#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_BAM_File	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_EVS_AA	i_EVS_All	i_EVS_EA	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_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
BAP1	8314	genome.wustl.edu	37	3	52440862	52440862	+	Missense_Mutation	SNP	G	G	C	rs200953639		TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr3:52440862G>C	ENST00000460680.1	-	8	1113	c.642C>G	c.(640-642)atC>atG	p.I214M	BAP1_ENST00000296288.5_Missense_Mutation_p.I214M	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TGGCGAGGCCGATACGCTCCA	0.587			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	dbGAP		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	0													58.0	46.0	50.0					3																	52440862		2195	4283	6478	-	-	-	SO:0001583	missense	0			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.642C>G	3.37:g.52440862G>C	ENSP00000417132:p.Ile214Met		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	pfam_Peptidase_C12,prints_Peptidase_C12	p.I214M	ENST00000460680.1	37	c.642	CCDS2853.1	3	.	.	.	.	.	.	.	.	.	.	G	14.14	2.447354	0.43429	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.56611	0.45;0.45	6.04	-10.7	0.00240	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.48786	0.1519	N	0.21282	0.65	0.45403	D	0.998387	D	0.60160	0.987	D	0.67231	0.95	T	0.79885	-0.1614	10	0.26408	T	0.33	-8.1917	19.0932	0.93238	0.3703:0.0:0.6297:0.0	.	214	Q92560	BAP1_HUMAN	M	214	ENSP00000417132:I214M;ENSP00000296288:I214M	ENSP00000296288:I214M	I	-	3	3	BAP1	52415902	0.000000	0.05858	0.162000	0.22713	0.912000	0.54170	-1.674000	0.01949	-2.486000	0.00520	-1.899000	0.00529	ATC	BAP1	-	pfam_Peptidase_C12	ENSG00000163930		0.587	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAP1	HGNC	protein_coding	OTTHUMT00000350895.1	58	0.00	0	G			52440862	52440862	-1	no_errors	ENST00000460680	ensembl	human	known	69_37n	missense	38	24.00	12	SNP	0.109	C
C1GALT1C1	29071	genome.wustl.edu	37	X	119760370	119760370	+	Missense_Mutation	SNP	A	A	T			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chrX:119760370A>T	ENST00000304661.5	-	2	890	c.652T>A	c.(652-654)Tct>Act	p.S218T	C1GALT1C1_ENST00000371313.2_Missense_Mutation_p.S218T	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	218					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						TTATCTTCAGATATCTTCCAA	0.373																																						dbGAP											0													107.0	100.0	102.0					X																	119760370		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.652T>A	X.37:g.119760370A>T	ENSP00000304364:p.Ser218Thr		A8K246|Q8WWS3|Q9NZX1	Missense_Mutation	SNP	NULL	p.S218T	ENST00000304661.5	37	c.652	CCDS14602.1	X	.	.	.	.	.	.	.	.	.	.	A	11.74	1.729829	0.30684	.	.	ENSG00000171155	ENST00000304661;ENST00000371313	T;T	0.42900	0.96;0.96	5.32	1.57	0.23409	.	0.219934	0.47093	D	0.000256	T	0.34687	0.0906	L	0.52011	1.625	0.43126	D	0.994856	P	0.39862	0.692	B	0.42522	0.39	T	0.05419	-1.0886	9	.	.	.	-19.1121	5.3485	0.16022	0.5665:0.2748:0.1587:0.0	.	218	Q96EU7	C1GLC_HUMAN	T	218	ENSP00000304364:S218T;ENSP00000360363:S218T	.	S	-	1	0	C1GALT1C1	119644398	0.999000	0.42202	1.000000	0.80357	0.941000	0.58515	1.317000	0.33631	0.248000	0.21435	-0.377000	0.06932	TCT	C1GALT1C1	-	NULL	ENSG00000171155		0.373	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1GALT1C1	HGNC	protein_coding	OTTHUMT00000058117.1	69	0.00	0	A	NM_152692		119760370	119760370	-1	no_errors	ENST00000304661	ensembl	human	known	69_37n	missense	59	10.61	7	SNP	0.953	T
