#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CLIC6	54102	broad.mit.edu	37	21	36088676	36088676	+	Missense_Mutation	SNP	A	A	G			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr21:36088676A>G	ENST00000360731.3	+	7	2011	c.2011A>G	c.(2011-2013)Aga>Gga	p.R671G	CLIC6_ENST00000349499.2_Missense_Mutation_p.R653G			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	671	GST C-terminal.					chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						TGGCATCTGGAGATACTTGAA	0.363																																						uc010gmt.1																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						c.(2011-2013)Aga>Gga		Homo sapiens chloride intracellular channel 6 (CLIC6), nuclear gene encoding mitochondrial protein, mRNA.							144.0	136.0	139.0					21																	36088676		2203	4300	6503	SO:0001583	missense	54102					chloride channel complex|cytoplasm|plasma membrane	voltage-gated chloride channel activity	g.chr21:36088676A>G	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"""Ion channels / Chloride channels : Intracellular"""	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.2011A>G	21.37:g.36088676A>G	ENSP00000353959:p.Arg671Gly		Somatic				CLIC6_uc002yuf.1_Missense_Mutation_p.R653G	p.R671G	NM_053277	NP_444507	WXS	Illumina GAIIx	Phase_I	Q96NY7	CLIC6_HUMAN			6	2011	+			671			GST C-terminal.		A8K0U8|Q8IX31	Missense_Mutation	SNP	ENST00000360731.3	37	c.2011A>G		.	.	.	.	.	.	.	.	.	.	A	18.47	3.630301	0.67015	.	.	ENSG00000159212	ENST00000360731;ENST00000349499	D;D	0.94092	-3.35;-3.35	5.85	4.68	0.58851	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96929	0.8997	M	0.88241	2.94	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.97089	0.9789	10	0.87932	D	0	-3.7579	13.2783	0.60200	0.8677:0.1323:0.0:0.0	.	671;653	Q96NY7;Q96NY7-2	CLIC6_HUMAN;.	G	671;653	ENSP00000353959:R671G;ENSP00000290332:R653G	ENSP00000290332:R653G	R	+	1	2	CLIC6	35010546	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.403000	0.66338	1.021000	0.39600	0.460000	0.39030	AGA		0.363	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			6	93	0	0	0	1	0	6	93				
PIAS2	9063	broad.mit.edu	37	18	44470887	44470887	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr18:44470887G>A	ENST00000585916.1	-	2	154	c.155C>T	c.(154-156)gCg>gTg	p.A52V	PIAS2_ENST00000545673.1_Intron|PIAS2_ENST00000324794.7_Missense_Mutation_p.A52V	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	52					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						AATCTGAACCGCAGGGCTGCA	0.448																																						uc002lck.3																			0				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						c.(154-156)gCg>gTg		Homo sapiens protein inhibitor of activated STAT, 2 (PIAS2), transcript variant beta, mRNA.							66.0	68.0	67.0					18																	44470887		2203	4300	6503	SO:0001583	missense	9063				androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body|nuclear speck	DNA binding|SUMO ligase activity|androgen receptor binding|protein binding|transcription coactivator activity|zinc ion binding	g.chr18:44470887G>A	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"""Zinc fingers, MIZ-type"""	17311	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 4"""	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.155C>T	18.37:g.44470887G>A	ENSP00000465676:p.Ala52Val		Somatic				PIAS2_uc010dnp.3_5'UTR|PIAS2_uc010xda.2_Intron|PIAS2_uc002lcl.3_Missense_Mutation_p.A52V|PIAS2_uc002lcm.3_Missense_Mutation_p.A52V|PIAS2_uc002lcn.1_Missense_Mutation_p.A56V	p.A52V	NM_004671	NP_004662	WXS	Illumina GAIIx	Phase_I	O75928	PIAS2_HUMAN			1	342	-			52					O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	37	c.155C>T	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.606423	0.46527	.	