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_alt_allele	validation_method	validation_status	validation_tumor_sample
LCE1F	353137	broad.mit.edu	37	1	152748962	152748962	+	Missense_Mutation	SNP	C	C	G	rs116630978	by1000genomes	TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr1:152748962C>G	ENST00000334371.2	+	1	115	c.115C>G	c.(115-117)Cct>Gct	p.P39A		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization			p.P39A(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			taagtgccctccTGTCTCTTC	0.677													14	84	---	---	---	---
LCE1F	353137	broad.mit.edu	37	1	152748963	152748963	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr1:152748963C>T	ENST00000334371.2	+	1	116	c.116C>T	c.(115-117)cCt>cTt	p.P39L		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization			p.P39L(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			aagtgccctccTGTCTCTTCC	0.672													13	84	---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197073334	197073334	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr1:197073334T>C	ENST00000367409.4	-	18	5303	c.5047A>G	c.(5047-5049)Ata>Gta	p.I1683V	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1683	IQ 5.				mitosis	cytoplasm|nucleus	calmodulin binding	p.I1683V(1)|p.I1683fs*7(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TGCAATTTTATTGTAGCATTT	0.303													4	125	---	---	---	---
CCDC142	84865	broad.mit.edu	37	2	74708964	74708964	+	Missense_Mutation	SNP	A	A	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr2:74708964A>T	ENST00000393965.3	-	1	1397	c.1001T>A	c.(1000-1002)cTg>cAg	p.L334Q	CCDC142_ENST00000471713.1_5'UTR|CCDC142_ENST00000290418.4_Missense_Mutation_p.L334Q	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	334								p.L334Q(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						TGCCTGACTCAGCTGTTGCGC	0.612													8	111	---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100199303	100199303	+	Missense_Mutation	SNP	G	G	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr2:100199303G>C	ENST00000409236.2	-	15	2862	c.2750C>G	c.(2749-2751)cCt>cGt	p.P917R	AFF3_ENST00000409579.1_Missense_Mutation_p.P942R|AFF3_ENST00000356421.2_Missense_Mutation_p.P942R|AFF3_ENST00000317233.4_Missense_Mutation_p.P917R			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	p.P942R(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GTCGGCCTTAGGCTTTTTGCT	0.478													8	158	---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211454904	211454904	+	Silent	SNP	G	G	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr2:211454904G>A	ENST00000233072.5	+	8	982	c.786G>A	c.(784-786)gcG>gcA	p.A262A	CPS1_ENST00000430249.2_Silent_p.A268A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	262	Glutamine amidotransferase type-1.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity	p.A262A(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		TTTTGATCGCGGGAGGACCGG	0.483													24	534	---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71179726	71179726	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr3:71179726C>A	ENST00000491238.1	-	1	262	c.109G>T	c.(109-111)Gaa>Taa	p.E37*	FOXP1_ENST00000318789.4_Intron|FOXP1_ENST00000484350.1_Intron|FOXP1_ENST00000493089.1_Intron|FOXP1_ENST00000498215.1_Intron|FOXP1_ENST00000475937.1_Intron|FOXP1_ENST00000468577.1_Intron	NM_001244815.1	NP_001231744.1	Q9H334	FOXP1_HUMAN	forkhead box P1	383					cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		TAGATGGGTTCTGGCTGTTTC	0.468			T	PAX5	ALL								4	77	---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160260299	160260299	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr4:160260299C>T	ENST00000264431.4	+	13	2263	c.1844C>T	c.(1843-1845)gCt>gTt	p.A615V		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	615	Ras-associating.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity	p.A615V(1)|p.A603V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GTTTTTAAGGCTGATCAGCAA	0.423													6	355	---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152639275	152639275	+	Missense_Mutation	SNP	T	T	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr6:152639275T>C	ENST00000367255.5	-	86	17114	c.16513A>G	c.(16513-16515)Act>Gct	p.T5505A	SYNE1_ENST00000448038.1_Missense_Mutation_p.T5434A|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.T5505A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T5434A|SYNE1_ENST00000356820.4_Missense_Mutation_p.T29A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5505					cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	p.T5505A(3)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGAAGTTCAGTCAGTTTTCCT	0.448										HNSCC(10;0.0054)			9	188	---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90801576	90801576	+	Missense_Mutation	SNP	A	A	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr8:90801576A>G	ENST00000220751.4	+	10	1465	c.1151A>G	c.(1150-1152)aAg>aGg	p.K384R	RIPK2_ENST00000540020.1_Missense_Mutation_p.K247R	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	384					activation of MAPK activity|anti-apoptosis|apoptosis|inflammatory response|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|CARD domain binding|LIM domain binding|protein homodimerization activity|protein serine/threonine kinase activity|signal transducer activity	p.K384R(2)		kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TATTTTATGAAGCTGCATCAC	0.398													6	259	---	---	---	---