DNTT	1791	genome.wustl.edu	37	10	98092260	98092260	+	Missense_Mutation	SNP	G	G	T			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr10:98092260G>T	ENST00000371174.2	+	9	1368	c.1266G>T	c.(1264-1266)caG>caT	p.Q422H	DNTT_ENST00000419175.1_Missense_Mutation_p.Q422H			P04053	TDT_HUMAN	DNA nucleotidylexotransferase	422	Mediates interaction with DNTTIP2.				DNA modification (GO:0006304)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA nucleotidylexotransferase activity (GO:0003912)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		CCAGCTGGCAGGAAGGAAAGA	0.517																																						dbGAP											0													171.0	150.0	157.0					10																	98092260		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB046378	CCDS7447.1	10q23-q24	2013-05-21	2013-05-21		ENSG00000107447	ENSG00000107447	2.7.7.31	"""DNA polymerases"""	2983	protein-coding gene	gene with protein product	"""Terminal deoxynucleotidyltransferase"""	187410	"""deoxynucleotidyltransferase, terminal"""				Standard	NM_004088		Approved	TDT	uc001kmf.3	P04053	OTTHUMG00000018832	ENST00000371174.2:c.1266G>T	10.37:g.98092260G>T	ENSP00000360216:p.Gln422His		Q53FH1|Q5W103|Q96E50	Missense_Mutation	SNP	pfam_DNA_pol_lambd_fingers_domain,pfam_BRCT_dom,pfam_Nucleotidyltransferase,superfamily_DNA-dir_DNA_pol_X_beta-like_N,superfamily_DNA_pol_lambd_fingers_domain,superfamily_BRCT_dom,smart_BRCT_dom,smart_DNA-dir_DNA_pol_X,pirsf_DNA_nucleotidylexotransferase,pfscan_BRCT_dom,prints_DNA_nucleotidylexotransferase,prints_DNA_pol_X,prints_DNA_pol_X_beta-like	p.Q422H	ENST00000371174.2	37	c.1266	CCDS7447.1	10	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858407	0.32791	.	.	ENSG00000107447	ENST00000419175;ENST00000371174	T;T	0.42131	0.98;0.98	5.81	3.73	0.42828	DNA-directed DNA polymerase X (1);	0.720493	0.13994	N	0.348579	T	0.27098	0.0664	N	0.20685	0.6	0.34226	D	0.675983	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.003	T	0.23084	-1.0198	10	0.42905	T	0.14	-10.1922	8.7438	0.34573	0.0:0.1391:0.5883:0.2726	.	422;422	P04053-2;P04053	.;TDT_HUMAN	H	422	ENSP00000401169:Q422H;ENSP00000360216:Q422H	ENSP00000360216:Q422H	Q	+	3	2	DNTT	98082250	0.988000	0.35896	1.000000	0.80357	0.689000	0.40095	0.300000	0.19156	2.750000	0.94351	0.655000	0.94253	CAG	DNTT	-	smart_DNA-dir_DNA_pol_X,pirsf_DNA_nucleotidylexotransferase	ENSG00000107447		0.517	DNTT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DNTT	HGNC	protein_coding	OTTHUMT00000049607.1	62	0.00	0	G	NM_004088		98092260	98092260	+1	no_errors	ENST00000371174	ensembl	human	known	69_37n	missense	62	10.14	7	SNP	0.975	T
FADS1	3992	genome.wustl.edu	37	11	61582572	61582572	+	5'UTR	SNP	G	G	A			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr11:61582572G>A	ENST00000542506.1	-	0	191				FADS2_ENST00000517839.1_5'Flank|FADS1_ENST00000433932.1_Intron|MIR1908_ENST00000410394.1_RNA|FADS2_ENST00000522056.1_5'Flank|FADS2_ENST00000522639.1_5'Flank|FADS2_ENST00000574708.1_Intron|FADS1_ENST00000541683.1_5'UTR|FADS2_ENST00000257261.6_5'Flank|FADS1_ENST00000350997.7_Intron			O60427	FADS1_HUMAN	fatty acid desaturase 1						alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TAAGGTCCATGGCGATAAGAT	0.662																																						dbGAP											0													2.0	3.0	3.0					11																	61582572		521	1286	1807	-	-	-	SO:0001623	5_prime_UTR_variant	0				CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"""Fatty acid desaturases"""	3574	protein-coding gene	gene with protein product	"""delta-5 desaturase"""	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000542506.1:c.-353C>T	11.37:g.61582572G>A			A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	RNA	SNP	-	NULL	ENST00000542506.1	37	NULL		11																																																																																			FADS1	-	-	ENSG00000149485		0.662	FADS1-012	PUTATIVE	basic	protein_coding	FADS1	HGNC	protein_coding	OTTHUMT00000398584.1	114	0.00	0	G	NM_013402		61582572	61582572	-1	no_errors	ENST00000541683	ensembl	human	known	69_37n	rna	59	27.16	22	SNP	0.000	A
