#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
KMT2B	9757	broad.mit.edu	37	19	36219029	36219029	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr19:36219029G>A	ENST00000222270.7	+	19	4528	c.4528G>A	c.(4528-4530)Gcc>Acc	p.A1510T	KMT2B_ENST00000420124.1_Missense_Mutation_p.A1510T|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1510					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTGGTTCGACGCCCACGACCC	0.627																																						uc021usv.1										"""N, F, Mis"""							"""medulloblastoma, renal"""		0				NS(1)|breast(4)|central_nervous_system(38)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(121)|kidney(35)|large_intestine(22)|lung(78)|ovary(3)|pancreas(2)|prostate(13)|skin(7)|stomach(3)|upper_aerodigestive_tract(9)|urinary_tract(5)	366						c.(4528-4530)Gcc>Acc		Homo sapiens myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), mRNA.							16.0	17.0	17.0					19																	36219029		2002	4171	6173	SO:0001583	missense	8085				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding	g.chr19:36219029G>A	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.4528G>A	19.37:g.36219029G>A	ENSP00000222270:p.Ala1510Thr	HNSCC(34;0.089)	Somatic				MLL2_uc021usu.1_Missense_Mutation_p.A324T	p.A1510T	NM_014727	NP_055542	WXS	Illumina GAIIx	Phase_I	O14686	MLL2_HUMAN			18	4528	+			0			Cys-rich.		O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	c.4528G>A	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219732	0.58560	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.83837	-1.77;-1.77	5.31	5.31	0.75309	.	0.000000	0.42053	D	0.000777	D	0.85978	0.5823	L	0.40543	1.245	0.41110	D	0.985733	D	0.76494	0.999	P	0.61533	0.89	D	0.86032	0.1514	10	0.49607	T	0.09	.	16.0062	0.80363	0.0:0.0:1.0:0.0	.	1510	Q9UMN6	MLL4_HUMAN	T	1510	ENSP00000222270:A1510T;ENSP00000398837:A1510T	ENSP00000222270:A1510T	A	+	1	0	AD000671.1	40910869	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.067000	0.50010	2.765000	0.95021	0.655000	0.94253	GCC		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		7	10	0	0	0	1	0	7	10				
CEP152	22995	broad.mit.edu	37	15	49052457	49052457	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr15:49052457T>C	ENST00000380950.2	-	19	2756	c.2569A>G	c.(2569-2571)Ata>Gta	p.I857V	CEP152_ENST00000399334.3_Missense_Mutation_p.I857V|CEP152_ENST00000325747.5_Missense_Mutation_p.I764V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	857					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TGCACAGCTATTTCTACCTGT	0.378																																						uc001zwz.3																			0				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63						c.(2569-2571)Ata>Gta		Homo sapiens centrosomal protein 152kDa (CEP152), transcript variant 1, mRNA.							116.0	107.0	110.0					15																	49052457		1854	4107	5961	SO:0001583	missense	22995				G2/M transition of mitotic cell cycle|centrosome duplication	centrosome|cytosol	protein kinase binding	g.chr15:49052457T>C	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2569A>G	15.37:g.49052457T>C	ENSP00000370337:p.Ile857Val		Somatic				CEP152_uc001zwy.3_Missense_Mutation_p.I857V|CEP152_uc001zxa.2_Missense_Mutation_p.I764V	p.I857V	NM_001194998	NP_001181927	WXS	Illumina GAIIx	Phase_I	O94986	CE152_HUMAN		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)	18	2762	-		all_lung(180;0.0428)	857					E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	c.2569A>G	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	T	6.395	0.441075	0.12164	.	.	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.50813	0.74;0.73;0.74	4.66	-0.456	0.12190	.	0.796636	0.11934	N	0.515418	T	0.25457	0.0619	N	0.11427	0.14	0.21220	N	0.999756	B;B;B	0.15141	0.002;0.001;0.012	B;B;B	0.08055	0.003;0.001;0.002	T	0.18650	-1.0330	10	0.27785	T	0.31	-2.0E-4	9.9434	0.41593	0.0:0.5788:0.0:0.4212	.	764;857;857	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	V	857;764;857	ENSP00000370337:I857V;ENSP00000321000:I764V;ENSP00000382271:I857V	ENSP00000321000:I764V	I	-	1	0	CEP152	46839749	0.347000	0.24853	0.990000	0.47175	0.565000	0.35776	0.061000	0.14366	0.009000	0.14813	-0.408000	0.06270	ATA		0.378	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		35	60	0	0	0	1	0	35	60				
