	p.G1054G	DUOX2_uc010bea.3_Silent_p.G1054G	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	Homo sapiens dual oxidase 2 (DUOX2), mRNA.	1054	Interaction with TXNDC11 (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTGCAAACACGCCAACACAGA	0.562												
FBXO22	26263	broad.mit.edu	37	15	76205599	76205599	+	Frame_Shift_Del	DEL	T	T	-			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr15:76205599delT	uc002bbk.3	+	2	440	c.335delT	c.(334-336)attfs	p.I112fs	FBXO22_uc002bbj.2_Frame_Shift_Del_p.I112fs|FBXO22_uc002bbl.3_Frame_Shift_Del_p.I8fs	NM_147188	NP_671717	Q8NEZ5	FBX22_HUMAN	Homo sapiens F-box protein 22 (FBXO22), transcript variant 1, mRNA.	112					ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GAAACTTTCATTAGTCTGGAA	0.358												
SYNM	23336	broad.mit.edu	37	15	99670079	99670079	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr15:99670079C>T	uc002bup.3	+	4	1631	c.1511C>T	c.(1510-1512)aCg>aTg	p.T504M	SYNM_uc002buo.3_Missense_Mutation_p.T504M|SYNM_uc002buq.3_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	Homo sapiens synemin, intermediate filament protein (SYNM), transcript variant A, mRNA.	505	Tail.				intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						GTGAAAGCCACGAGGGAGCAA	0.488												
LRRK1	79705	broad.mit.edu	37	15	101586198	101586198	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr15:101586198C>T	uc002bwr.3	+	20	3295	c.2976C>T	c.(2974-2976)ccC>ccT	p.P992P	LRRK1_uc010usb.2_Non-coding_Transcript|LRRK1_uc010usc.2_Non-coding_Transcript	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	Homo sapiens leucine-rich repeat kinase 1 (LRRK1), mRNA.	992					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACCTCCTGCCCCATCTCCTTC	0.592												
SPIRE2	84501	broad.mit.edu	37	16	89916966	89916966	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr16:89916966delC	uc002foz.1	+	2	595	c.543delC	c.(541-543)gacfs	p.D181fs	SPIRE2_uc010civ.1_Frame_Shift_Del_p.D96fs|SPIRE2_uc010ciw.1_Frame_Shift_Del_p.D181fs|SPIRE2_uc002fpa.1_Frame_Shift_Del_p.D133fs|SPIRE2_uc010cix.1_Frame_Shift_Del_p.D50fs	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	Homo sapiens spire homolog 2 (Drosophila) (SPIRE2), mRNA.	181	KIND.				transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		GGCTGACCGACCCCCGGGGCG	0.751												
OR3A2	4995	broad.mit.edu	37	17	3181738	3181738	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr17:3181738G>A	uc002fvg.3	-	0	531	c.492C>T	c.(490-492)aaC>aaT	p.N164N		NM_002551	NP_002542	P47893	OR3A2_HUMAN	Homo sapiens olfactory receptor, family 3, subfamily A, member 2 (OR3A2), mRNA.	164					sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)	1						GGGTCAGTGCGTTGGTGAAGG	0.582												
DNAH2	146754	broad.mit.edu	37	17	7736507	7736507	+	Missense_Mutation	SNP	G	G	A	rs145226741		TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr17:7736507G>A	uc002giu.1	+	83	13111	c.13097G>A	c.(13096-13098)cGg>cAg	p.R4366Q		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	Homo sapiens dynein, axonemal, heavy chain 2 (DNAH2), mRNA.	4366					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				ATCCACTTCCGGCCTGCAGAG	0.622												
MLLT6	4302	broad.mit.edu	37	17	36873166	36873166	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr17:36873166C>T	uc002hqi.4	+	9	1596	c.1583C>T	c.(1582-1584)tCc>tTc	p.S528F	MLLT6_uc002hqj.3_Intron|MLLT6_uc002hqk.4_5'Flank|MIR4726_uc021twg.1_5'Flank	NM_005937	NP_005928	P55198	AF17_HUMAN	Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (MLLT6), mRNA.	528					regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					GGAGGTCTGTCCTCCCGAACC	0.637			T	MLL	AL							
OR4D2	124538	broad.mit.edu	37	17	56247707	56247707	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr17:56247707G>A	uc010wnp.2	+	0	691	c.691G>A	c.(691-693)Gag>Aag	p.E231K		NM_001004707	NP_001004707	P58180	OR4D2_HUMAN	Homo sapiens olfactory receptor, family 4, subfamily D, member 2 (OR4D2), mRNA.	231					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						ACATCCAGGGGAGGCAAGAAG	0.537												