HTT	3064	genome.wustl.edu	37	4	3221994	3221994	+	Missense_Mutation	SNP	A	A	C			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr4:3221994A>C	ENST00000355072.5	+	53	7473	c.7328A>C	c.(7327-7329)aAg>aCg	p.K2443T		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2443					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CTCCAGGAAAAGGAAGTCTTT	0.517																																						dbGAP											0													111.0	109.0	110.0					4																	3221994		1888	4114	6002	-	-	-	SO:0001583	missense	0			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7328A>C	4.37:g.3221994A>C	ENSP00000347184:p.Lys2443Thr		Q9UQB7	Missense_Mutation	SNP	pfam_Huntingtin_middle-repeat,pfam_HEAT,superfamily_ARM-type_fold,prints_Huntingtin	p.K2443T	ENST00000355072.5	37	c.7328	CCDS43206.1	4	.	.	.	.	.	.	.	.	.	.	a	22.5	4.297709	0.81025	.	.	ENSG00000197386	ENST00000355072	T	0.05855	3.38	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.04454	-1.0950	10	0.20046	T	0.44	.	15.0977	0.72247	1.0:0.0:0.0:0.0	.	2443	P42858	HD_HUMAN	T	2443	ENSP00000347184:K2443T	ENSP00000347184:K2443T	K	+	2	0	HTT	3191792	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	9.234000	0.95347	1.977000	0.57605	0.524000	0.50904	AAG	HTT	-	NULL	ENSG00000197386		0.517	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTT	HGNC	protein_coding	OTTHUMT00000358234.2	47	0.00	0	A	NM_002111		3221994	3221994	+1	no_errors	ENST00000355072	ensembl	human	known	69_37n	missense	41	24.07	13	SNP	1.000	C
OR52B2	255725	genome.wustl.edu	37	11	6191379	6191379	+	Missense_Mutation	SNP	G	G	A			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr11:6191379G>A	ENST00000530810.1	-	1	259	c.178C>T	c.(178-180)Ccc>Tcc	p.P60S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001004052.1	NP_001004052.1	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B, member 2	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(15)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAATACATGGGCACATGAAGG	0.478																																					NSCLC(5;186 261 1778 7098 14207)	dbGAP											0													196.0	196.0	196.0					11																	6191379		2091	4237	6328	-	-	-	SO:0001583	missense	0			AB065763	CCDS53598.1	11p15.4	2012-08-09				ENSG00000255307		"""GPCR / Class A : Olfactory receptors"""	15207	protein-coding gene	gene with protein product							Standard	NM_001004052		Approved		uc010qzy.2	Q96RD2		ENST00000530810.1:c.178C>T	11.37:g.6191379G>A	ENSP00000432011:p.Pro60Ser		Q8NGM7	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.P60S	ENST00000530810.1	37	c.178	CCDS53598.1	11	.	.	.	.	.	.	.	.	.	.	G	17.24	3.338363	0.60963	.	.	ENSG00000255307	ENST00000530810	T	0.02015	4.5	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.23611	0.0571	H	0.97390	3.995	0.47476	D	0.999431	D	0.89917	1.0	D	0.77004	0.989	T	0.40776	-0.9545	9	0.72032	D	0.01	.	17.5353	0.87829	0.0:0.0:1.0:0.0	.	60	Q96RD2	O52B2_HUMAN	S	60	ENSP00000432011:P60S	ENSP00000432011:P60S	P	-	1	0	OR52B2	6147955	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	9.477000	0.97925	2.608000	0.88229	0.643000	0.83706	CCC	OR52B2	-	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam	ENSG00000255307		0.478	OR52B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR52B2	HGNC	protein_coding	OTTHUMT00000385977.1	63	0.00	0	G	NM_001004052		6191379	6191379	-1	no_errors	ENST00000530810	ensembl	human	known	69_37n	missense	61	14.08	10	SNP	1.000	A
