#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
TEAD1	7003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	12901386	12901386	+	Silent	SNP	G	G	A			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr11:12901386G>A	ENST00000526600.1	+	1	397	c.174G>A	c.(172-174)ccG>ccA	p.P58P	TEAD1_ENST00000527636.1_Silent_p.P154P|TEAD1_ENST00000527575.1_Silent_p.P154P|TEAD1_ENST00000361905.4_Silent_p.P139P|TEAD1_ENST00000334310.6_Silent_p.P143P|TEAD1_ENST00000361985.2_Silent_p.P154P			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	154					gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P139P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CAGGGGCGCCGGGGGTAAGTC	0.597																																																1	Substitution - coding silent(1)	lung(1)											45.0	47.0	46.0					11																	12901386		2200	4294	6494	SO:0001819	synonymous_variant	7003			X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079			11714	protein-coding gene	gene with protein product		189967	"""atrophia areata, peripapillary chorioretinal degeneration"""	TCF13, AA		1851669, 9889009, 15016762	Standard	NM_021961		Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.174G>A	11.37:g.12901386G>A			A4FUP2|E7EV65	Silent	SNP	ENST00000526600.1	37																																																																																					0.597	TEAD1-007	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000387220.1	NM_021961		50	87	50	87
VRTN	55237	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	74825020	74825020	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr14:74825020C>T	ENST00000256362.4	+	2	1775	c.1534C>T	c.(1534-1536)Cgc>Tgc	p.R512C		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	512					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GAGGCGTCTGCGCAGGGCTGC	0.677																																																0													56.0	60.0	59.0					14																	74825020		2202	4299	6501	SO:0001583	missense	55237			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1534C>T	14.37:g.74825020C>T	ENSP00000256362:p.Arg512Cys		Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.364730	0.61513	.	.	ENSG00000133980	ENST00000256362	T	0.58060	0.36	4.29	3.4	0.38934	.	0.000000	0.64402	U	0.000001	T	0.39145	0.1067	L	0.32530	0.975	0.28678	N	0.905262	B	0.26445	0.149	B	0.12837	0.008	T	0.41734	-0.9492	10	0.87932	D	0	-7.5069	10.6671	0.45736	0.0:0.9101:0.0:0.0899	.	512	Q9H8Y1	VRTN_HUMAN	C	512	ENSP00000256362:R512C	ENSP00000256362:R512C	R	+	1	0	VRTN	73894773	0.992000	0.36948	0.982000	0.44146	0.958000	0.62258	2.356000	0.44116	1.012000	0.39366	0.491000	0.48974	CGC		0.677	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		67	83	67	83
EML1	2009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	100367314	100367314	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr14:100367314C>G	ENST00000262233.6	+	9	1085	c.946C>G	c.(946-948)Ctc>Gtc	p.L316V	EML1_ENST00000327921.9_Missense_Mutation_p.L304V|EML1_ENST00000334192.4_Missense_Mutation_p.L335V	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	316	Tandem atypical propeller in EMLs.				brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				ATTGAATACTCTCCACGTCAT	0.433																																																0													320.0	276.0	291.0					14																	100367314		2203	4300	6503	SO:0001583	missense	2009			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.946C>G	14.37:g.100367314C>G	ENSP00000262233:p.Leu316Val		Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.29|19.29	3.798373|3.798373	0.70567|0.70567	.|.	.|.	ENSG00000066629|ENSG00000066629	ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138;ENST00000556714|ENST00000554386	T;T;T;T;T|.	0.59224|.	4.98;0.99;0.99;0.99;0.28|.	5.34|5.34	4.45|4.45	0.53987|0.53987	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60470|0.60470	0.2271|0.2271	L|L	0.56396|0.56396	1.775|1.775	0.80722|0.80722	D|D	1|1	D;D;P;D;D|.	0.76494|.	0.999;0.998;0.584;0.999;0.999|.	D;D;B;D;D|.	0.87578|.	0.995;0.985;0.145;0.998;0.99|.	T|T	0.58216|0.58216	-0.7675|-0.7675	10|5	0.62326|.	D|.	