TMEM241	85019	broad.mit.edu	37	18	20979531	20979531	+	Missense_Mutation	SNP	A	A	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr18:20979531A>T	uc002kuf.3	-	4	388	c.279_splice	c.e4+1	p.L93_splice	TMEM241_uc010xaq.2_Intron|TMEM241_uc010xar.2_Splice_Site|TMEM241_uc002kug.3_Splice_Site|TMEM241_uc002kuh.3_Splice_Site	NM_032933	NP_116322	Q24JQ0	CR045_HUMAN	Homo sapiens transmembrane protein 241 (TMEM241), mRNA.	93						integral to membrane											AATACTTACCAGTCTGGACAA	0.443												
LGALS13	29124	broad.mit.edu	37	19	40095888	40095888	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr19:40095888C>T	uc002omb.3	+	2	203	c.163C>T	c.(163-165)Cga>Tga	p.R55*		NM_013268	NP_037400	Q9UHV8	PP13_HUMAN	Homo sapiens lectin, galactoside-binding, soluble, 13 (LGALS13), mRNA.	55	Galectin.				lipid catabolic process|phospholipid metabolic process		carboxylesterase activity|lysophospholipase activity|sugar binding	p.F54F(1)		lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CTTCCGTTTCCGAGTGCACTT	0.498												
CEACAM7	1087	broad.mit.edu	37	19	42187746	42187746	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr19:42187746G>A	uc002ori.1	-	2	678	c.676C>T	c.(676-678)Cgc>Tgc	p.R226C	CEACAM7_uc010ehx.2_Missense_Mutation_p.R226C|CEACAM7_uc010ehy.1_Intron	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	Homo sapiens carcinoembryonic antigen-related cell adhesion molecule 7 (CEACAM7), mRNA.	226	Ig-like C2-type.					anchored to membrane|integral to membrane|plasma membrane				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		GGGTCACTGCGGCTGGCACCC	0.552												
BCAM	4059	broad.mit.edu	37	19	45322967	45322967	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr19:45322967C>T	uc002ozu.3	+	12	1791	c.1747C>T	c.(1747-1749)Cgg>Tgg	p.R583W	BCAM_uc002ozt.1_Missense_Mutation_p.R583W	NM_005581	NP_005572	P50895	BCAM_HUMAN	Homo sapiens basal cell adhesion molecule (Lutheran blood group) (BCAM), transcript variant 1, mRNA.	583					cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCGCCAGCGGCGGGAGAAGGG	0.642												
FPR2	2358	broad.mit.edu	37	19	52272072	52272072	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr19:52272072G>A	uc002pxr.3	+	1	206	c.161G>A	c.(160-162)cGg>cAg	p.R54Q	FPR2_uc002pxs.4_Missense_Mutation_p.R54Q|FPR2_uc010epf.3_Missense_Mutation_p.R54Q|FPR2_uc021uyp.1_Missense_Mutation_p.R54Q	NM_001005738	NP_001453	P25090	FPR2_HUMAN	Homo sapiens formyl peptide receptor 2 (FPR2), transcript variant 2, mRNA.	54					cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						GCTGGATTCCGGATGACACGC	0.562												
CCDC88A	55704	broad.mit.edu	37	2	55561635	55561635	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr2:55561635G>C	uc002ryv.2	-	14	3164	c.2322C>G	c.(2320-2322)aaC>aaG	p.N774K	CCDC88A_uc010ypa.1_Missense_Mutation_p.N774K|CCDC88A_uc010yoz.1_Missense_Mutation_p.N774K|CCDC88A_uc010ypb.1_Missense_Mutation_p.N676K|CCDC88A_uc002ryu.2_Missense_Mutation_p.N57K|CCDC88A_uc002ryw.3_Missense_Mutation_p.N57K	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	Homo sapiens coiled-coil domain containing 88A (CCDC88A), transcript variant 1, mRNA.	774					activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						TTTTATTGCTGTTCTCTAAAG	0.338												
RMND5A	64795	broad.mit.edu	37	2	86992995	86992995	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr2:86992995G>A	uc002srr.2	+	5	1079	c.702G>A	c.(700-702)ttG>ttA	p.L234L	RMND5A_uc002srs.4_Intron	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	Homo sapiens required for meiotic nuclear division 5 homolog A (S. cerevisiae) (RMND5A), mRNA.	234										kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						TTCAGGTTTTGATGGGAAGCC	0.428												
DDX18	8886	broad.mit.edu	37	2	118587005	118587005	+	Silent	SNP	G	G	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr2:118587005G>T	uc002tlh.1	+	12	1932	c.1833G>T	c.(1831-1833)ctG>ctT	p.L611L		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 (DDX18), mRNA.	611							ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGGTTGCTCTGTCATTTGGTT	0.403												