OR7D2	162998	genome.wustl.edu	37	19	9297079	9297080	+	Frame_Shift_Ins	INS	-	-	T	rs145118134	byFrequency	TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr19:9297079_9297080insT	ENST00000344248.2	+	1	801_802	c.622_623insT	c.(622-624)gttfs	p.V208fs		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	208					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V208I(1)		breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TGTGCTGGGCGTTTTTCCCCTC	0.46																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.627dupT	19.37:g.9297084_9297084dupT	ENSP00000345563:p.Val208fs		Q6IFJ7|Q8N133	Frame_Shift_Ins	INS	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.P210fs	ENST00000344248.2	37	c.622_623	CCDS32900.1	19																																																																																			OR7D2	-	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000188000		0.460	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR7D2	HGNC	protein_coding	OTTHUMT00000449002.1	65	0.00	0	-			9297079	9297080	+1	no_errors	ENST00000344248	ensembl	human	known	69_37n	frame_shift_ins	34	20.93	9	INS	0.001:0.001	T
PIK3CA	5290	genome.wustl.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; 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). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		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.E542K(545)|p.E542Q(10)		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)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)											56.0	56.0	56.0					3																	178936082		1809	4069	5878	-	-	-	SO:0001583	missense	0				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.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E542K	ENST00000263967.3	37	c.1624	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	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	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	53	0.00	0	G			178936082	178936082	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	48	26.15	17	SNP	1.000	A
RGS12	6002	genome.wustl.edu	37	4	3319691	3319691	+	Silent	SNP	G	G	A			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr4:3319691G>A	ENST00000344733.5	+	2	2698	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	RGS12_ENST00000336727.3_Silent_p.P598P|RGS12_ENST00000382788.3_Silent_p.P598P|RGS12_ENST00000543385.1_Silent_p.P598P	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	598					positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TGAATGCCCCGAAGAGGGAGT	0.567																																						dbGAP											0													84.0	101.0	95.0					4																	3319691		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.1794G>A	4.37:g.3319691G>A			B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Silent	SNP	pfam_Raf-like_ras-bd,pfam_Regulat_G_prot_signal,pfam_PDZ,pfam_GoLoco_motif,superfamily_Regulat_G_prot_signal_superfam,superfamily_PDZ,smart_PDZ,smart_PTyr_interaction_dom,smart_Regulat_G_prot_signal,smart_Raf-like_ras-bd,smart_GoLoco_motif,pfscan_GoLoco_motif,pfscan_PDZ,pfscan_PTyr_interaction_dom,pfscan_Raf-like_ras-bd,pfscan_Regulat_G_prot_signal,prints_Regulat_G_prot_signal	p.P598	ENST00000344733.5	37	c.1794	CCDS3366.1	4																																																																																			RGS12	-	NULL	ENSG00000159788		0.567	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RGS12	HGNC	protein_coding	OTTHUMT00000206602.1	56	0.00	0	G	NM_002926		3319691	3319691	+1	no_errors	ENST00000344733	ensembl	human	known	69_37n	silent	35	10.26	4	SNP	0.128	A
