#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_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	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
NPAS2	4862	broad.mit.edu	37	2	101598737	101598737	+	Silent	SNP	A	A	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr2:101598737A>G	ENST00000335681.5	+	16	1812	c.1527A>G	c.(1525-1527)ctA>ctG	p.L509L	NPAS2_ENST00000542504.1_Silent_p.L574L	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	509					cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGACCAGCTAGAGCAGCGGA	0.527																																						ENST00000335681.5																			0				cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(1525-1527)ctA>ctG		neuronal PAS domain protein 2							83.0	76.0	78.0					2																	101598737		2203	4300	6503	SO:0001819	synonymous_variant	4862				central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr2:101598737A>G	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1527A>G	2.37:g.101598737A>G						NPAS2_ENST00000542504.1_Silent_p.L574L	p.L509L	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN			16	1812	+			509					Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	c.1527A>G	CCDS2048.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.476941	0.26511	.	.	ENSG00000170485	ENST00000433408	.	.	.	5.56	2.65	0.31530	.	.	.	.	.	T	0.45617	0.1351	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32428	-0.9907	4	.	.	.	.	2.6869	0.05110	0.27:0.1127:0.5018:0.1154	.	.	.	.	G	8	.	.	R	+	1	2	NPAS2	100965169	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.938000	0.28965	0.703000	0.31848	-0.177000	0.13119	AGA		0.527	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			4	55	0	0	0	0.014758	0	4	55				
EXPH5	23086	broad.mit.edu	37	11	108384325	108384325	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr11:108384325C>T	ENST00000265843.4	-	6	2019	c.1909G>A	c.(1909-1911)Gac>Aac	p.D637N	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.D561N|EXPH5_ENST00000525344.1_Missense_Mutation_p.D630N|EXPH5_ENST00000443411.1_Missense_Mutation_p.D449N	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	637					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTCCTTCTGTCATCAGAAATC	0.408																																						ENST00000265843.4																			0				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91						c.(1909-1911)Gac>Aac		exophilin 5							98.0	101.0	100.0					11																	108384325		2201	4298	6499	SO:0001583	missense	23086				intracellular protein transport		Rab GTPase binding	g.chr11:108384325C>T		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1909G>A	11.37:g.108384325C>T	ENSP00000265843:p.Asp637Asn					EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.D561N|EXPH5_ENST00000443411.1_Missense_Mutation_p.D449N|EXPH5_ENST00000525344.1_Missense_Mutation_p.D630N	p.D637N	NM_015065.2	NP_055880.2	Q149M6	Q149M6_HUMAN		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)	6	2019	-		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)	637					Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	c.1909G>A	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461079	0.43736	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04970	4.22;4.15;4.0;4.22;4.06;3.52	6.03	2.63	0.31362	.	0.874697	0.10070	N	0.719837	T	0.15176	0.0366	M	0.67953	2.075	0.09310	N	1	D	0.63880	0.993	P	0.54140	0.743	T	0.13019	-1.0525	10	0.54805	T	0.06	-0.3658	8.3452	0.32268	0.0:0.7118:0.0:0.2882	.	637	Q8NEV8	EXPH5_HUMAN	N	637;561;449;630;481;561;449	ENSP00000265843:D637N;ENSP00000391966:D561N;ENSP00000411390:D449N;ENSP00000432546:D630N;ENSP00000432683:D561N;ENSP00000446434:D449N	ENSP00000265843:D637N	D	-	1	0	EXPH5	107889535	0.024000	0.19004	0.215000	0.23724	0.022000	0.10575	0.549000	0.23329	0.832000	0.34804	0.557000	0.71058	GAC		0.408	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		10	91	0	0	0	0.069234	0	10	91				