0.03|.	-14.2931|-14.2931	8.9052|8.9052	0.35519|0.35519	0.15:0.7758:0.0:0.0743|0.15:0.7758:0.0:0.0743	.|.	304;304;316;335;335|.	F8W717;B7Z650;O00423;O00423-3;B3KXA3|.	.;.;EMAL1_HUMAN;.;.|.	V|C	303;304;316;335;335;285|40	ENSP00000451346:L303V;ENSP00000327384:L304V;ENSP00000262233:L316V;ENSP00000334314:L335V;ENSP00000452089:L285V|.	ENSP00000262233:L316V|.	L|S	+|+	1|2	0|0	EML1|EML1	99437067|99437067	0.993000|0.993000	0.37304|0.37304	0.338000|0.338000	0.25549|0.25549	0.979000|0.979000	0.70002|0.70002	2.986000|2.986000	0.49370|0.49370	1.230000|1.230000	0.43646|0.43646	0.591000|0.591000	0.81541|0.81541	CTC|TCT		0.433	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		45	74	45	74
C17orf77	146723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	72588190	72588190	+	Missense_Mutation	SNP	A	A	T			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr17:72588190A>T	ENST00000392620.1	+	3	367	c.5A>T	c.(4-6)gAt>gTt	p.D2V	CD300LD_ENST00000375352.1_Intron|C17orf77_ENST00000328023.2_Missense_Mutation_p.D2V	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	2						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						GCATGGATGGATGAATTGGCG	0.438																																																0													103.0	105.0	105.0					17																	72588190		2203	4300	6503	SO:0001583	missense	0				CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.5A>T	17.37:g.72588190A>T	ENSP00000376396:p.Asp2Val			Missense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	A	4.024	0.001939	0.07819	.	.	ENSG00000182352	ENST00000524389;ENST00000392620;ENST00000328023	T;T	0.56776	0.44;0.44	2.95	-5.06	0.02946	.	.	.	.	.	T	0.26011	0.0634	N	0.08118	0	0.09310	N	1	P	0.42908	0.793	B	0.34385	0.181	T	0.28459	-1.0043	9	0.87932	D	0	.	11.1743	0.48590	0.3233:0.0:0.6767:0.0	.	2	Q96MU5	CQ077_HUMAN	V	2	ENSP00000376396:D2V;ENSP00000329353:D2V	ENSP00000329353:D2V	D	+	2	0	C17orf77	70099785	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.532000	0.06164	-1.342000	0.02222	-0.363000	0.07495	GAT		0.438	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460		49	140	49	140
LLGL2	3993	hgsc.bcm.edu;broad.mit.edu	37	17	73570548	73570548	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr17:73570548A>G	ENST00000392550.3	+	24	3085	c.2968A>G	c.(2968-2970)Atc>Gtc	p.I990V	LLGL2_ENST00000577200.1_Missense_Mutation_p.I990V|LLGL2_ENST00000167462.5_Intron	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	990					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CCTGAAGGAAATCCAGAGCAC	0.697																																																0													14.0	17.0	16.0					17																	73570548		2152	4225	6377	SO:0001583	missense	3993			X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2968A>G	17.37:g.73570548A>G	ENSP00000376333:p.Ile990Val		Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	A	9.741	1.164787	0.21538	.	.	ENSG00000073350	ENST00000392550	T	0.05081	3.5	5.05	2.76	0.32466	.	0.241449	0.41097	N	0.000943	T	0.04452	0.0122	N	0.25426	0.745	0.35473	D	0.797475	B;B	0.10296	0.003;0.001	B;B	0.12156	0.007;0.006	T	0.39860	-0.9593	10	0.13108	T	0.6	-1.5982	9.6288	0.39768	0.8537:0.0:0.1463:0.0	.	617;990	B4DVR9;Q6P1M3	.;L2GL2_HUMAN	V	990	ENSP00000376333:I990V	ENSP00000376333:I990V	I	+	1	0	LLGL2	71082143	1.000000	0.71417	0.980000	0.43619	0.564000	0.35744	3.564000	0.53791	0.238000	0.21222	-0.572000	0.04151	ATC		0.697	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		4	7	4	7
PALM	5064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	746735	746735	+	Missense_Mutation	SNP	C	C	T	rs202021174		TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr19:746735C>T	ENST00000338448.5	+	9	1131	c.1085C>T	c.(1084-1086)gCg>gTg	p.A362V	PALM_ENST00000264560.7_Missense_Mutation_p.A318V|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	362					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		GAGAATCAGGCGGGGCCCGAG	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		11382	0.001		0.0	False		,,,				2504	0.0															0													12.0	13.0	13.0					19																	746735		2192	4287	6479	SO:0001583	missense	5064			Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.1085C>T	19.37:g.746735C>T	ENSP00000341911:p.Ala362Val		O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	37	CCDS32857.