RNF170	81790	genome.wustl.edu	37	8	42729139	42729139	+	Missense_Mutation	SNP	G	G	C			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr8:42729139G>C	ENST00000534961.1	-	3	624	c.148C>G	c.(148-150)Caa>Gaa	p.Q50E	RNF170_ENST00000319073.4_De_novo_Start_InFrame|RNF170_ENST00000526349.1_De_novo_Start_OutOfFrame|RNF170_ENST00000319104.3_Missense_Mutation_p.Q50E|RNF170_ENST00000527424.1_Missense_Mutation_p.Q50E	NM_001160223.1	NP_001153695.1	Q96K19	RN170_HUMAN	ring finger protein 170	50					protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			lung(3)	3	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			TGAATGTTTTGATGTACATTT	0.313																																						dbGAP											0													117.0	109.0	112.0					8																	42729139		2203	4300	6503	-	-	-	SO:0001583	missense	0			AL136620	CCDS6138.1, CCDS55229.1, CCDS55230.1	8p11.21	2014-01-29				ENSG00000120925		"""RING-type (C3HC4) zinc fingers"""	25358	protein-coding gene	gene with protein product		614649	"""sensory ataxia 1 (autosomal dominant)"""	SNAX1		11230166, 21115467	Standard	NR_027668		Approved	DKFZP564A022, ADSA	uc003xpm.3	Q96K19		ENST00000534961.1:c.148C>G	8.37:g.42729139G>C	ENSP00000445725:p.Gln50Glu		D3DSY6|E9PIL4|Q7Z483|Q86YC0|Q8IXR7|Q8N2B5|Q8N5G9|Q8NG30|Q9H0V6	Missense_Mutation	SNP	pfam_DUF1232,pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	p.Q50E	ENST00000534961.1	37	c.148	CCDS6138.1	8	.	.	.	.	.	.	.	.	.	.	G	15.38	2.817284	0.50633	.	.	ENSG00000120925	ENST00000319104;ENST00000534961;ENST00000527424;ENST00000531440	D;D;D;T	0.84370	-1.84;-1.68;-1.68;1.53	5.69	5.69	0.88448	.	0.050174	0.85682	D	0.000000	D	0.88149	0.6359	M	0.61703	1.905	0.80722	D	1	P;P;B	0.52316	0.48;0.952;0.435	B;P;B	0.49922	0.132;0.626;0.15	D	0.87476	0.2417	10	0.44086	T	0.13	-3.5517	19.3918	0.94585	0.0:0.0:1.0:0.0	.	50;50;50	Q96K19-3;Q96K19-2;Q96K19	.;.;RN170_HUMAN	E	50	ENSP00000326138:Q50E;ENSP00000445725:Q50E;ENSP00000434797:Q50E;ENSP00000436416:Q50E	ENSP00000240159:Q50E	Q	-	1	0	RNF170	42848296	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.419000	0.90253	2.681000	0.91329	0.591000	0.81541	CAA	RNF170	-	NULL	ENSG00000120925		0.313	RNF170-202	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF170	HGNC	protein_coding	OTTHUMT00000383166.1	57	0.00	0	G	NM_030954		42729139	42729139	-1	no_errors	ENST00000527424	ensembl	human	known	69_37n	missense	55	12.70	8	SNP	1.000	C
SPON1	10418	genome.wustl.edu	37	11	14281248	14281248	+	RNA	SNP	G	G	A	rs112977335		TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr11:14281248G>A	ENST00000310358.7	+	0	2366							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		CCAGAGTGCCGTGAGTGAGAG	0.582																																						dbGAP											0													20.0	21.0	20.0					11																	14281248		2168	4255	6423	-	-	-			0			AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"""spondin 1, (f-spondin) extracellular matrix protein"""			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		11.37:g.14281248G>A			A8K6W5|O94862|Q8NCD7|Q8WUR5	Splice_Site	SNP	-	NULL	ENST00000310358.7	37	c.NULL		11	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771183	0.90108	.	.	ENSG00000152268	ENST00000310358	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1531	0.86782	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPON1	14237824	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	9.455000	0.97625	2.658000	0.90341	0.561000	0.74099	.	SPON1	-	-	ENSG00000152268		0.582	SPON1-201	KNOWN	basic	processed_transcript	SPON1	HGNC	processed_transcript		91	0	0	G	NM_145584		14281248	14281248	+1	no_errors	ENST00000310358	ensembl	human	known	69_37n	splice_site	59	13.24	9	SNP	1.000	A