THEMIS	387357	broad.mit.edu	37	6	128135044	128135044	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr6:128135044G>T	ENST00000368248.2	-	4	890	c.742C>A	c.(742-744)Cta>Ata	p.L248I	THEMIS_ENST00000543064.1_Missense_Mutation_p.L248I|THEMIS_ENST00000368250.1_Missense_Mutation_p.L169I|THEMIS_ENST00000537166.1_Missense_Mutation_p.L213I	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	248	CABIT 1.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TCGACATCTAGACTGGGGAGG	0.343																																						uc011ebt.2																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						c.(742-744)Cta>Ata		Homo sapiens thymocyte selection associated (THEMIS), transcript variant 1, mRNA.							100.0	108.0	105.0					6																	128135044		2202	4300	6502	SO:0001583	missense	387357				T cell receptor signaling pathway|negative T cell selection|positive T cell selection	cytoplasm|nucleus		g.chr6:128135044G>T	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"""thymocyte expressed molecule involved in selection"""	613607	"""chromosome 6 open reading frame 207"", ""chromosome 6 open reading frame 190"", ""thymocyte selection pathway associated"""	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.742C>A	6.37:g.128135044G>T	ENSP00000357231:p.Leu248Ile		Somatic				THEMIS_uc010kfa.3_Missense_Mutation_p.L151I|THEMIS_uc021zfa.1_Missense_Mutation_p.L248I|THEMIS_uc010kfb.3_Missense_Mutation_p.L213I	p.L248I	NM_001164685	NP_001158157	WXS	Illumina GAIIx	Phase_I	Q8N1K5	THMS1_HUMAN			3	891	-			248			CABIT 1.		A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	37	c.742C>A	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.898330	0.52227	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166;ENST00000434358	T;T;T;T;T	0.63580	2.35;2.35;2.35;2.35;-0.05	5.59	0.512	0.16994	.	0.000000	0.64402	D	0.000003	T	0.68192	0.2974	M	0.80422	2.495	0.37282	D	0.907871	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.71192	-0.4665	10	0.72032	D	0.01	-12.7023	9.2931	0.37800	0.4537:0.0:0.5463:0.0	.	248;248	F5H1J9;Q8N1K5	.;THMS1_HUMAN	I	169;248;248;213;16	ENSP00000357233:L169I;ENSP00000439594:L248I;ENSP00000357231:L248I;ENSP00000439863:L213I;ENSP00000387740:L16I	ENSP00000357231:L248I	L	-	1	2	THEMIS	128176737	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	1.453000	0.35167	0.097000	0.17492	-0.391000	0.06502	CTA		0.343	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		42	48	0	0	0	1	0	42	48				
GSTM3	2947	broad.mit.edu	37	1	110280288	110280288	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr1:110280288G>A	ENST00000540225.1	-	7	768	c.458C>T	c.(457-459)gCc>gTc	p.A153V	GSTM3_ENST00000361066.2_Missense_Mutation_p.A153V|GSTM3_ENST00000256594.3_Missense_Mutation_p.A153V|GSTM3_ENST00000488824.1_5'UTR|RP4-735C1.4_ENST00000431955.1_RNA			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	153	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	CTTTTCCCCGGCAAACCATGA	0.433																																						uc001dyo.2																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9						c.(457-459)gCc>gTc		Homo sapiens glutathione S-transferase mu 3 (brain) (GSTM3), transcript variant 1, mRNA.	