SPATA31A3	727830	broad.mit.edu	37	9	40702847	40702847	+	Silent	SNP	C	C	A			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr9:40702847C>A	ENST00000356699.5	+	4	533	c.504C>A	c.(502-504)acC>acA	p.T168T	SPATA31A3_ENST00000463536.1_3'UTR	NM_001083124.1	NP_001076593.1			SPATA31 subfamily A, member 3									p.T168T(2)									TGGCCTCCACCCCATCACCAG	0.597													20	445	---	---	---	---
LPAR1	1902	broad.mit.edu	37	9	113703743	113703743	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr9:113703743C>T	ENST00000374431.3	-	4	1134	c.751G>A	c.(751-753)Gat>Aat	p.D251N	LPAR1_ENST00000538760.1_Missense_Mutation_p.D252N|LPAR1_ENST00000541779.1_Missense_Mutation_p.D252N|LPAR1_ENST00000374430.2_Missense_Mutation_p.D251N|LPAR1_ENST00000358883.4_Missense_Mutation_p.D251N	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	251					positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane		p.D251N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						ATCATGGTATCCCGATTCCGC	0.443													24	98	---	---	---	---
OR9G4	283189	broad.mit.edu	37	11	56511197	56511197	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr11:56511197C>T	ENST00000302957.3	-	1	90	c.91G>A	c.(91-93)Ggt>Agt	p.G31S		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	31					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.G31S(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						GCTGAGAAACCCAACAAGATG	0.428													4	107	---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134054637	134054637	+	Silent	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr11:134054637C>T	ENST00000534548.2	-	19	2410	c.2346G>A	c.(2344-2346)aaG>aaA	p.K782K	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	782					cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding	p.K782K(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TCAGCTTACACTTGACAGCAT	0.448													19	96	---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76374992	76374992	+	Missense_Mutation	SNP	A	A	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr13:76374992A>G	ENST00000357063.3	+	8	2051	c.791A>G	c.(790-792)gAt>gGt	p.D264G	RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Missense_Mutation_p.D173G|LMO7_ENST00000377534.3_Missense_Mutation_p.D264G|LMO7_ENST00000341547.4_Missense_Mutation_p.D264G|LMO7_ENST00000465261.2_5'UTR|LMO7_ENST00000321797.8_5'UTR			Q8WWI1	LMO7_HUMAN	LIM domain 7	264						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding	p.D264G(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TGCTCCTCTGATATCACGTTG	0.458													14	328	---	---	---	---
CPNE6	9362	broad.mit.edu	37	14	24543288	24543288	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr14:24543288C>T	ENST00000397016.2	+	5	688	c.377C>T	c.(376-378)cCa>cTa	p.P126L	CPNE6_ENST00000216775.2_Missense_Mutation_p.P126L|CPNE6_ENST00000537691.1_Missense_Mutation_p.P181L|CPNE6_ENST00000560092.1_3'UTR	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	126					lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport		calcium ion binding|transporter activity			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		GTCACTAAGCCATTATTGCTG	0.532													18	90	---	---	---	---
ALDOC	230	broad.mit.edu	37	17	26901519	26901519	+	Missense_Mutation	SNP	G	G	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr17:26901519G>T	ENST00000226253.4	-	6	1092	c.617C>A	c.(616-618)aCa>aAa	p.T206K	ALDOC_ENST00000395319.3_Intron|ALDOC_ENST00000395321.2_Missense_Mutation_p.T206K	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	206					fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis	cytosol	cytoskeletal protein binding|fructose-bisphosphate aldolase activity	p.T206K(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Lung NSC(42;0.00431)					CACCTTCTCTGTAACATACTG	0.517													12	314	---	---	---	---
ZNF181	339318	broad.mit.edu	37	19	35232875	35232875	+	Nonsense_Mutation	SNP	C	C	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr19:35232875C>G	ENST00000392232.3	+	6	1889	c.1721C>G	c.(1720-1722)tCa>tGa	p.S574*	ZNF181_ENST00000459757.2_Nonsense_Mutation_p.S529*|ZNF181_ENST00000492450.1_Nonsense_Mutation_p.S530*			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	530					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.S466*(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AGCAAAGGCTCAAATCTTACT	0.388													5	201	---	---	---	---