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.761	-0.769352	0.02974	.	.	ENSG00000099864	ENST00000338448;ENST00000264560;ENST00000538247	T;T	0.16324	2.35;2.35	4.19	0.3	0.15776	.	0.848256	0.10621	N	0.653317	T	0.06050	0.0157	N	0.03209	-0.39	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.12156	0.006;0.007	T	0.44483	-0.9325	10	0.12766	T	0.61	-11.8796	5.8252	0.18550	0.0:0.6382:0.1554:0.2065	.	318;362	O75781-2;O75781	.;PALM_HUMAN	V	362;318;227	ENSP00000341911:A362V;ENSP00000264560:A318V	ENSP00000264560:A318V	A	+	2	0	PALM	697735	0.003000	0.15002	0.001000	0.08648	0.047000	0.14425	0.418000	0.21230	0.234000	0.21139	0.462000	0.41574	GCG		0.672	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		15	11	15	11
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	42799051	42799051	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr19:42799051G>A	ENST00000575354.2	+	20	4575	c.4535G>A	c.(4534-4536)cGt>cAt	p.R1512H	CIC_ENST00000572681.2_Missense_Mutation_p.R2418H|CIC_ENST00000160740.3_Missense_Mutation_p.R1510H	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			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)				TTGAAGATCCGTGAGGTGCGC	0.627			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													51.0	51.0	51.0					19																	42799051		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4535G>A	19.37:g.42799051G>A	ENSP00000458663:p.Arg1512His		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529376	0.85706	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.65037	0.2653	L	0.29908	0.895	0.47009	D	0.999284	D	0.76494	0.999	D	0.74674	0.984	T	0.68911	-0.5284	8	0.87932	D	0	-6.0224	15.0527	0.71888	0.0:0.0:1.0:0.0	.	1512	Q96RK0	CIC_HUMAN	H	1512	.	ENSP00000160740:R1512H	R	+	2	0	CIC	47490891	1.000000	0.71417	0.993000	0.49108	0.974000	0.67602	8.215000	0.89762	2.513000	0.84729	0.491000	0.48974	CGT		0.627	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			62	27	62	27
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78429937	78429937	+	Splice_Site	SNP	A	A	C			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr1:78429937A>C	ENST00000370768.2	-	11	1022		c.e11+1		FUBP1_ENST00000370767.1_Splice_Site|FUBP1_ENST00000436586.2_Splice_Site	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1						positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						ATATGTACTCACCTGGCTTAA	0.333			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													103.0	100.0	101.0					1																	78429937		2203	4300	6503	SO:0001630	splice_region_variant	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.940+1T>G	1.37:g.78429937A>C			Q12828	Splice_Site	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.788585	0.70337	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	.	.	.	5.81	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9919	0.53180	0.9321:0.0:0.0679:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FUBP1	78202525	1.000000	0.71417	0.972000	0.41901	0.947000	0.59692	5.036000	0.64164	1.008000	0.39264	0.528000	0.53228	.		0.333	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Intron	18	13	18	13
DCAF6	55827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	167956741	167956741	+	Silent	SNP	T	T	C			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr1:167956741T>C	ENST00000312263.6	+	5	651	c.447T>C	c.(445-447)acT>acC	p.T149T	DCAF6_ENST00000432587.2_Silent_p.T118T|DCAF6_ENST00000367840.3_Silent_p.T149T|DCAF6_ENST00000367843.3_Silent_p.T149T|DCAF6_ENST00000470919.1_3'UTR	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	149					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						AGATTATGACTGTACCCAATG	0.358																																																0													86.0	81.0	83.0					1																	167956741		2203	4299	6502	SO:0001819	synonymous_variant	55827			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.447T>C	1.37:g.167956741T>C			A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Silent	SNP	ENST00000312263.6	37	CCDS30933.1																																																																																				0.358	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		7	43	7	43