RP11-156P1.3	0	broad.mit.edu	37	17	45128742	45128742	+	RNA	SNP	T	T	G	rs34655963	byFrequency	TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr17:45128742T>G	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							TAATGATTTTTATTATACTTT	0.328													g|||	2160	0.43131	0.3593	0.4986	5008	,	,		16551	0.3482		0.4861	False		,,,				2504	0.5102					ENST00000575173.1																			0																																																			0							g.chr17:45128742T>G																													17.37:g.45128742T>G														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.328	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			3	52	0	0	0	0.115264	0	3	52				
CDH12	1010	broad.mit.edu	37	5	22078769	22078769	+	Missense_Mutation	SNP	C	C	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr5:22078769C>G	ENST00000382254.1	-	5	1103	c.17G>C	c.(16-18)tGt>tCt	p.C6S	CDH12_ENST00000504376.2_Missense_Mutation_p.C6S|CDH12_ENST00000522262.1_Missense_Mutation_p.C6S	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	6					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						CAGGGATAAACAGTTCCTTGT	0.448										HNSCC(59;0.17)																												ENST00000382254.1																			0				NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						c.(16-18)tGt>tCt		cadherin 12, type 2 (N-cadherin 2)							125.0	130.0	128.0					5																	22078769		2203	4300	6503	SO:0001583	missense	1010				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:22078769C>G	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.17G>C	5.37:g.22078769C>G	ENSP00000371689:p.Cys6Ser	HNSCC(59;0.17)				CDH12_ENST00000504376.2_Missense_Mutation_p.C6S|CDH12_ENST00000522262.1_Missense_Mutation_p.C6S	p.C6S	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN			5	1103	-			6					B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	c.17G>C	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595277	0.46318	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.56611	0.58;0.58;0.45	5.53	3.72	0.42706	.	0.488476	0.25135	N	0.032866	T	0.31827	0.0809	N	0.08118	0	0.36079	D	0.842668	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21381	-1.0247	10	0.51188	T	0.08	.	10.9808	0.47492	0.1339:0.5929:0.2733:0.0	.	6;6	B7Z2U6;P55289	.;CAD12_HUMAN	S	6	ENSP00000423577:C6S;ENSP00000371689:C6S;ENSP00000428786:C6S	ENSP00000371689:C6S	C	-	2	0	CDH12	22114526	1.000000	0.71417	0.979000	0.43373	0.993000	0.82548	3.648000	0.54410	0.689000	0.31550	-0.233000	0.12211	TGT		0.448	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		29	55	0	0	0	0.108266	0	29	55				
LPL	4023	broad.mit.edu	37	8	19811648	19811648	+	Missense_Mutation	SNP	C	C	T	rs200669137		TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr8:19811648C>T	ENST00000311322.8	+	5	1029	c.559C>T	c.(559-561)Cct>Tct	p.P187S		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	187					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	TCCAGCTGGACCTAACTTTGA	0.453																																						ENST00000311322.8																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36						c.(559-561)Cct>Tct		lipoprotein lipase	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)						111.0	105.0	107.0					8																	19811648		2203	4300	6503	SO:0001583	missense	4023				fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity	g.chr8:19811648C>T		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.559C>T	8.37:g.19811648C>T	ENSP00000309757:p.Pro187Ser						p.P187S	NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN		Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	5	1029	+			187					B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	37	c.559C>T	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.704181	0.88924	.	.	ENSG00000175445	ENST00000520959;ENST00000311322;ENST00000538071;ENST00000535763	D;D	0.92149	-2.98;-2.98	6.17	6.17	0.99709	Lipase, N-terminal (1);	0.089217	0.85682	D	0.000000	D	0.97275	0.9109	M	0.94021	3.485	0.40553	D	0.981137	D	0.89917	1.0	D	0.97110	1.0	D	0.97596	1.0120	8	.	.	.	-22.4702	18.3732	0.90420	0.0:1.0:0.0:0.0	.	187	P06858	LIPL_HUMAN	S	111;187;111;173	ENSP00000428496:P111S;ENSP00000309757:P187S	.	P	+	1	0	LPL	19855928	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	5.699000	0.68310	2.941000	0.99782	0.655000	0.94253	CCT		0.453	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			27	50	0	0	0	0.099896	0	27	50				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		14	40	0	0	0	0.146539	0	14	40				