.	ENSG00000078043	ENST00000398654;ENST00000262161;ENST00000398651;ENST00000324794	T	0.34275	1.37	6.06	5.19	0.71726	DNA-binding SAP (1);	0.110818	0.64402	N	0.000012	T	0.29976	0.0750	L	0.38838	1.175	0.80722	D	1	B;B;B;B	0.25169	0.119;0.008;0.029;0.007	B;B;B;B	0.23018	0.043;0.008;0.029;0.013	T	0.04565	-1.0942	10	0.25106	T	0.35	-4.3726	15.1526	0.72713	0.0671:0.0:0.9329:0.0	.	56;52;52;52	O75928-3;Q2TA77;O75928-2;O75928	.;.;.;PIAS2_HUMAN	V	52;52;48;52	ENSP00000317163:A52V	ENSP00000262161:A52V	A	-	2	0	PIAS2	42724885	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	6.550000	0.73905	1.578000	0.49821	0.650000	0.86243	GCG		0.448	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		3	53	0	0	0	1	0	3	53				
SERPINB4	6318	broad.mit.edu	37	18	61309020	61309020	+	Missense_Mutation	SNP	C	C	T	rs267605228		TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr18:61309020C>T	ENST00000341074.5	-	4	440	c.325G>A	c.(325-327)Gga>Aga	p.G109R	SERPINB4_ENST00000356424.6_Missense_Mutation_p.G109R	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	109					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G109*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GTCTTTTCTCCGAAGAGCTTG	0.413													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20596	0.0		0.0	False		,,,				2504	0.0					uc002ljf.3																			1	Substitution - Nonsense(1)	p.G109*(1)|p.G109V(1)	lung(1)	breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						c.(325-327)Gga>Aga		Homo sapiens serpin peptidase inhibitor, clade B (ovalbumin), member 4 (SERPINB4), mRNA.							237.0	219.0	225.0					18																	61309020		2203	4300	6503	SO:0001583	missense	6317				regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity	g.chr18:61309020C>T	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"""Serine (or cysteine) peptidase inhibitors"""	10570	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.325G>A	18.37:g.61309020C>T	ENSP00000343445:p.Gly109Arg		Somatic				SERPINB3_uc002lje.3_Missense_Mutation_p.G109R|SERPINB3_uc002ljg.3_Intron	p.G109R	NM_002974	NP_002965	WXS	Illumina GAIIx	Phase_I	P29508	SPB3_HUMAN			3	411	-			109					A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	c.325G>A	CCDS11986.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220669	0.58560	.	.	ENSG00000206073	ENST00000341074;ENST00000356424	D;D	0.84873	-1.91;-1.91	3.76	1.93	0.25924	Serpin domain (3);	1.026050	0.07803	N	0.956916	D	0.91925	0.7443	M	0.92169	3.28	0.30751	N	0.745066	D;D	0.61080	0.975;0.989	P;P	0.55508	0.541;0.777	D	0.83714	0.0189	10	0.72032	D	0.01	.	8.7289	0.34487	0.0:0.8059:0.0:0.1941	.	109;109	P48594;Q9BYF7	SPB4_HUMAN;.	R	109	ENSP00000343445:G109R;ENSP00000348795:G109R	ENSP00000343445:G109R	G	-	1	0	SERPINB4	59460000	0.000000	0.05858	0.015000	0.15790	0.001000	0.01503	0.399000	0.20916	0.373000	0.24621	0.603000	0.83216	GGA		0.413	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		74	116	0	0	0	1	0	74	116				