KIDINS220	57498	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	8872066	8872066	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr2:8872066T>C	ENST00000256707.3	-	30	4281	c.4100A>G	c.(4099-4101)gAt>gGt	p.D1367G	KIDINS220_ENST00000427284.1_Missense_Mutation_p.D1348G|KIDINS220_ENST00000473731.1_Missense_Mutation_p.D1348G|KIDINS220_ENST00000418530.1_Missense_Mutation_p.D1268G	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1367					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AATACTGGAATCCTGGGAATT	0.388																																																0													82.0	79.0	80.0					2																	8872066		1828	4099	5927	SO:0001583	missense	57498			AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4100A>G	2.37:g.8872066T>C	ENSP00000256707:p.Asp1367Gly		A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.635062	0.87760	.	.	ENSG00000134313	ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731	T;T;T;T	0.69435	-0.4;-0.39;-0.38;-0.39	5.86	5.86	0.93980	.	0.050067	0.85682	D	0.000000	T	0.70133	0.3189	N	0.24115	0.695	0.49798	D	0.999821	P;P;D	0.62365	0.849;0.859;0.991	P;P;P	0.61275	0.755;0.574;0.886	T	0.74657	-0.3592	10	0.87932	D	0	.	16.2644	0.82568	0.0:0.0:0.0:1.0	.	1268;1367;221	Q9ULH0-2;Q9ULH0;B4DG84	.;KDIS_HUMAN;.	G	1367;1348;1268;1348	ENSP00000256707:D1367G;ENSP00000411849:D1348G;ENSP00000414923:D1268G;ENSP00000418974:D1348G	ENSP00000256707:D1367G	D	-	2	0	KIDINS220	8789517	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.499000	0.81566	2.244000	0.73946	0.528000	0.53228	GAT		0.388	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		45	70	45	70
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	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	NM_001282387.1	NP_001269316.1	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). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|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). {ECO:0000269|PubMed:18772396}.|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). {ECO:0000269|PubMed:19117336}.|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). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	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	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			27	40	27	40
POLQ	10721	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	121186388	121186388	+	Silent	SNP	T	T	A			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr3:121186388T>A	ENST00000264233.5	-	24	7073	c.6945A>T	c.(6943-6945)cgA>cgT	p.R2315R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2315					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CAAAGGCATGTCGCATGCTAA	0.443								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)											0													174.0	156.0	162.0					3																	121186388		2203	4300	6503	SO:0001819	synonymous_variant	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.6945A>T	3.37:g.121186388T>A			O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																				0.443	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		15	21	15	21
XRN1	54464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	142136035	142136035	+	Silent	SNP	C	C	T			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr3:142136035C>T	ENST00000264951.4	-	13	1500	c.1383G>A	c.(1381-1383)caG>caA	p.Q461Q	XRN1_ENST00000392981.2_Silent_p.Q461Q	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	461					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						ACTGTATTGCCTGAACATAAC	0.348																																																0													90.0	92.0	91.0					3																	142136035		2203	4300	6503	SO:0001819	synonymous_variant	54464			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1383G>A	3.37:g.142136035C>T			Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																				0.348	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		28	53	28	53