MAST2	23139	broad.mit.edu	37	1	46501483	46501483	+	Silent	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:46501483C>T	ENST00000361297.2	+	29	5425	c.5142C>T	c.(5140-5142)gcC>gcT	p.A1714A	MAST2_ENST00000372009.2_Silent_p.A1524A	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCAGACTGGCCCATCCATCTT	0.577																																						ENST00000361297.2																			0				breast(1)|lung(3)|ovary(5)|stomach(2)	11						c.(5140-5142)gcC>gcT		microtubule associated serine/threonine kinase 2							57.0	65.0	63.0					1																	46501483		1966	4150	6116	SO:0001819	synonymous_variant	23139				regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity	g.chr1:46501483C>T	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.5142C>T	1.37:g.46501483C>T						MAST2_ENST00000372008.1_Intron|MAST2_ENST00000372009.2_Silent_p.A1524A	p.A1714A	NM_015112.2	NP_055927.2	Q6P0Q8	MAST2_HUMAN			29	5425	+	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)		1714						Silent	SNP	ENST00000361297.2	37	c.5142C>T	CCDS41326.1																																																																																				0.577	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		4	85	0	0	0	0.150653	0	4	85				
CEACAM5	1048	broad.mit.edu	37	19	42213808	42213808	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr19:42213808G>C	ENST00000221992.6	+	2	388	c.274G>C	c.(274-276)Ggg>Cgg	p.G92R	CEACAM5_ENST00000405816.1_Missense_Mutation_p.G92R|CEACAM5_ENST00000398599.4_Missense_Mutation_p.G92R|CEA_ENST00000598976.1_Missense_Mutation_p.G92R|CEACAM7_ENST00000599715.1_5'Flank	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	92	Ig-like 1.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		AGCTACCCCAGGGCCCGCATA	0.473																																						ENST00000221992.6																			0				breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34						c.(274-276)Ggg>Cgg		carcinoembryonic antigen-related cell adhesion molecule 5							193.0	199.0	197.0					19																	42213808		2203	4300	6503	SO:0001583	missense	1048					anchored to membrane|basolateral plasma membrane|integral to plasma membrane		g.chr19:42213808G>C	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.274G>C	19.37:g.42213808G>C	ENSP00000221992:p.Gly92Arg					CEACAM5_ENST00000398599.4_Missense_Mutation_p.G92R|CEACAM5_ENST00000405816.1_Missense_Mutation_p.G92R|CEA_ENST00000598976.1_Missense_Mutation_p.G92R	p.G92R	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN		OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)	2	388	+			92			Ig-like 1.		H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	c.274G>C	CCDS12584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	12.63|12.63	1.994462|1.994462	0.35226|0.35226	.|.	.|.	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181|ENST00000398599	T;T|.	0.67698|.	-0.28;-0.28|.	2.56|2.56	1.49|1.49	0.22878|0.22878	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.73063|0.73063	0.3539|0.3539	H|H	0.95917|0.95917	3.74|3.74	0.09310|0.09310	N|N	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.63409|0.63409	-0.6644|-0.6644	9|5	0.87932|.	D|.	0|.	.|.	6.5806|6.5806	0.22591|0.22591	0.0:0.0:0.7141:0.2859|0.0:0.0:0.7141:0.2859	.|.	92;92;92|.	Q8N4D0;P06731;Q53G30|.	.;CEAM5_HUMAN;.|.	R|T	92|88	ENSP00000221992:G92R;ENSP00000385072:G92R|.	ENSP00000221992:G92R|.	G|R	+|+	1|2	0|0	CEACAM5|CEACAM5	46905648|46905648	0.089000|0.089000	0.21612|0.21612	0.005000|0.005000	0.12908|0.12908	0.011000|0.011000	0.07611|0.07611	1.563000|1.563000	0.36364|0.36364	0.628000|0.628000	0.30357|0.30357	0.305000|0.305000	0.20034|0.20034	GGG|AGG		0.473	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		6	223	0	0	0	0.021553	0	6	223				