TTN	7273	broad.mit.edu	37	2	179556814	179556814	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr2:179556814G>T	uc021vsy.1	-	117	28184	c.27959C>A	c.(27958-27960)cCc>cAc	p.P9320H	TTN_uc021vsz.1_Intron|TTN_uc021vta.1_Intron|TTN_uc021vtb.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P5981H|TTN_uc010fre.1_Missense_Mutation_p.P431H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	Homo sapiens titin (TTN), transcript variant N2-A, mRNA.	10247	Ig-like 76.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGGTTTCTTGGGAACCTCAGG	0.433												
TTN	7273	broad.mit.edu	37	2	179569962	179569962	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr2:179569962C>T	uc021vsy.1	-	99	26036	c.25811G>A	c.(25810-25812)cGa>cAa	p.R8604Q	TTN_uc021vsz.1_Intron|TTN_uc021vta.1_Intron|TTN_uc021vtb.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.R5265Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	Homo sapiens titin (TTN), transcript variant N2-A, mRNA.	9531							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGAAGACCTCGGAAGTCAGT	0.383												
SPTLC3	55304	broad.mit.edu	37	20	13029756	13029756	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr20:13029756C>A	uc002wod.1	+	1	570	c.281C>A	c.(280-282)gCt>gAt	p.A94D	SPTLC3_uc002woc.3_Missense_Mutation_p.A94D	NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	Homo sapiens serine palmitoyltransferase, long chain base subunit 3 (SPTLC3), mRNA.	94					sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25					Pyridoxal Phosphate(DB00114)	TGCAACGCAGCTGTGGAAAGA	0.423												
PLCG1	5335	broad.mit.edu	37	20	39788360	39788360	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr20:39788360A>G	uc002xjp.1	+	1	453	c.332A>G	c.(331-333)tAt>tGt	p.Y111C	PLCG1_uc002xjo.1_Missense_Mutation_p.Y111C	NM_182811	NP_877963	P19174	PLCG1_HUMAN	Homo sapiens phospholipase C, gamma 1 (PLCG1), transcript variant 2, mRNA.	111	PH 1.				activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				GTCATTCTCTATGGAATGGAA	0.537												
RRP1B	23076	broad.mit.edu	37	21	45107441	45107441	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr21:45107441C>T	uc002zdk.3	+	12	1300	c.1186C>T	c.(1186-1188)Ctt>Ttt	p.L396F	RRP1B_uc002zdl.3_5'UTR	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	Homo sapiens ribosomal RNA processing 1 homolog B (S. cerevisiae) (RRP1B), mRNA.	396					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		TGAAAGCAGTCTTCAAAAGAG	0.532												
CABIN1	23523	broad.mit.edu	37	22	24487684	24487684	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr22:24487684G>A	uc002zzi.1	+	23	3800	c.3673G>A	c.(3673-3675)Gtt>Att	p.V1225I	CABIN1_uc021wnc.1_Missense_Mutation_p.V1175I|CABIN1_uc002zzj.1_Missense_Mutation_p.V1175I|CABIN1_uc002zzl.2_Missense_Mutation_p.V1225I	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	Homo sapiens calcineurin binding protein 1 (CABIN1), transcript variant 2, mRNA.	1225					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GCCACCCACCGTTTACTTGCT	0.612												
FGD5	152273	broad.mit.edu	37	3	14862435	14862435	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr3:14862435C>T	uc003bzc.3	+	0	1967	c.1857C>T	c.(1855-1857)ttC>ttT	p.F619F	FGD5_uc011avk.2_Silent_p.F619F	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	Homo sapiens FYVE, RhoGEF and PH domain containing 5 (FGD5), mRNA.	619					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CACCTCCTTTCGACCTGGCCT	0.557												
GCET2	257144	broad.mit.edu	37	3	111842437	111842437	+	Silent	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr3:111842437A>G	uc021xcl.1	-	5	593	c.408T>C	c.(406-408)ccT>ccC	p.P136P	C3orf52_uc011bht.1_Intron|C3orf52_uc003dyr.1_Intron|GCET2_uc003dys.2_Silent_p.P134P|GCET2_uc021xcm.1_Silent_p.P119P	NM_001190259	NP_001177188	Q8N6F7	GCET2_HUMAN	Homo sapiens germinal center expressed transcript 2 (GCET2), transcript variant 3, mRNA.	134						mitochondrion		p.S135S(1)		endometrium(3)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	8						GGTCTGTAGAAGGCATATGTA	0.483												