LYZL2	119180	broad.mit.edu	37	10	30915131	30915131	+	Silent	SNP	G	G	A	rs374503421		TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr10:30915131G>A	ENST00000375318.2	-	3	395	c.339C>T	c.(337-339)gaC>gaT	p.D113D		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	67					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				CGATGCTGCCGTCATCCAGGA	0.587																																						uc001ivk.3																			0				NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19						c.(337-339)gaC>gaT		Homo sapiens lysozyme-like 2 (LYZL2), mRNA.		G		0,4406		0,0,2203	157.0	118.0	131.0		339	-4.5	0.0	10		131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LYZL2	NM_183058.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		113/195	30915131	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	119180				cell wall macromolecule catabolic process	extracellular region	lysozyme activity	g.chr10:30915131G>A	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.339C>T	10.37:g.30915131G>A			Somatic					p.D113D	NM_183058	NP_898881	WXS	Illumina GAIIx	Phase_I	Q7Z4W2	LYZL2_HUMAN			2	352	-		Prostate(175;0.151)	67					Q6NZ69	Silent	SNP	ENST00000375318.2	37	c.339C>T	CCDS7167.2																																																																																				0.587	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058		24	53	0	0	0	1	0	24	53				
POLQ	10721	broad.mit.edu	37	3	121179063	121179063	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr3:121179063G>A	ENST00000264233.5	-	25	7114	c.6986C>T	c.(6985-6987)gCt>gTt	p.A2329V		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2329					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)		AGAGTAGTCAGCAGCCAGTAT	0.393								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)	uc003eee.4																			0				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						c.(6985-6987)gCt>gTt	DNA polymerases (catalytic subunits)	Homo sapiens polymerase (DNA directed), theta (POLQ), mRNA.							75.0	71.0	72.0					3																	121179063		2203	4300	6503	SO:0001583	missense	10721				DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA-directed DNA polymerase activity|damaged DNA binding|single-stranded DNA-dependent ATPase activity	g.chr3:121179063G>A	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.6986C>T	3.37:g.121179063G>A	ENSP00000264233:p.Ala2329Val		Somatic				POLQ_uc003eed.3_Missense_Mutation_p.A1501V	p.A2329V	NM_199420	NP_955452	WXS	Illumina GAIIx	Phase_I	O75417	DPOLQ_HUMAN		GBM - Glioblastoma multiforme(114;0.0915)	24	7115	-			2329					O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	c.6986C>T	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532622	0.85812	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.97209	-4.29	5.6	5.6	0.85130	DNA-directed DNA polymerase, family A, palm domain (2);	0.111909	0.64402	D	0.000011	D	0.97980	0.9335	M	0.63843	1.955	0.42902	D	0.994235	D;D	0.71674	0.996;0.998	P;D	0.68039	0.873;0.955	D	0.98083	1.0405	10	0.45353	T	0.12	.	19.6126	0.95616	0.0:0.0:1.0:0.0	.	2329;1501	O75417;O75417-2	DPOLQ_HUMAN;.	V	1952;2329;2465	ENSP00000264233:A2329V	ENSP00000264233:A2329V	A	-	2	0	POLQ	122661753	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.217000	0.77982	2.630000	0.89119	0.591000	0.81541	GCT		0.393	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		3	67	0	0	0	1	0	3	67				
BCL2L12	83596	broad.mit.edu	37	19	50170383	50170383	+	Missense_Mutation	SNP	C	C	G			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr19:50170383C>G	ENST00000246785.3	+	3	725	c.467C>G	c.