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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
XPA	7507	broad.mit.edu	37	9	100459557	100459557	+	Silent	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr9:100459557C>T	ENST00000375128.4	-	1	82	c.18G>A	c.(16-18)ggG>ggA	p.G6G		NM_000380.3	NP_000371.1	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	6	Interaction with CEP164 and required for UV resistance.				nucleotide-excision repair, DNA damage removal	nucleoplasm	damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity			breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11		Acute lymphoblastic leukemia(62;0.158)				CCGGCAAAGCCCCGTCGGCCG	0.731000			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				6	22					0	0	1	0	0
LCE2B	26239	broad.mit.edu	37	1	152659435	152659435	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr1:152659435C>T	ENST00000368780.3	+	2	170	c.116C>T	c.(115-117)cCa>cTa	p.P39L	LCE2B_ENST00000417924.2_Missense_Mutation_p.P39L	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	39	Cys-rich.|Pro-rich.				keratinization					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCCAGCTCCATGTTCCCCT	0.622000													8	175					0	0	1	0	0
ZFHX3	463	broad.mit.edu	37	16	72831385	72831385	+	Silent	SNP	T	T	C	rs76691369	byFrequency	TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr16:72831385T>C	ENST00000268489.5	-	9	5868	c.5196A>G	c.(5194-5196)caA>caG	p.Q1732Q	ZFHX3_ENST00000397992.5_Silent_p.Q818Q	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1732	Poly-Gln.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				gttgttgttgttgctgttgct	0.537000													3	13					0	0	1	0	0
KRT75	9119	broad.mit.edu	37	12	52822482	52822482	+	Nonsense_Mutation	SNP	G	G	A	rs151328629		TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr12:52822482G>A	ENST00000252245.5	-	6	1301	c.1081C>T	c.(1081-1083)Cga>Tga	p.R361*		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	361	Coil 2.|Rod.					keratin filament	structural molecule activity			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TTGGTGTTTCGAAGGTCATCC	0.532000													7	43					0	0	1	0	0
CIC	23152	broad.mit.edu	37	19	42791393	42791393	+	Splice_Site	SNP	G	G	A			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr19:42791393G>A	ENST00000572681.2	+	4	3247		c.e4+1		CIC_ENST00000575354.2_Splice_Site|CIC_ENST00000160740.3_Splice_Site			Q96RK0	CIC_HUMAN	capicua transcriptional repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ATGATGATGCGTGAGTTCCCT	0.647000			"""Mis, F, S"""		oligodendroglioma								11	7					0	0	1	0	0
POLK	51426	broad.mit.edu	37	5	74892057	74892057	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr5:74892057A>G	ENST00000241436.4	+	13	1711	c.1539A>G	c.(1537-1539)atA>atG	p.I513M	POLK_ENST00000506928.1_3'UTR|POLK_ENST00000504026.1_Intron|POLK_ENST00000380481.3_Missense_Mutation_p.I423M|POLK_ENST00000352007.5_Missense_Mutation_p.I315M|POLK_ENST00000508526.1_Missense_Mutation_p.I315M	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	513					DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		GTGTTCGGATATCTAGTTTTC	0.378000								DNA polymerases (catalytic subunits)					7	28					0	0	1	0	0
ACSM2B	348158	broad.mit.edu	37	16	20556560	20556560	+	Missense_Mutation	SNP	G	G	C			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr16:20556560G>C	ENST00000329697.6	-	10	1368	c.1200C>G	c.(1198-1200)aaC>aaG	p.N400K	ACSM2B_ENST00000567288.1_5'UTR|ACSM2B_ENST00000565232.1_Missense_Mutation_p.N400K|ACSM2B_ENST00000567001.1_Missense_Mutation_p.N400K|ACSM2B_ENST00000565322.1_Missense_Mutation_p.N321K	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	400					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						GGGGCAGGACGTTGCCCTTAT	0.507000													23	26					0	0	1	0	0