ABCF3	55324	broad.mit.edu	37	3	183907351	183907351	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr3:183907351C>A	uc003fmz.2	+	12	1253	c.1120C>A	c.(1120-1122)Ccc>Acc	p.P374T	ABCF3_uc003fna.2_Missense_Mutation_p.P368T|ABCF3_uc003fnb.2_Missense_Mutation_p.P55T	NM_018358	NP_060828	Q9NUQ8	ABCF3_HUMAN	Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 3 (ABCF3), mRNA.	374	ABC transporter 1.						ATP binding|ATPase activity			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCAGACGTGGCCCTCCACCAT	0.617												
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr3:195505836G>C	uc021xjp.1	-	1	12771	c.12615C>G	c.(12613-12615)caC>caG	p.H4205Q	MUC4_uc003fva.3_5'Flank|MUC4_uc003fvb.3_5'Flank|MUC4_uc003fvc.3_5'Flank|MUC4_uc003fvd.3_5'Flank|MUC4_uc003fve.3_5'Flank|MUC4_uc010hzr.3_5'Flank|MUC4_uc021xjm.1_Intron|MUC4_uc021xjn.1_Intron|MUC4_uc021xjo.1_Intron|MUC4_uc021xjg.1_Intron|MUC4_uc021xjh.1_Intron|MUC4_uc021xji.1_Intron|MUC4_uc021xjj.1_Intron|MUC4_uc021xjk.1_Intron|MUC4_uc021xjl.1_Intron|MUC4_uc003fvo.3_Intron|MUC4_uc003fvp.3_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	Homo sapiens mucin 4, cell surface associated (MUC4), transcript variant 1, mRNA.	968					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity	p.H4205Q(10)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597												
EVC2	132884	broad.mit.edu	37	4	5630350	5630350	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:5630350G>A	uc003gij.3	-	11	1876	c.1822C>T	c.(1822-1824)Cgt>Tgt	p.R608C	EVC2_uc003gik.3_Missense_Mutation_p.R528C|EVC2_uc011bwb.2_Missense_Mutation_p.R48C	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	Homo sapiens Ellis van Creveld syndrome 2 (EVC2), transcript variant 1, mRNA.	608						integral to membrane		p.R608H(2)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CCCTGCACACGGGTCTCTGAT	0.507												
SLC2A9	56606	broad.mit.edu	37	4	9889261	9889261	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:9889261G>A	uc003gmc.3	-	9	1282	c.1221C>T	c.(1219-1221)caC>caT	p.H407H	SLC2A9_uc003gmd.3_Silent_p.H378H	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	Homo sapiens solute carrier family 2 (facilitated glucose transporter), member 9 (SLC2A9), transcript variant 1, mRNA.	407					glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35						CCCAGGGGGCGTGGTCCTGGG	0.632												
PCDH7	5099	broad.mit.edu	37	4	30724267	30724267	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:30724267A>G	uc003gsk.1	+	0	2231	c.1223A>G	c.(1222-1224)gAg>gGg	p.E408G	PCDH7_uc011bxx.2_Missense_Mutation_p.E408G|PCDH7_uc021xnd.1_Missense_Mutation_p.E408G|PCDH7_uc021xnc.1_Missense_Mutation_p.E408G	NM_002589	NP_002580	O60245	PCDH7_HUMAN	Homo sapiens protocadherin 7 (PCDH7), transcript variant a, mRNA.	408	Cadherin 3.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ATCAAAGACGAGAACGACAAC	0.642												
CXCL6	6372	broad.mit.edu	37	4	74702791	74702791	+	Missense_Mutation	SNP	C	C	A	rs149811429		TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:74702791C>A	uc003hhf.3	+	1	415	c.220C>A	c.(220-222)Cag>Aag	p.Q74K		NM_002993	NP_002984	P80162	CXCL6_HUMAN	Homo sapiens chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) (CXCL6), mRNA.	74					cell-cell signaling|chemotaxis|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity|heparin binding	p.P73P(1)		large_intestine(1)|lung(7)	8	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CGCAGGCCCGCAGTGCTCCAA	0.542												
NPNT	255743	broad.mit.edu	37	4	106863540	106863540	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:106863540C>A	uc011cfd.2	+	8	1143	c.930C>A	c.(928-930)gaC>gaA	p.D310E	NPNT_uc011cfc.2_Missense_Mutation_p.D297E|NPNT_uc011cfe.2_Missense_Mutation_p.D310E|NPNT_uc003hya.3_Missense_Mutation_p.D280E|NPNT_uc011cff.2_Missense_Mutation_p.D280E	NM_001184691	NP_001171620	Q6UXI9	NPNT_HUMAN	Homo sapiens nephronectin (NPNT), transcript variant 3, mRNA.	280	Pro-rich.				cell differentiation	membrane	calcium ion binding			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		TAAAGGGTGACACAGGAAATA	0.393												