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			8	23	8	23
HSPA4L	22824	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	128739562	128739562	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr4:128739562G>A	ENST00000296464.4	+	13	2072	c.1661G>A	c.(1660-1662)gGa>gAa	p.G554E	HSPA4L_ENST00000439123.2_Missense_Mutation_p.G585E|HSPA4L_ENST00000515262.1_3'UTR|HSPA4L_ENST00000508776.1_Missense_Mutation_p.G554E|HSPA4L_ENST00000505726.1_Missense_Mutation_p.G528E	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	554					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GATCATACAGGAGCCAAAACA	0.313																																																0													83.0	87.0	86.0					4																	128739562		2203	4299	6502	SO:0001583	missense	22824			AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"""Heat shock proteins / HSP70"""	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1661G>A	4.37:g.128739562G>A	ENSP00000296464:p.Gly554Glu		A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	.	.	.	.	.	.	.	.	.	.	g	1.414	-0.574715	0.03882	.	.	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000508549;ENST00000505726	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	5.11	4.27	0.50696	.	0.627359	0.16599	N	0.207428	T	0.00608	0.0020	N	0.14661	0.345	0.33818	D	0.628709	B;B;B	0.33413	0.411;0.297;0.021	B;B;B	0.32211	0.134;0.142;0.019	T	0.25950	-1.0117	10	0.02654	T	1	.	6.1171	0.20132	0.154:0.0:0.695:0.151	.	528;554;554	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	E	554;585;554;513;528	ENSP00000422482:G554E;ENSP00000393926:G585E;ENSP00000296464:G554E;ENSP00000427305:G513E;ENSP00000425645:G528E	ENSP00000296464:G554E	G	+	2	0	HSPA4L	128959012	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.250000	0.51445	1.162000	0.42619	-0.127000	0.14921	GGA		0.313	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		30	47	30	47
ENPP1	5167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	132198210	132198210	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr6:132198210C>T	ENST00000360971.2	+	18	1822	c.1802C>T	c.(1801-1803)aCg>aTg	p.T601M		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	601	Linker. {ECO:0000250}.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	CCTGTTTATACGCCAAAGCAT	0.448																																					Colon(104;336 1535 5856 11019 33782)											0													89.0	73.0	78.0					6																	132198210		2203	4300	6503	SO:0001583	missense	5167			M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.1802C>T	6.37:g.132198210C>T	ENSP00000354238:p.Thr601Met		Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	c	6.381	0.438456	0.12104	.	.	ENSG00000197594	ENST00000360971	T	0.73363	-0.74	5.75	-2.45	0.06481	.	0.784631	0.12041	N	0.505097	T	0.39708	0.1088	M	0.64676	1.99	0.09310	N	1	P;B	0.34909	0.475;0.313	B;B	0.26416	0.069;0.035	T	0.21759	-1.0236	10	0.44086	T	0.13	-0.6455	1.1311	0.01746	0.2193:0.3034:0.1083:0.369	.	601;231	P22413;Q7Z3P5	ENPP1_HUMAN;.	M	601	ENSP00000354238:T601M	ENSP00000354238:T601M	T	+	2	0	ENPP1	132239903	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.756000	0.04777	-0.131000	0.11578	-0.224000	0.12420	ACG		0.448	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			15	14	15	14
GLT6D1	360203	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	138516117	138516117	+	Silent	SNP	C	C	T	rs201383603		TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr9:138516117C>T	ENST00000371763.1	-	5	910	c.657G>A	c.(655-657)ccG>ccA	p.P219P		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	219			P -> S (in dbSNP:rs17040344). {ECO:0000269|PubMed:19218399}.		carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)	p.P219P(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		CCTGTCCAAACGGGATGCAAG	0.493													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20088	0.0		0.0	False		,,,				2504	0.0															1	Substitution - coding silent(1)	endometrium(1)											105.0	104.0	104.0					9																	138516117		1915	4127	6042	SO:0001819	synonymous_variant	360203			AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.657G>A	9.37:g.138516117C>T				Silent	SNP	ENST00000371763.1	37	CCDS43900.1																																																																																				0.493	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		50	86	50	86