RP11-798G7.5	0	broad.mit.edu	37	17	43587576	43587576	+	RNA	SNP	A	A	G	rs145439557	by1000genomes	TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr17:43587576A>G	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							tctgaaaagaaaagaaaaaaa	0.428000													4	29					0	0	1	0	0
PRMT1	0	broad.mit.edu	37	19	50185264	50185264	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr19:50185264C>T	ENST00000532489.1	+	4	658	c.152C>T	c.(151-153)tCg>tTg	p.S51L	PRMT1_ENST00000454376.2_Missense_Mutation_p.S97L|PRMT1_ENST00000391851.4_Missense_Mutation_p.S79L			Q8WUW5	Q8WUW5_HUMAN	protein arginine methyltransferase 1	78						cytoplasm	protein methyltransferase activity			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GACGTCGGCTCGGGCACCGGC	0.637000													3	24					0	0	1	0	0
SNHG14	0	broad.mit.edu	37	15	25488832	25488832	+	RNA	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr15:25488832C>T	ENST00000453082.2	+	0	2332				SNORD115-40_ENST00000606510.1_RNA	NR_003343.1																						AATAGGATTACGCTGAGGCCC	0.498000													4	295					0	0	1	0	0
PRDM8	56978	broad.mit.edu	37	4	81122620	81122620	+	Missense_Mutation	SNP	A	A	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr4:81122620A>T	ENST00000339711.4	+	9	1627	c.396A>T	c.(394-396)aaA>aaT	p.K132N	PRDM8_ENST00000415738.2_Missense_Mutation_p.K132N|PRDM8_ENST00000504452.1_Missense_Mutation_p.K132N	NM_020226.3	NP_064611.3	Q9NQV8	PRDM8_HUMAN	PR domain containing 8	132	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GGTACGGGAAAGAACTGACTG	0.517000											OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	40					0	0	1	0	0
IGHV3-48	0	broad.mit.edu	37	14	106994047	106994047	+	RNA	SNP	A	A	G			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr14:106994047A>G	ENST00000390624.2	-	0	196																											GCTGCACAGGAGAGTCTCAGG	0.562000													61	91					0	0	1	0	0
PHLPP2	23035	broad.mit.edu	37	16	71689222	71689222	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr16:71689222C>T	ENST00000393524.2	-	15	3038	c.2305G>A	c.(2305-2307)Gca>Aca	p.A769T	PHLPP2_ENST00000568954.1_Missense_Mutation_p.A836T|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000540628.1_Missense_Mutation_p.A46T|PHLPP2_ENST00000360429.3_Missense_Mutation_p.A836T|PHLPP2_ENST00000567016.1_Missense_Mutation_p.A871T|PHLPP2_ENST00000356272.3_Missense_Mutation_p.A836T			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	836						cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						AGCACATCTGCCATCGTACAC	0.488000													7	119					0	0	1	0	0
UBR3	130507	broad.mit.edu	37	2	170937133	170937133	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr2:170937133C>T	ENST00000272793.5	+	38	5538	c.5488C>T	c.(5488-5490)Cgc>Tgc	p.R1830C	UBR3_ENST00000418381.1_Missense_Mutation_p.R1830C|UBR3_ENST00000392631.1_Missense_Mutation_p.R651C			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1830					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TCGAGGTCACCGCTTCTGCCT	0.398000													22	22					0	0	1	0	0
ZNF407	55628	broad.mit.edu	37	18	72343568	72343568	+	Missense_Mutation	SNP	G	G	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr18:72343568G>T	ENST00000299687.5	+	1	593	c.593G>T	c.(592-594)tGc>tTc	p.C198F	ZNF407_ENST00000577538.1_Missense_Mutation_p.C198F|ZNF407_ENST00000309902.6_Missense_Mutation_p.C198F|ZNF407_ENST00000582337.1_Missense_Mutation_p.C198F	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	198					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TTTTCTTCTTGCTCTGACTTG	0.448000													10	140					0.00621372	0.00640201	1	1	0