Glutathione(DB00143)						126.0	145.0	138.0					1																	110280288		2203	4300	6503	SO:0001583	missense	2947				establishment of blood-nerve barrier|glutathione metabolic process|response to estrogen stimulus	cytoplasm	glutathione transferase activity|identical protein binding	g.chr1:110280288G>A	BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4635	protein-coding gene	gene with protein product		138390	"""glutathione S-transferase M3 (brain)"""			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.458C>T	1.37:g.110280288G>A	ENSP00000444978:p.Ala153Val		Somatic				GSTM3_uc001dyp.2_Missense_Mutation_p.A150V|GSTM3_uc010ovv.2_Missense_Mutation_p.A153V	p.A153V	NM_000849	NP_000840	WXS	Illumina GAIIx	Phase_I	P21266	GSTM3_HUMAN		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	6	768	-		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)	153			GST C-terminal.		O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	37	c.458C>T	CCDS812.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153126	0.78001	.	.	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.01725	4.67;4.67;4.67	5.53	5.53	0.82687	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.01661	0.0053	L	0.39326	1.205	0.80722	D	1	B;P;B	0.42248	0.313;0.774;0.313	B;B;B	0.43194	0.09;0.411;0.09	T	0.67260	-0.5715	10	0.48119	T	0.1	2.0E-4	18.4034	0.90525	0.0:0.0:1.0:0.0	.	153;159;153	Q6FGJ9;Q59EJ5;P21266	.;.;GSTM3_HUMAN	V	153	ENSP00000444978:A153V;ENSP00000256594:A153V;ENSP00000354357:A153V	ENSP00000256594:A153V	A	-	2	0	GSTM3	110081811	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.936000	0.75892	2.871000	0.98454	0.655000	0.94253	GCC		0.433	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849		5	255	0	0	0	1	0	5	255				
REV3L	5980	broad.mit.edu	37	6	111652902	111652902	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr6:111652902G>A	ENST00000358835.3	-	25	8465	c.8011C>T	c.(8011-8013)Ccc>Tcc	p.P2671S	REV3L_ENST00000368805.1_Missense_Mutation_p.P2671S|REV3L_ENST00000368802.3_Missense_Mutation_p.P2671S|REV3L_ENST00000435970.1_Missense_Mutation_p.P2593S			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2671					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ACTCCATTGGGGGACACTGTG	0.373								DNA polymerases (catalytic subunits)																														uc003puy.4																			0				NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88						c.(8011-8013)Ccc>Tcc	DNA polymerases (catalytic subunits)	Homo sapiens REV3-like, catalytic subunit of DNA polymerase zeta (yeast) (REV3L), mRNA.							136.0	132.0	133.0					6																	111652902		2203	4300	6503	SO:0001583	missense	5980				DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding	g.chr6:111652902G>A	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8011C>T	6.37:g.111652902G>A	ENSP00000351697:p.Pro2671Ser		Somatic				REV3L_uc003pux.4_Missense_Mutation_p.P2593S|REV3L_uc003puz.4_Missense_Mutation_p.P2593S|REV3L_uc003pva.1_Non-coding_Transcript	p.P2671S	NM_002912	NP_002903	WXS	Illumina GAIIx	Phase_I	O60673	DPOLZ_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)	23	8352	-		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)	2671					O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	c.8011C>T	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	G	33	5.193682	0.94960	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.19105	2.17;2.17;2.17;2.17	5.93	5.93	0.95920	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.246544	0.41712	D	0.000837	T	0.46444	0.1393	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.46527	-0.9185	10	0.87932	D	0	-3.5269	20.3368	0.98748	0.0:0.0:1.0:0.0	.	2671	O60673	DPOLZ_HUMAN	S	2671;2671;2671;2593;744	ENSP00000357792:P2671S;ENSP00000357795:P2671S;ENSP00000351697:P2671S;ENSP00000402003:P2593S	ENSP00000351697:P2671S	P	-	1	0	REV3L	111759595	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.352000	0.97076	2.805000	0.96524	0.655000	0.94253	CCC		0.373	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		7	129	0	0	0	1	0	7	129				