TLL1	7092	broad.mit.edu	37	4	166960565	166960565	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:166960565C>T	uc003irh.2	+	9	1880	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D	TLL1_uc011cjn.2_Silent_p.D411D|TLL1_uc011cjo.2_Silent_p.D235D	NM_012464	NP_036596	O43897	TLL1_HUMAN	Homo sapiens tolloid-like 1 (TLL1), transcript variant 1, mRNA.	411	CUB 1.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AAGTAAGAGACGGGTACTGGA	0.388												
ODZ3	55714	broad.mit.edu	37	4	183594220	183594220	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:183594220C>T	uc003ivd.1	+	5	1249	c.1174C>T	c.(1174-1176)Cga>Tga	p.R392*		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	Homo sapiens odz, odd Oz/ten-m homolog 3 (Drosophila) (ODZ3), mRNA.	392					signal transduction	integral to membrane				NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(35)|lung(56)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(4)	129		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TGATATTGGCCGAAGAGCAAT	0.388												
ODZ3	55714	broad.mit.edu	37	4	183594343	183594343	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:183594343C>T	uc003ivd.1	+	5	1372	c.1297C>T	c.(1297-1299)Cgg>Tgg	p.R433W		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	Homo sapiens odz, odd Oz/ten-m homolog 3 (Drosophila) (ODZ3), mRNA.	433					signal transduction	integral to membrane				NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(35)|lung(56)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(4)	129		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		AGTATATGGCCGGAAAGGCTT	0.388												
FAT1	2195	broad.mit.edu	37	4	187557880	187557880	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr4:187557880G>A	uc003izf.3	-	4	4019	c.3831C>T	c.(3829-3831)acC>acT	p.T1277T		NM_005245	NP_005236	Q14517	FAT1_HUMAN	Homo sapiens FAT tumor suppressor homolog 1 (Drosophila) (FAT1), mRNA.	1277	Cadherin 11.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CATCCTTGTCGGTGGCTATGA	0.493										HNSCC(5;0.00058)		
TTC37	9652	broad.mit.edu	37	5	94856458	94856458	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:94856458G>A	uc003klb.3	-	19	2373	c.2076C>T	c.(2074-2076)gcC>gcT	p.A692A		NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	Homo sapiens tetratricopeptide repeat domain 37 (TTC37), mRNA.	692							binding			breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						TGTAGTCTACGGCTTTTCCAT	0.299												
DMXL1	1657	broad.mit.edu	37	5	118503534	118503534	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:118503534A>G	uc010jcl.1	+	22	5554	c.5373A>G	c.(5371-5373)atA>atG	p.I1791M	DMXL1_uc003ksd.2_Missense_Mutation_p.I1791M|DMXL1_uc021ycw.1_Missense_Mutation_p.I1618M	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Homo sapiens Dmx-like 1 (DMXL1), mRNA.	1791										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AAACATTAATAAAGCAACCTA	0.343												
ABLIM3	22885	broad.mit.edu	37	5	148620291	148620291	+	Silent	SNP	C	C	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:148620291C>G	uc003lpy.2	+	13	1508	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	ABLIM3_uc003lpz.1_Silent_p.S419S|ABLIM3_uc003lqa.1_Intron|ABLIM3_uc003lqb.3_Intron|ABLIM3_uc003lqc.1_Intron|ABLIM3_uc003lqd.1_Intron|ABLIM3_uc003lqe.1_Intron|ABLIM3_uc003lqf.3_Intron	NM_014945	NP_055760	O94929	ABLM3_HUMAN	Homo sapiens actin binding LIM protein family, member 3 (ABLIM3), mRNA.	419					axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTGAGGTCCTCCACTCCAA	0.572												
SLIT3	6586	broad.mit.edu	37	5	168112727	168112727	+	Missense_Mutation	SNP	C	C	T	rs150873620	by1000genomes	TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:168112727C>T	uc010jjg.3	-	30	3961	c.3541G>A	c.(3541-3543)Gcc>Acc	p.A1181T	SLIT3_uc003mab.3_Missense_Mutation_p.A1174T	NM_003062	NP_003053	O75094	SLIT3_HUMAN	Homo sapiens slit homolog 3 (Drosophila) (SLIT3), mRNA.	1174	Laminin G-like.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding	p.A1174T(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGACCTTGGCGGAGGCCAGT	0.627												