AP005901.1	0	broad.mit.edu	37	18	15323276	15323276	+	RNA	SNP	A	A	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr18:15323276A>T	ENST00000455308.2	-	0	572					NR_027417.1																						ATCAACTGCAATTGCATTTGC	0.308000													3	13					0	0	1	0	0
PKP1	5317	broad.mit.edu	37	1	201291189	201291189	+	Silent	SNP	G	G	A			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr1:201291189G>A	ENST00000263946.3	+	9	1745	c.1494G>A	c.(1492-1494)gaG>gaA	p.E498E	PKP1_ENST00000367324.3_Silent_p.E477E|PKP1_ENST00000352845.3_Silent_p.E498E	NM_000299.3	NP_000290.2	Q13835	PKP1_HUMAN	plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)	498					cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GCCAGCTGGAGTATAACGCCC	0.607000													6	19					0	0	1	0	0
DHX29	54505	broad.mit.edu	37	5	54577289	54577289	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr5:54577289T>C	ENST00000251636.5	-	12	2168	c.2020A>G	c.(2020-2022)Agg>Ggg	p.R674G	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	674	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|translation initiation factor activity			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TAGAGTAACCTGGTAGATTCA	0.388000													11	33					0	0	1	0	0
LMNA	4000	broad.mit.edu	37	1	156105907	156105907	+	Silent	SNP	G	G	A			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr1:156105907G>A	ENST00000368300.4	+	6	1364	c.1152G>A	c.(1150-1152)gaG>gaA	p.E384E	LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368297.1_Silent_p.E303E|LMNA_ENST00000473598.2_Silent_p.E285E|LMNA_ENST00000448611.2_Silent_p.E272E|LMNA_ENST00000392353.3_Silent_p.E303E|LMNA_ENST00000368299.3_Silent_p.E384E|LMNA_ENST00000368301.2_Silent_p.E384E|LMNA_ENST00000361308.4_Silent_p.E384E|LMNA_ENST00000347559.2_Silent_p.E384E	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	384	Tail.				cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration	cytoplasm|lamin filament|nuclear envelope|perinuclear region of cytoplasm	protein binding|structural molecule activity			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					AGGGCGAGGAGGAGAGGTGGG	0.642000									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				8	21					0	0	1	0	0
APOB	338	broad.mit.edu	37	2	21245798	21245798	+	Silent	SNP	G	G	A	rs72653068		TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr2:21245798G>A	ENST00000233242.1	-	18	2848	c.2721C>T	c.(2719-2721)caC>caT	p.H907H		NM_000384.2	NP_000375.2	P04114	APOB_HUMAN	apolipoprotein B	907	Heparin-binding.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	GACCCGACTCGTGGAAGAAGT	0.507000													8	15					0	0	1	0	0
IRAK2	3656	broad.mit.edu	37	3	10255186	10255186	+	Nonsense_Mutation	SNP	G	G	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr3:10255186G>T	ENST00000256458.4	+	6	832	c.742G>T	c.(742-744)Gga>Tga	p.G248*		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	248	Protein kinase.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						TTCAAGTCCAGGATCAATCGA	0.463000													7	55					8.12818e-05	8.91478e-05	1	1	0
WDR90	197335	broad.mit.edu	37	16	705148	705148	+	Splice_Site	SNP	G	G	A			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr16:705148G>A	ENST00000549091.1	+	14	1648		c.e14+1		WDR90_ENST00000293879.4_Splice_Site|LA16c-349E10.1_ENST00000573609.1_RNA	NM_145294.4	NP_660337.3	Q96KV7	WDR90_HUMAN	WD repeat domain 90											endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				ATGAAACCAGGTGATGCAGCC	0.657000													7	48					0	0	1	0	0