(466-468)tCt>tGt	p.S156C	IRF3_ENST00000309877.7_5'Flank|IRF3_ENST00000596765.1_5'Flank|BCL2L12_ENST00000246784.3_Intron|IRF3_ENST00000593922.1_5'Flank|IRF3_ENST00000599223.1_5'Flank|IRF3_ENST00000601291.1_5'Flank|BCL2L12_ENST00000441864.2_Missense_Mutation_p.S155C|IRF3_ENST00000599144.1_5'Flank|IRF3_ENST00000596822.1_5'Flank|IRF3_ENST00000377135.4_5'Flank|IRF3_ENST00000600911.1_5'Flank|IRF3_ENST00000377139.3_5'Flank|IRF3_ENST00000597198.1_5'Flank|IRF3_ENST00000598808.1_5'Flank|IRF3_ENST00000442265.2_5'Flank|IRF3_ENST00000600022.1_5'Flank	NM_001040668.1|NM_138639.1	NP_001035758.1|NP_619580.1	Q9HB09	B2L12_HUMAN	BCL2-like 12 (proline rich)	156					inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	8		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)		CGGCCTTGCTCTCTGCCCATC	0.567																																						uc002ppa.3																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	8						c.(466-468)tCt>tGt		Homo sapiens BCL2-like 12 (proline rich) (BCL2L12), transcript variant 1, mRNA.							111.0	123.0	119.0					19																	50170383		2203	4300	6503	SO:0001583	missense	83596				apoptosis			g.chr19:50170383C>G	AF289220	CCDS12776.1, CCDS46144.1, CCDS74424.1, CCDS74423.1	19q13.3	2014-03-07				ENSG00000126453			13787	protein-coding gene	gene with protein product		610837					Standard	NM_001040668		Approved		uc002ppa.3	Q9HB09		ENST00000246785.3:c.467C>G	19.37:g.50170383C>G	ENSP00000246785:p.Ser156Cys		Somatic				IRF3_uc002poy.2_5'Flank|IRF3_uc021uxp.1_5'Flank|IRF3_uc021uxq.1_5'Flank|IRF3_uc002pot.2_5'Flank|IRF3_uc021uxr.1_5'Flank|IRF3_uc021uxs.1_5'Flank|IRF3_uc002pow.3_5'Flank|IRF3_uc021uxo.1_5'Flank|IRF3_uc002pou.3_5'Flank|IRF3_uc010end.2_5'Flank|IRF3_uc002poz.1_5'Flank|IRF3_uc010ene.1_5'Flank|BCL2L12_uc002ppb.3_Missense_Mutation_p.S155C	p.S156C	NM_138639	NP_619580	WXS	Illumina GAIIx	Phase_I	Q9HB09	B2L12_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)	2	1149	+		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)	156					Q3SY11|Q3SY13|Q96I96|Q9HB08	Missense_Mutation	SNP	ENST00000246785.3	37	c.467C>G	CCDS12776.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347528	0.61183	.	.	ENSG00000126453	ENST00000246785;ENST00000441864	T;T	0.50813	0.73;0.73	3.53	2.49	0.30216	.	0.436858	0.17115	N	0.186458	T	0.38825	0.1055	N	0.19112	0.55	0.80722	D	1	D;D	0.61697	0.99;0.99	P;P	0.53450	0.726;0.726	T	0.11842	-1.0571	10	0.35671	T	0.21	-11.9185	6.1719	0.20422	0.0:0.8573:0.0:0.1427	.	155;156	Q3SY13;Q9HB09	.;B2L12_HUMAN	C	156;155	ENSP00000246785:S156C;ENSP00000393803:S155C	ENSP00000246785:S156C	S	+	2	0	BCL2L12	54862195	0.985000	0.35326	0.991000	0.47740	0.942000	0.58702	0.842000	0.27627	1.041000	0.40125	0.561000	0.74099	TCT		0.567	BCL2L12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465770.1	NM_052842		20	343	0	0	0	1	0	20	343				
TBC1D14	57533	broad.mit.edu	37	4	7032081	7032081	+	Missense_Mutation	SNP	C	C	T			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr4:7032081C>T	ENST00000409757.4	+	14	2168	c.2044C>T	c.(2044-2046)Cgg>Tgg	p.R682W	TBC1D14_ENST00000451522.2_Missense_Mutation_p.R402W|TBC1D14_ENST00000446947.2_Missense_Mutation_p.R329W|RP11-367J11.2_ENST00000500031.1_RNA|TBC1D14_ENST00000410031.1_Missense_Mutation_p.R454W|TBC1D14_ENST00000448507.1_Missense_Mutation_p.R682W	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	682					negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						GAAAGACAGCCGGGAAATGGA	0.577																																						uc011bwg.2																			0				breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						c.