STK10	6793	broad.mit.edu	37	5	171479966	171479966	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:171479966C>T	uc003mbo.1	-	17	3033	c.2733G>A	c.(2731-2733)aaG>aaA	p.K911K		NM_005990	NP_005981	O94804	STK10_HUMAN	Homo sapiens serine/threonine kinase 10 (STK10), mRNA.	911							ATP binding|protein serine/threonine kinase activity			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCCGCCATTCCTTCAGGTTCT	0.567												
LMAN2	10960	broad.mit.edu	37	5	176765541	176765541	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:176765541G>A	uc003mge.3	-	2	618	c.381C>T	c.(379-381)aaC>aaT	p.N127N		NM_006816	NP_006807	Q12907	LMAN2_HUMAN	Homo sapiens lectin, mannose-binding 2 (LMAN2), mRNA.	127	L-type lectin-like.				protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	metal ion binding|sugar binding			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCATGGAGGTTCTTCTTCC	0.632												
CANX	821	broad.mit.edu	37	5	179132740	179132740	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr5:179132740G>A	uc011dgp.2	+	1	238	c.163G>A	c.(163-165)Gct>Act	p.A55T	CANX_uc010jlb.1_Missense_Mutation_p.A20T|CANX_uc003mkk.3_Missense_Mutation_p.A20T|CANX_uc003mkl.3_Missense_Mutation_p.A20T|CANX_uc011dgq.2_5'UTR	NM_001746	NP_001737	P27824	CALX_HUMAN	Homo sapiens calnexin (CANX), transcript variant 1, mRNA.	20					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	tattgttgaggctcatgatgg	0.423												
ABCF1	23	broad.mit.edu	37	6	30552069	30552069	+	Frame_Shift_Del	DEL	G	G	-			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr6:30552069delG	uc003nql.3	+	12	1298	c.1203delG	c.(1201-1203)ctgfs	p.L401fs	ABCF1_uc003nqk.2_Frame_Shift_Del_p.L402fs|ABCF1_uc003nqm.3_Frame_Shift_Del_p.L363fs|MIR877_uc021yud.1_5'Flank	NM_001025091	NP_001020262	Q8NE71	ABCF1_HUMAN	Homo sapiens ATP-binding cassette, sub-family F (GCN20), member 1 (ABCF1), transcript variant 1, mRNA.	401	ABC transporter 1.				inflammatory response|translational initiation	nuclear envelope|nucleoplasm|polysomal ribosome	ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						AGGGACAGCTGGAACAAGGGG	0.592												
LRFN2	57497	broad.mit.edu	37	6	40359856	40359856	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr6:40359856C>T	uc003oph.1	-	2	2661	c.2196G>A	c.(2194-2196)gcG>gcA	p.A732A		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	Homo sapiens leucine rich repeat and fibronectin type III domain containing 2 (LRFN2), mRNA.	732						cell junction|integral to membrane|postsynaptic membrane				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTCCCGCCGCCGCAGCAGCAA	0.682												
UNC5CL	222643	broad.mit.edu	37	6	40996138	40996138	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr6:40996138C>T	uc003opi.3	-	8	1630	c.1531G>A	c.(1531-1533)Ggc>Agc	p.G511S		NM_173561	NP_775832	Q8IV45	UN5CL_HUMAN	Homo sapiens unc-5 homolog C (C. elegans)-like (UNC5CL), mRNA.	511					signal transduction	cytoplasm|integral to membrane				endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGCTCCAGGCCCTGGTTATCC	0.687											OREG0017423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
SMPD2	6610	broad.mit.edu	37	6	109764877	109764877	+	Silent	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr6:109764877A>G	uc003pti.3	+	9	1435	c.1041A>G	c.(1039-1041)ggA>ggG	p.G347G	PPIL6_uc010kdp.3_5'Flank|PPIL6_uc003ptg.4_5'Flank|PPIL6_uc021zdq.1_5'Flank|PPIL6_uc003pth.1_5'Flank	NM_003080	NP_003071	O60906	NSMA_HUMAN	Homo sapiens sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase) (SMPD2), mRNA.	347					induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|sphingomyelin metabolic process	integral to plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		TGGCGGCTGGAGGAGGGGCCG	0.632												
UTRN	7402	broad.mit.edu	37	6	144809879	144809879	+	Missense_Mutation	SNP	T	T	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr6:144809879T>A	uc003qkt.3	+	28	4135	c.4043T>A	c.(4042-4044)gTc>gAc	p.V1348D		NM_007124	NP_009055	P46939	UTRO_HUMAN	Homo sapiens utrophin (UTRN), mRNA.	1348	Interaction with SYNM.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATGCTTCAAGTCTTGCAAGAG	0.483												