SPON1	10418	genome.wustl.edu	37	11	14281248	14281248	+	RNA	SNP	G	G	A	rs112977335		TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr11:14281248G>A	ENST00000310358.7	+	0	2366							Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	21				Epithelial(150;0.00898)		CCAGAGTGCCGTGAGTGAGAG	0.582																																						dbGAP											0													20.0	21.0	20.0					11																	14281248		2168	4255	6423	-	-	-			0			AB018305	CCDS73262.1	11p15.2	2014-05-06	2004-03-05		ENSG00000152268	ENSG00000262655			11252	protein-coding gene	gene with protein product		604989	"""spondin 1, (f-spondin) extracellular matrix protein"""			9872452	Standard	NM_006108		Approved	KIAA0762, f-spondin	uc001mle.3	Q9HCB6	OTTHUMG00000181576		11.37:g.14281248G>A			A8K6W5|O94862|Q8NCD7|Q8WUR5	Splice_Site	SNP	-	NULL	ENST00000310358.7	37	c.NULL		11	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771183	0.90108	.	.	ENSG00000152268	ENST00000310358	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1531	0.86782	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPON1	14237824	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	9.455000	0.97625	2.658000	0.90341	0.561000	0.74099	.	SPON1	-	-	ENSG00000152268		0.582	SPON1-201	KNOWN	basic	processed_transcript	SPON1	HGNC	processed_transcript		91	0.00	0	G	NM_145584		14281248	14281248	+1	no_errors	ENST00000310358	ensembl	human	known	69_37n	splice_site	59	13.24	9	SNP	1.000	A
SRM	6723	genome.wustl.edu	37	1	11116774	11116774	+	Missense_Mutation	SNP	G	G	A			TCGA-HN-A2OB-01A-21D-A27P-09	TCGA-HN-A2OB-10B-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9c888118-477d-4f12-afb7-653f05afa824	d739bf12-a886-410b-bc7b-22edf99c393d	g.chr1:11116774G>A	ENST00000376957.2	-	4	502	c.422C>T	c.(421-423)gCc>gTc	p.A141V		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	141	PABS.				cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)|spermidine synthase activity (GO:0004766)			large_intestine(1)|lung(1)|urinary_tract(1)	3	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)	GTAGCCAATGGCCATGCCTGG	0.562																																						dbGAP											0													98.0	86.0	90.0					1																	11116774		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC033106	CCDS125.1	1p36-p22	2010-11-08			ENSG00000116649	ENSG00000116649	2.5.1.16		11296	protein-coding gene	gene with protein product		182891		SRML1		2344393	Standard	NM_003132		Approved	SPS1	uc001arz.1	P19623	OTTHUMG00000002119	ENST00000376957.2:c.422C>T	1.37:g.11116774G>A	ENSP00000366156:p.Ala141Val		B1AKP9|Q15511	Missense_Mutation	SNP	pfam_Spermidine/spermine_synthase,pfscan_Spermidine/spermine_synthase,tigrfam_Spermidine/spermine_synthase	p.A141V	ENST00000376957.2	37	c.422	CCDS125.1	1	.	.	.	.	.	.	.	.	.	.	G	34	5.301565	0.95601	.	.	ENSG00000116649	ENST00000376957	T	0.78003	-1.14	5.35	5.35	0.76521	.	0.105714	0.64402	D	0.000005	D	0.90045	0.6891	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	D	0.91814	0.5462	10	0.87932	D	0	.	18.4201	0.90587	0.0:0.0:1.0:0.0	.	141	P19623	SPEE_HUMAN	V	141	ENSP00000366156:A141V	ENSP00000366156:A141V	A	-	2	0	SRM	11039361	1.000000	0.71417	0.968000	0.41197	0.909000	0.53808	7.686000	0.84128	2.663000	0.90544	0.561000	0.74099	GCC	SRM	-	pfam_Spermidine/spermine_synthase,pfscan_Spermidine/spermine_synthase,tigrfam_Spermidine/spermine_synthase	ENSG00000116649		0.562	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SRM	HGNC	protein_coding	OTTHUMT00000006056.1	65	0.00	0	G	NM_003132		11116774	11116774	-1	no_errors	ENST00000376957	ensembl	human	known	69_37n	missense	50	21.88	14	SNP	1.000	A