(2044-2046)Cgg>Tgg		Homo sapiens TBC1 domain family, member 14 (TBC1D14), transcript variant 2, mRNA.							95.0	85.0	88.0					4																	7032081		2203	4300	6503	SO:0001583	missense	57533					intracellular	Rab GTPase activator activity	g.chr4:7032081C>T	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.2044C>T	4.37:g.7032081C>T	ENSP00000386921:p.Arg682Trp		Somatic				TBC1D14_uc003gjs.4_Missense_Mutation_p.R682W|TBC1D14_uc010idh.3_Missense_Mutation_p.R402W|TBC1D14_uc011bwh.2_Missense_Mutation_p.R329W|TBC1D14_uc003gju.4_Missense_Mutation_p.R173W	p.R682W	NM_001113361	NP_065824	WXS	Illumina GAIIx	Phase_I	Q9P2M4	TBC14_HUMAN			13	2123	+			682					B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	c.2044C>T	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	C	17.95	3.512988	0.64522	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000446947	T;T;T;T;T	0.08896	3.45;3.45;3.43;3.45;3.04	5.01	2.31	0.28768	.	0.220514	0.31312	N	0.007861	T	0.18383	0.0441	L	0.51422	1.61	0.45791	D	0.998671	D;D;D	0.89917	0.999;0.998;1.0	D;D;D	0.74023	0.963;0.928;0.982	T	0.00379	-1.1777	10	0.49607	T	0.09	-17.0223	8.1902	0.31363	0.2797:0.6461:0.0:0.0742	.	329;402;682	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	W	682;682;454;402;329	ENSP00000404041:R682W;ENSP00000386921:R682W;ENSP00000386343:R454W;ENSP00000388886:R402W;ENSP00000405875:R329W	ENSP00000386921:R682W	R	+	1	2	TBC1D14	7082982	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	1.502000	0.35704	0.286000	0.22352	-0.324000	0.08512	CGG		0.577	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		29	58	0	0	0	1	0	29	58				
TRAF1	7185	broad.mit.edu	37	9	123673658	123673658	+	Missense_Mutation	SNP	C	C	A			TCGA-FY-A3WA-01A-11D-A22D-08	TCGA-FY-A3WA-10A-01D-A22D-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d6c94a2f-7b2f-4067-9d0b-7606c893f9e9	2184c4d7-dcda-4c5d-ae4e-ee823a887d79	g.chr9:123673658C>A	ENST00000373887.3	-	6	3284	c.839G>T	c.(838-840)tGc>tTc	p.C280F	TRAF1_ENST00000540010.1_Missense_Mutation_p.C280F|TRAF1_ENST00000546084.1_Missense_Mutation_p.C158F	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	280	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						CGACTCATGGCACCGCCTGGT	0.637																																						uc004bku.2																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						c.(838-840)tGc>tTc		Homo sapiens TNF receptor-associated factor 1 (TRAF1), transcript variant 1, mRNA.							49.0	42.0	45.0					9																	123673658		2203	4300	6503	SO:0001583	missense	7185				apoptosis|positive regulation of NF-kappaB transcription factor activity|protein complex assembly|regulation of apoptosis|signal transduction	cytoplasm	protein binding|zinc ion binding	g.chr9:123673658C>A	AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.839G>T	9.37:g.123673658C>A	ENSP00000362994:p.Cys280Phe		Somatic				TRAF1_uc011lyg.2_Missense_Mutation_p.C158F|TRAF1_uc010mvl.2_Missense_Mutation_p.C280F	p.C280F	NM_005658	NP_001177876	WXS	Illumina GAIIx	Phase_I	Q13077	TRAF1_HUMAN			5	1411	-			280			MATH.		B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	37	c.839G>T	CCDS6825.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882024	0.51908	.	.	ENSG00000056558	ENST00000373887;ENST00000540010;ENST00000546084	T;T;T	0.41758	0.99;0.99;0.99	4.64	4.64	0.57946	TRAF-type (1);TRAF-like (1);MATH (3);	0.297563	0.33753	N	0.004593	T	0.22820	0.0551	N	0.12182	0.205	0.36665	D	0.878193	B	0.17852	0.024	B	0.11329	0.006	T	0.14952	-1.0454	10	0.09590	T	0.72	-21.8104	12.6316	0.56661	0.1769:0.8231:0.0:0.0	.	280	Q13077	TRAF1_HUMAN	F	280;280;158	ENSP00000362994:C280F;ENSP00000443183:C280F;ENSP00000438583:C158F	ENSP00000362994:C280F	C	-	2	0	TRAF1	122713479	0.903000	0.30736	1.000000	0.80357	0.990000	0.78478	2.013000	0.40942	2.286000	0.76751	0.563000	0.77884	TGC		0.637	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658		3	37	0	0	0	1	0	3	37				