SLC29A4	222962	broad.mit.edu	37	7	5330480	5330480	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr7:5330480A>G	uc003sod.3	+	2	448	c.287A>G	c.(286-288)cAt>cGt	p.H96R	SLC29A4_uc011jwg.1_Non-coding_Transcript|SLC29A4_uc003soc.3_Missense_Mutation_p.H96R|SLC29A4_uc003soe.3_Missense_Mutation_p.H96R	NM_153247	NP_694979	Q7RTT9	S29A4_HUMAN	Homo sapiens solute carrier family 29 (nucleoside transporters), member 4 (SLC29A4), transcript variant 2, mRNA.	96					nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)		GACTACCTGCATCACAAGTAC	0.627												
STK31	56164	broad.mit.edu	37	7	23830449	23830449	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr7:23830449C>T	uc003sws.4	+	21	2711	c.2644C>T	c.(2644-2646)Cga>Tga	p.R882*	STK31_uc003swt.4_Nonsense_Mutation_p.R859*|STK31_uc011jze.2_Nonsense_Mutation_p.R882*|STK31_uc010kuq.3_Nonsense_Mutation_p.R859*|STK31_uc003swv.1_Nonsense_Mutation_p.R48*	NM_031414	NP_116562	Q9BXU1	STK31_HUMAN	Homo sapiens serine/threonine kinase 31 (STK31), transcript variant 1, mRNA.	882	Protein kinase.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GCAGAGTCAGCGAGCCTCGGT	0.378												
EGFR	1956	broad.mit.edu	37	7	55233035	55233035	+	Silent	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr7:55233035C>T	uc003tqk.3	+	14	2031	c.1785C>T	c.(1783-1785)tgC>tgT	p.C595C	EGFR_uc003tqi.3_Silent_p.C595C|EGFR_uc003tqj.3_Silent_p.C595C|EGFR_uc022adm.1_Silent_p.C595C|EGFR_uc010kzg.2_Silent_p.C550C|EGFR_uc022adn.1_Silent_p.C550C|EGFR_uc011kco.2_Silent_p.C542C|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_Non-coding_Transcript|EGFR_uc003tqn.3_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	Homo sapiens epidermal growth factor receptor (EGFR), transcript variant 1, mRNA.	595					activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	TCAAGACCTGCCCGGCAGGAG	0.567		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)		
LOC407835	407835	broad.mit.edu	37	7	128767702	128767702	+	Frame_Shift_Del	DEL	T	T	-			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr7:128767702delT	uc003voo.3	+	0	1378	c.1131delT	c.(1129-1131)gatfs	p.D377fs						Homo sapiens mitogen-activated protein kinase kinase 2 pseudogene (LOC407835), non-coding RNA.																		AAGAAGCGGATTTTGCCTGCT	0.582												
MCM4	4173	broad.mit.edu	37	8	48889249	48889249	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr8:48889249A>G	uc003xqk.2	+	16	3329	c.2503A>G	c.(2503-2505)Att>Gtt	p.I835V	MCM4_uc003xql.2_Missense_Mutation_p.I835V|MCM4_uc011ldi.2_Missense_Mutation_p.I822V	NM_182746	NP_877423	P33991	MCM4_HUMAN	Homo sapiens minichromosome maintenance complex component 4 (MCM4), transcript variant 2, mRNA.	835					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding	p.A834T(1)		biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				CCCACAGGCAATTACTAAAGA	0.423												
TTC39B	158219	broad.mit.edu	37	9	15185345	15185345	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:15185345G>A	uc003zlr.2	-	15	1584	c.1547C>T	c.(1546-1548)gCt>gTt	p.A516V	TTC39B_uc003zlq.2_Missense_Mutation_p.A419V|TTC39B_uc011lmp.2_Missense_Mutation_p.A351V|TTC39B_uc010mie.2_Missense_Mutation_p.A514V|TTC39B_uc011lmr.2_Missense_Mutation_p.A447V|TTC39B_uc011lmq.2_Missense_Mutation_p.A503V|TTC39B_uc003zlp.2_Missense_Mutation_p.A33V	NM_152574	NP_001161814	Q5VTQ0	TT39B_HUMAN	Homo sapiens tetratricopeptide repeat domain 39B (TTC39B), transcript variant 1, mRNA.	450							binding	p.D516Y(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						CTTCCTCACAGCAAACTTCTC	0.507												
FAM75D4	389761	broad.mit.edu	37	9	84547688	84547688	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:84547688G>A	uc004amh.2	+	3	2698	c.2612G>A	c.(2611-2613)cGa>cAa	p.R871Q	AK097447_uc004ami.1_Intron|DQ577940_uc004amj.1_5'Flank	NM_001145197	NP_001138669	Q6ZUB0	YI020_HUMAN	Homo sapiens family with sequence similarity 75, member D4 (FAM75D4), mRNA.	871						integral to membrane				cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(57)|ovary(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	83						ATTAAACATCGAAATTTGGCA	0.458												