ITIH6	347365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	54777673	54777673	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chrX:54777673A>G	ENST00000218436.6	-	12	3522	c.3493T>C	c.(3493-3495)Tct>Cct	p.S1165P		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1165					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CCTCGCAAAGATATAGAACTG	0.592																																																0													81.0	66.0	71.0					X																	54777673		2203	4300	6503	SO:0001583	missense	347365			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3493T>C	X.37:g.54777673A>G	ENSP00000218436:p.Ser1165Pro		A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	A	1.972	-0.436150	0.04636	.	.	ENSG00000102313	ENST00000218436	T	0.12361	2.69	3.58	-2.56	0.06268	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	7779.790000	0.00166	N	0.000000	T	0.09113	0.0225	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33954	-0.9848	10	0.40728	T	0.16	.	0.5916	0.00729	0.2063:0.1514:0.209:0.4334	.	1165	Q6UXX5	ITH5L_HUMAN	P	1165	ENSP00000218436:S1165P	ENSP00000218436:S1165P	S	-	1	0	ITIH5L	54794398	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	0.538000	0.23160	0.195000	0.20347	-0.973000	0.02599	TCT		0.592	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		36	50	36	50
TREML2	79865	broad.mit.edu;ucsc.edu	37	6	41165879	41165879	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chr6:41165879G>A	ENST00000483722.1	-	2	529	c.344C>T	c.(343-345)cCc>cTc	p.P115L		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	115	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCCCATCAAGGGGTACAGGAT	0.612																																																0													40.0	40.0	40.0					6																	41165879		2203	4299	6502	SO:0001583	missense	79865			AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.344C>T	6.37:g.41165879G>A	ENSP00000418767:p.Pro115Leu		Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	G	15.06	2.720147	0.48728	.	.	ENSG00000112195	ENST00000483722	T	0.19938	2.11	4.68	4.68	0.58851	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000028	T	0.33000	0.0848	M	0.63843	1.955	0.50467	D	0.999879	D	0.89917	1.0	D	0.97110	1.0	T	0.03433	-1.1037	10	0.49607	T	0.09	-21.7432	13.4773	0.61316	0.0:0.0:1.0:0.0	.	115	Q5T2D2	TRML2_HUMAN	L	115	ENSP00000418767:P115L	ENSP00000418767:P115L	P	-	2	0	TREML2	41273857	0.998000	0.40836	0.944000	0.38274	0.170000	0.22686	4.280000	0.58959	2.309000	0.77851	0.563000	0.77884	CCC		0.612	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		6	52	6	52
RGAG4	340526	broad.mit.edu;hgsc.bcm.edu	37	X	71351107	71351107	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DB-A64Q-01A-11D-A29Q-08	TCGA-DB-A64Q-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fb1dc195-0b41-4ff7-8364-7fdcb4a96521	62bd6123-d070-4bde-af89-8177daee0949	g.chrX:71351107delT	ENST00000545866.1	-	1	651	c.284delA	c.(283-285)gagfs	p.E95fs	NHSL2_ENST00000510661.1_5'Flank|NHSL2_ENST00000373677.1_5'Flank|NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Frame_Shift_Del_p.E95fs|NHSL2_ENST00000535692.1_5'Flank	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	95										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					ACAGTCGGGCTCCGCGCGTGG	0.647																																																0													23.0	27.0	26.0					X																	71351107		1924	4115	6039	SO:0001589	frameshift_variant	340526			AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.284delA	X.37:g.71351107delT	ENSP00000441366:p.Glu95fs		A7E2W7|Q8NCM4|Q9NPX1	Frame_Shift_Del	DEL	ENST00000545866.1	37	CCDS55446.1																																																																																				0.647	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		28	24	28	24