PRODH2	58510	broad.mit.edu	37	19	36297714	36297714	+	Missense_Mutation	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr19:36297714C>T	ENST00000301175.3	-	7	942	c.925G>A	c.(925-927)Gtg>Atg	p.V309M		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	309					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity	p.V309M(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGGAGCCGCACGTGCTGGGCC	0.682													4	17	---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	31021261	31021261	+	Silent	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr20:31021261C>T	ENST00000375687.4	+	12	1684	c.1260C>T	c.(1258-1260)gcC>gcT	p.A420A	ASXL1_ENST00000306058.5_Silent_p.A415A	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 (Drosophila)	420					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	p.A420A(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GAACCAGAGCCAGAAGGAATC	0.527			"""F, N, Mis"""		"""MDS, CMML"""								5	169	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34458923	34458923	+	Silent	SNP	A	A	G			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr20:34458923A>G	ENST00000374012.3	+	8	1098	c.969A>G	c.(967-969)ttA>ttG	p.L323L	PHF20_ENST00000439301.1_3'UTR|PHF20_ENST00000481202.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	323					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding	p.L323L(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					ACAAAGACTTATCGAGGAGAC	0.423													7	149	---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45797830	45797830	+	Missense_Mutation	SNP	A	A	C	rs143610627		TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr20:45797830A>C	ENST00000327619.5	+	11	1396	c.1022A>C	c.(1021-1023)aAt>aCt	p.N341T	EYA2_ENST00000357410.3_Missense_Mutation_p.N341T|EYA2_ENST00000317304.6_Missense_Mutation_p.N311T	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	eyes absent homolog 2 (Drosophila)	341					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity	p.N341T(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				TCAGATGACAATGGCCAAGAT	0.428													43	196	---	---	---	---
MT-ND5	4540	broad.mit.edu	37	M	13326	13326	+	Silent	SNP	T	T	C			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chrM:13326T>C	ENST00000361567.2	+	1	990	c.990T>C	c.(988-990)tgT>tgC	p.C330C				P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	330					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74					NADH(DB00157)	CTGCACATCTGTACCCACGCC	0.423													2	8	---	---	---	---
MT-ND5	4540	broad.mit.edu	37	M	13680	13680	+	Silent	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chrM:13680C>T	ENST00000361567.2	+	1	1344	c.1344C>T	c.(1342-1344)ccC>ccT	p.P448P				P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	448					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74					NADH(DB00157)	GAAAATAACCCCACCCTACTA	0.488													5	6	---	---	---	---
MT-CYB	4519	broad.mit.edu	37	M	14872	14872	+	Silent	SNP	C	C	T			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chrM:14872C>T	ENST00000361789.2	+	1	126	c.126C>T	c.(124-126)atC>atT	p.I42I						mitochondrially encoded cytochrome b											breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GCCTGCCTGATCCTCCAAATC	0.488													3	13	---	---	---	---
FASTKD2	22868	broad.mit.edu	37	2	207636634	207636634	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr2:207636634delA	ENST00000236980.6	+	5	1355	c.1007delA	c.(1006-1008)gaafs	p.E336fs	FASTKD2_ENST00000402774.3_Frame_Shift_Del_p.E336fs|FASTKD2_ENST00000403094.3_Frame_Shift_Del_p.E336fs	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	336					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		GCCTTGAGGGAATTAGACAGA	0.318													38	164	---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113275870	113275870	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr8:113275870delA	ENST00000297405.5	-	61	10104	c.9860delT	c.(9859-9861)ttafs	p.L3287fs	CSMD3_ENST00000455883.2_Frame_Shift_Del_p.L3118fs|CSMD3_ENST00000343508.3_Frame_Shift_Del_p.L3247fs|CSMD3_ENST00000352409.3_Frame_Shift_Del_p.L3217fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3287	Sushi 25.					integral to membrane|plasma membrane				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATACTTACGTAAGCACTGCGG	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			20	58	---	---	---	---
NINL	22981	broad.mit.edu	37	20	25436392	25436392	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EJ-5497-01A-02D-1576-08	TCGA-EJ-5497-10A-01D-1577-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	924c20dd-38c1-48a7-83c6-fd1bdffda680	f6c01a65-6505-4d90-a07f-9c7285b4cf58	g.chr20:25436392delC	ENST00000278886.6	-	23	3947	c.3874delG	c.(3874-3876)gaafs	p.E1293fs	NINL_ENST00000464285.1_5'UTR|NINL_ENST00000422516.1_Frame_Shift_Del_p.E944fs	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1293					G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						ACCCGCTCTTCTGTGGCTTTC	0.527													11	428	---	---	---	---