TMEM246	84302	broad.mit.edu	37	9	104238682	104238682	+	Silent	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:104238682G>A	uc004bbm.3	-	1	1015	c.693C>T	c.(691-693)cgC>cgT	p.R231R	AK094413_uc004bbl.1_5'Flank|TMEM246_uc022blf.1_Silent_p.R231R	NM_032342	NP_115718	Q9BRR3	CI125_HUMAN	Homo sapiens chromosome 9 open reading frame 125 (C9orf125), mRNA.	231						integral to membrane											GCTCAGAGAAGCGAGCCCGCA	0.542												
SMC2	10592	broad.mit.edu	37	9	106885401	106885401	+	Silent	SNP	A	A	G			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:106885401A>G	uc004bbv.3	+	16	2433	c.2145A>G	c.(2143-2145)ctA>ctG	p.L715L	SMC2_uc004bbu.1_Silent_p.L715L|SMC2_uc004bbw.3_Silent_p.L715L|SMC2_uc011lvl.2_Silent_p.L715L|SMC2_uc004bbx.3_Silent_p.L715L	NM_001042551	NP_006435	O95347	SMC2_HUMAN	Homo sapiens structural maintenance of chromosomes 2 (SMC2), transcript variant 2, mRNA.	715					cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						ATCGCCAACTAAAACAGCAGT	0.348												
COL27A1	85301	broad.mit.edu	37	9	117071558	117071558	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:117071558C>T	uc011lxl.2	+	59	5236	c.5236C>T	c.(5236-5238)Cgg>Tgg	p.R1746W	COL27A1_uc004bii.3_Non-coding_Transcript|COL27A1_uc011lxn.2_Missense_Mutation_p.R61W	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	Homo sapiens collagen, type XXVII, alpha 1 (COL27A1), mRNA.	1746	Fibrillar collagen NC1.				cell adhesion		extracellular matrix structural constituent	p.R1746L(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGCCATCAGCCGGGTCCAGAT	0.607												
ATP6V1G1	9550	broad.mit.edu	37	9	117359986	117359986	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:117359986G>A	uc004bjc.3	+	2	445	c.320G>A	c.(319-321)cGg>cAg	p.R107Q		NM_004888	NP_004879	O75348	VATG1_HUMAN	Homo sapiens ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 (ATP6V1G1), mRNA.	107					cellular iron ion homeostasis|insulin receptor signaling pathway|proton transport|transferrin transport	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase complex	ATPase binding|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	p.R107R(1)		endometrium(1)|lung(2)|prostate(1)|skin(1)	5						TGTGACATTCGGCCAGAAATC	0.478												
NELF	26012	broad.mit.edu	37	9	140351900	140351900	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chr9:140351900C>T	uc004cna.3	-	2	819	c.587G>A	c.(586-588)cGc>cAc	p.R196H	NELF_uc011mex.2_5'Flank|NELF_uc010nci.3_5'Flank|NELF_uc011mey.2_Non-coding_Transcript|NELF_uc004cnb.3_Missense_Mutation_p.R196H|NELF_uc004cmz.3_Missense_Mutation_p.R196H|NELF_uc011mez.2_Missense_Mutation_p.R196H|NELF_uc004cnc.3_Missense_Mutation_p.R196H|NELF_uc022bqi.1_Missense_Mutation_p.R196H	NM_001130969	NP_001124441	Q6X4W1	NELF_HUMAN	Homo sapiens nasal embryonic LHRH factor (NELF), transcript variant 1, mRNA.	196						nucleus|plasma membrane				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	10	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)		CAGCTTCTTGCGGCGACCGGA	0.652												
SHOX	6473	broad.mit.edu	37	X	591909	591909	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chrX:591909G>A	uc004cph.1	+	2	968	c.277_splice	c.e2+1	p.G93_splice	SHOX_uc004cpi.3_Splice_Site_p.G93_splice	NM_000451	NP_000442	O15266	SHOX_HUMAN	Homo sapiens short stature homeobox (SHOX), transcript variant 1, mRNA.	93					skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			endometrium(3)|lung(9)|prostate(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGTGGCAGAAGGTAAGTTCCT	0.647												
FOXR2	139628	broad.mit.edu	37	X	55650926	55650926	+	Missense_Mutation	SNP	A	A	C			TCGA-06-0648-01A-01W-0323-08	TCGA-06-0648-10A-01W-0323-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33f8304e-11c3-4a9d-ad21-ffea555309dc	7a88c445-24c5-4dfd-9064-de5dc2a47b41	g.chrX:55650926A>C	uc004duo.3	+	0	1094	c.782A>C	c.(781-783)gAt>gCt	p.D261A		NM_198451	NP_940853	Q6PJQ5	FOXR2_HUMAN	Homo sapiens forkhead box R2 (FOXR2), mRNA.	261					embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	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			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						AAGGATGAAGATAATGCAAGA	0.517