RGS21	431704	broad.mit.edu	37	1	192321267	192321267	+	Missense_Mutation	SNP	C	C	T	rs369430749		TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:192321267C>T	ENST00000417209.2	+	4	353	c.179C>T	c.(178-180)aCg>aTg	p.T60M		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	60	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						TTTAAGAAAACGAAAAATGCA	0.348													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0					ENST00000417209.2																			0				NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						c.(178-180)aCg>aTg		regulator of G-protein signaling 21		C	MET/THR	0,3690		0,0,1845	67.0	64.0	65.0		179	5.8	1.0	1		65	1,8223		0,1,4111	no	missense	RGS21	NM_001039152.3	81	0,1,5956	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	60/153	192321267	1,11913	1845	4112	5957	SO:0001583	missense	431704				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity	g.chr1:192321267C>T	AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"""Regulators of G-protein signaling"""	26839	protein-coding gene	gene with protein product		612407	"""regulator of G-protein signalling 21"""			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.179C>T	1.37:g.192321267C>T	ENSP00000428343:p.Thr60Met						p.T60M	NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN			4	353	+			60			RGS.			Missense_Mutation	SNP	ENST00000417209.2	37	c.179C>T	CCDS41448.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.288527	0.59976	0.0	1.22E-4	ENSG00000253148	ENST00000417209	T	0.29655	1.56	5.77	5.77	0.91146	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.000000	0.34828	U	0.003657	T	0.49064	0.1535	L	0.46885	1.475	0.34163	D	0.668843	D	0.69078	0.997	D	0.63793	0.918	T	0.57734	-0.7760	10	0.62326	D	0.03	.	18.5418	0.91031	0.0:1.0:0.0:0.0	.	60	Q2M5E4	RGS21_HUMAN	M	60	ENSP00000428343:T60M	ENSP00000428343:T60M	T	+	2	0	RGS21	190587890	1.000000	0.71417	0.994000	0.49952	0.670000	0.39368	2.937000	0.48979	2.733000	0.93635	0.557000	0.71058	ACG		0.348	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2			3	16	0	0	0	0.115264	0	3	16				
SLC25A3	5250	broad.mit.edu	37	12	98991696	98991696	+	Silent	SNP	T	T	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr12:98991696T>G	ENST00000228318.3	+	4	465	c.345T>G	c.(343-345)ggT>ggG	p.G115G	SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Silent_p.G114G|SLC25A3_ENST00000549338.1_Silent_p.G114G|SLC25A3_ENST00000551917.1_Silent_p.G115G|SLC25A3_ENST00000547534.1_Silent_p.G114G|SLC25A3_ENST00000401722.3_Silent_p.G114G|SLC25A3_ENST00000548847.1_Silent_p.G114G|SLC25A3_ENST00000552981.1_Silent_p.G114G	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	115					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		AAGAGGATGGTGTTCGTGGTT	0.393																																						ENST00000188376.5																			0				breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16						c.(340-342)ggT>ggG		solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3							162.0	148.0	153.0					12																	98991696		2203	4300	6503	SO:0001819	synonymous_variant	5250				generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity	g.chr12:98991696T>G		CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"""Solute carriers"""	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.345T>G	12.37:g.98991696T>G						SLC25A3_ENST00000549338.1_Silent_p.G114G|SLC25A3_ENST00000548847.1_Silent_p.G114G|SLC25A3_ENST00000228318.3_Silent_p.G115G|SLC25A3_ENST00000401722.3_Silent_p.G114G|SLC25A3_ENST00000547534.1_Silent_p.G114G|SLC25A3_ENST00000552981.1_Silent_p.G114G|SLC25A3_ENST00000551917.1_Silent_p.G115G	p.G114G	NM_002635.3|NM_213611.2	NP_002626.1|NP_998776.1	Q00325	MPCP_HUMAN		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)	3	696	+		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)	115					B3KS34|Q7Z7N7|Q96A03	Silent	SNP	ENST00000228318.3	37	c.342T>G	CCDS9066.1																																																																																				0.393	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		27	51	0	0	0	0.134883	0	27	51				