SI	6476	broad.mit.edu	37	3	164781241	164781241	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr3:164781241C>T	ENST00000264382.3	-	8	958	c.896G>A	c.(895-897)aGc>aAc	p.S299N		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	299	Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CATTGCATTGCTATTCATTAA	0.264000										HNSCC(35;0.089)			17	56					0	0	1	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H			O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma								25	37					0	0	1	0	0
MPV17L	255027	broad.mit.edu	37	16	15501855	15501855	+	Missense_Mutation	SNP	C	C	G			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr16:15501855C>G	ENST00000287594.6	+	3	550	c.406C>G	c.(406-408)Ctg>Gtg	p.L136V	RP11-1021N1.1_ENST00000568222.1_Intron|MPV17L_ENST00000396385.3_Silent_p.L159L	NM_173803.3	NP_776164.2	Q2QL34	MP17L_HUMAN	MPV17 mitochondrial membrane protein-like	0						integral to membrane|peroxisomal membrane				kidney(2)|large_intestine(1)|skin(1)	4						GTGGTTTTCTCTGGGCCACCT	0.502000													3	60					0	0	1	0	0
ACTG1	71	broad.mit.edu	37	17	79478121	79478121	+	Silent	SNP	G	G	A			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr17:79478121G>A	ENST00000575842.1	-	4	1242	c.816C>T	c.(814-816)tgC>tgT	p.C272C	ACTG1_ENST00000575087.1_Silent_p.C272C|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000331925.2_Silent_p.C272C|ACTG1_ENST00000573283.1_Silent_p.C272C			P63261	ACTG_HUMAN	actin, gamma 1	272					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			CGTGGATGCCGCAAGATTCCA	0.542000													4	79					0	0	1	0	0
RP11-798G7.5	0	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs149697015	by1000genomes	TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr17:43587569G>C	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							aactccgtctgaaaagaaaag	0.443000													3	24					0	0	1	0	0
FUBP1	8880	broad.mit.edu	37	1	78444659	78444659	+	Frame_Shift_Del	DEL	G	G	-			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr1:78444659delG	ENST00000370767.1	-	1	117	c.30delC	c.(28-30)ccfs	p.P10fs	FUBP1_ENST00000436586.2_Frame_Shift_Del_p.P10fs|FUBP1_ENST00000370768.2_Frame_Shift_Del_p.P10fs			Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	10					transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						AGCCAGAAGAGGGGGGAGGCA	0.557			"""F, N"""		oligodendroglioma								9	12	---	---	---	---					
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr1:120612003_120612004delGG	ENST00000256646.2	-	1	236_237	c.17_18delCC	c.(16-18)cfs	p.P6fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	6					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity	p.P6fs*27(2)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.762			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				4	5	---	---	---	---					
SKIDA1	387640	broad.mit.edu	37	10	21805466	21805467	+	In_Frame_Ins	INS	-	-	CCTCCT	rs138084841	by1000genomes	TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr10:21805466_21805467insCCTCCT	ENST00000449193.2	-	4	3537_3538	c.1285_1286insAGGAGG	c.(1285-1287)ggg>AGGAGGggg	p.428_429insRR	SKIDA1_ENST00000444772.3_In_Frame_Ins_p.349_350insRR	NM_207371.3	NP_997254.3			SKI/DACH domain containing 1									p.E428_G429insEE(2)									CCCGCTGCccccctcctcctcc	0.619													2	4	---	---	---	---					
NELFCD	51497	broad.mit.edu	37	20	57556343	57556343	+	Frame_Shift_Del	DEL	G	G	-			TCGA-QH-A86X-01A-11D-A36O-08	TCGA-QH-A86X-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d987213e-8137-4aff-9332-890b683cea2f	54b51d95-2a98-444a-9c72-6196b1788ec4	g.chr20:57556343delG	ENST00000602795.1	+	1	81	c.33delG	c.(31-33)gcfs	p.A11fs	NELFCD_ENST00000344018.3_Frame_Shift_Del_p.A2fs					negative elongation factor complex member C/D																		AGGGCATGGCGGGGGCCGTGC	0.821													2	4	---	---	---	---					