MT-CO1	4512	broad.mit.edu	37	M	3248	3248	+	5'Flank	SNP	G	G	A			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chrM:3248G>A	ENST00000361624.2	+	0	0				MT-TW_ENST00000387382.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						tggcagagcccggtaatcgca	0.438																																						ENST00000386347.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chrM:3248G>A			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395			M.37:g.3248G>A	Exception_encountered													0	19	+								Q34770	RNA	SNP	ENST00000361624.2	37																																																																																						0.438	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028		7	46	0	0	0	0.038147	0	7	46				
LIFR	3977	broad.mit.edu	37	5	38511959	38511959	+	Silent	SNP	G	G	A			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr5:38511959G>A	ENST00000263409.4	-	6	831	c.669C>T	c.(667-669)taC>taT	p.Y223Y	LIFR_ENST00000453190.2_Silent_p.Y223Y|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	223					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GATTGTCAATGTAGCATCTAA	0.393			T	PLAG1	salivary adenoma																																Melanoma(13;4 730 6426 9861 34751)	ENST00000263409.4				Dom	yes		5	5p13-p12	3977	T	leukemia inhibitory factor receptor			E	PLAG1		salivary adenoma		0				NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78						c.(667-669)taC>taT		leukemia inhibitory factor receptor alpha							93.0	79.0	84.0					5																	38511959		2203	4300	6503	SO:0001819	synonymous_variant	3977				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity	g.chr5:38511959G>A	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.669C>T	5.37:g.38511959G>A						LIFR_ENST00000503088.1_5'UTR|LIFR_ENST00000453190.2_Silent_p.Y223Y	p.Y223Y	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN			6	831	-	all_lung(31;0.00021)		223					Q6LCD9	Silent	SNP	ENST00000263409.4	37	c.669C>T	CCDS3927.1																																																																																				0.393	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		12	29	0	0	0	0.080935	0	12	29				
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	RNA	INS	-	-	AGCT	rs141324796|rs79472512	byFrequency	TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:17034125_17034126insAGCT	ENST00000492551.1	-	0	477_478					NR_026567.1				espin pseudogene																		CAGCAGCAGCCAGCTGAGCACC	0.718														1500	0.299521	0.1188	0.3444	5008	,	,		24180	0.4177		0.3101	False		,,,				2504	0.3793					ENST00000492551.1																			0																																																			0							g.chr1:17034125_17034126insAGCT	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17034126_17034129dupAGCT								NR_026567.1						0	477_478	-									RNA	INS	ENST00000492551.1	37																																																																																						0.718	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			7	8						7	8	---	---	---	---
TMCO2	127391	broad.mit.edu	37	1	40713708	40713709	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:40713708_40713709delTC	ENST00000372766.3	+	1	136_137	c.43_44delTC	c.(43-45)tctfs	p.S15fs	TMCO2_ENST00000468258.1_Intron	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	transmembrane and coiled-coil domains 2	15						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			CCTCTTAGAGTCTCTCTCTCTC	0.406																																						ENST00000372766.3																			0				kidney(1)|large_intestine(3)|lung(1)|ovary(1)	6						c.(43-45)tfs		transmembrane and coiled-coil domains 2																																				SO:0001589	frameshift_variant	127391					integral to membrane		g.chr1:40713708_40713709delTC	AL050341	CCDS30684.1	1p34.2	2014-02-12			ENSG00000188800	ENSG00000188800			23312	protein-coding gene	gene with protein product							Standard	NM_001008740		Approved	dJ39G22.2	uc001cfe.2	Q7Z6W1	OTTHUMG00000005764	ENST00000372766.3:c.43_44delTC	1.37:g.40713718_40713719delTC	ENSP00000361852:p.Ser15fs					TMCO2_ENST00000468258.1_Intron	p.S15fs	NM_001008740.3	NP_001008740.1	Q7Z6W1	TMCO2_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)		1	136_137	+	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	15						Frame_Shift_Del	DEL	ENST00000372766.3	37	c.43_44delTC	CCDS30684.1																																																																																				0.406	TMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015769.1	NM_001008740		7	170						7	170	---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102738795	102738796	+	RNA	INS	-	-	T	rs200787919|rs68192524|rs5003690		TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr11:102738795_102738796insT	ENST00000532855.1	-	0	725_726							P39900	MMP12_HUMAN	matrix metallopeptidase 12 (macrophage elastase)						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|proteolysis (GO:0006508)|wound healing, spreading of epidermal cells (GO:0035313)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.N211fs*20(2)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	26		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)|Marimastat(DB00786)	AGGAACAAGTGGTGCCTAAGAA	0.416																																						ENST00000532855.1																			2	Insertion - Frameshift(2)	p.N211fs*20(2)	upper_aerodigestive_tract(1)|prostate(1)	autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	26								matrix metallopeptidase 12 (macrophage elastase)	Acetohydroxamic Acid(DB00551)			3692,6		1844,4,1						-0.2	0.9		dbSNP_113	54	7905,5		3951,3,1	no	frameshift	MMP12	NM_002426.4		5795,7,2	A1A1,A1R,RR		0.0632,0.1622,0.0948				11597,11						4321				positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding	g.chr11:102738795_102738796insT	L23808	CCDS73375.1	11q22.3	2009-02-26	2005-08-08			ENSG00000262406			7158	protein-coding gene	gene with protein product		601046	"""matrix metalloproteinase 12 (macrophage elastase)"""				Standard	NM_002426		Approved	HME	uc001phk.3	P39900			11.37:g.102738795_102738796insT										P39900	MMP12_HUMAN		BRCA - Breast invasive adenocarcinoma(274;0.014)	0	725_726	-		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)						B2R9X8|B7ZLF6|Q2M1L9	RNA	INS	ENST00000532855.1	37																																																																																						0.416	MMP12-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000386646.1	NM_002426		2	4						2	4	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	8962361	8962361	+	Frame_Shift_Del	DEL	C	C	-			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr19:8962361delC	ENST00000397910.4	-	82	43541	c.43338delG	c.(43336-43338)gggfs	p.G14446fs	MUC16_ENST00000380951.5_Frame_Shift_Del_p.G1087fs	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22091	SEA 16. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TACCAGAATTCCCAGTTAAGG	0.478																																						ENST00000397910.4																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(43336-43338)ggfs		mucin 16, cell surface associated							26.0	27.0	27.0					19																	8962361		1793	3965	5758	SO:0001589	frameshift_variant	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:8962361delC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.43338delG	19.37:g.8962361delC	ENSP00000381008:p.Gly14446fs					MUC16_ENST00000380951.5_Frame_Shift_Del_p.G1087fs	p.G14446fs	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN			82	43541	-			13920	Missing (in Ref. 3; AAK74120).		SEA 16.		Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	37	c.43338delG	CCDS54212.1																																																																																				0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		2	4						2	4	---	---	---	---
MIR3687-2	103504728	broad.mit.edu	37	21	9825838	9825839	+	RNA	INS	-	-	GCG	rs372061766|rs369177681|rs563875271	byFrequency	TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr21:9825838_9825839insGCG	ENST00000577708.1	+	0	0				MIR3648_ENST00000581792.1_RNA	NR_037458.1																						cggccgcgactgcggcggcggt	0.842																																						ENST00000581792.1																			0																																																			0							g.chr21:9825838_9825839insGCG																													21.37:g.9825845_9825847dupGCG								NR_037421.1						0	7_8	+									RNA	INS	ENST00000577708.1	37																																																																																						0.842	MIR3687-201	KNOWN	basic	miRNA	miRNA				7	15						7	15	---	---	---	---