LNX1	84708	broad.mit.edu	37	4	54440038	54440038	+	Missense_Mutation	SNP	G	G	C			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr4:54440038G>C	ENST00000263925.7	-	2	446	c.132C>G	c.(130-132)tgC>tgG	p.C44W	FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000504605.1_5'Flank	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	44					protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AAGCCTGCAGGCAGATGTGGC	0.567																																						uc003hag.4																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32						c.(130-132)tgC>tgG		Homo sapiens ligand of numb-protein X 1 (LNX1), transcript variant 1, mRNA.							43.0	40.0	40.0					4																	54440038		1568	3582	5150	SO:0001583	missense	84708					cytoplasm	zinc ion binding	g.chr4:54440038G>C	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.132C>G	4.37:g.54440038G>C	ENSP00000263925:p.Cys44Trp		Somatic				PDGFRA_uc003haa.3_Intron|LNX1_uc003hah.4_Non-coding_Transcript	p.C44W	NM_001126328	NP_001119800	WXS	Illumina GAIIx	Phase_I	Q8TBB1	LNX1_HUMAN	GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)		1	388	-	all_neural(26;0.153)		44					Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	c.132C>G	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.178195	0.57692	.	.	ENSG00000072201	ENST00000263925;ENST00000513421;ENST00000510143;ENST00000512247	D;D;D;D	0.99695	-6.43;-6.43;-6.43;-6.43	5.98	2.88	0.33553	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97490	1.0053	10	0.87932	D	0	.	12.0885	0.53710	0.2665:0.0:0.7335:0.0	.	44	Q8TBB1	LNX1_HUMAN	W	44	ENSP00000263925:C44W;ENSP00000426445:C44W;ENSP00000421897:C44W;ENSP00000424364:C44W	ENSP00000263925:C44W	C	-	3	2	LNX1	54134795	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	2.890000	0.48609	0.847000	0.35167	0.591000	0.81541	TGC		0.567	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			5	30	0	0	0	1	0	5	30				
KIAA1549	57670	broad.mit.edu	37	7	138597183	138597183	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr7:138597183C>T	ENST00000422774.1	-	3	2950	c.2902G>A	c.(2902-2904)Gag>Aag	p.E968K	KIAA1549_ENST00000242365.4_Missense_Mutation_p.E918K|KIAA1549_ENST00000440172.1_Missense_Mutation_p.E968K			Q9HCM3	K1549_HUMAN	KIAA1549	968						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						ATGATGTACTCCTGCACAGCT	0.468			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)	uc011kql.2				Dom	yes		7	7q34	57670	O	KIAA1549			O	BRAF		pilocytic astrocytoma	KIAA1549/BRAF(703)	0				large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						c.(2902-2904)Gag>Aag		Homo sapiens KIAA1549 (KIAA1549), transcript variant 2, mRNA.							138.0	133.0	134.0					7																	138597183		2038	4209	6247	SO:0001583	missense	57670					integral to membrane		g.chr7:138597183C>T		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.2902G>A	7.37:g.138597183C>T	ENSP00000416040:p.Glu968Lys		Somatic				KIAA1549_uc011kqj.2_Missense_Mutation_p.E968K	p.E968K	NM_001164665	NP_001158137	WXS	Illumina GAIIx	Phase_I	Q9HCM3	K1549_HUMAN			2	2951	-			968					B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	c.2902G>A	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.441581	0.83993	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.26223	1.76;1.76;1.75	5.38	5.38	0.77491	.	0.153934	0.43416	D	0.000576	T	0.30854	0.0778	L	0.32530	0.975	0.30689	N	0.751499	P;D	0.55800	0.954;0.973	P;P	0.53593	0.541;0.73	T	0.05886	-1.0858	10	0.30854	T	0.27	.	14.5742	0.68235	0.0:0.8428:0.1572:0.0	.	968;968	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	K	968;918;968	ENSP00000406661:E968K;ENSP00000242365:E918K;ENSP00000416040:E968K	ENSP00000242365:E918K	E	-	1	0	KIAA1549	138247723	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.458000	0.53014	2.793000	0.96121	0.655000	0.94253	GAG		0.468	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			22	43	0	0	0	1	0	22	43				
TBCK	93627	broad.mit.edu	37	4	107216253	107216253	+	Silent	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr4:107216253C>T	ENST00000273980.5	-	4	711	c.264G>A	c.(262-264)gtG>gtA	p.V88V	TBCK_ENST00000394706.3_Silent_p.V88V|TBCK_ENST00000432496.2_Silent_p.V88V|TBCK_ENST00000361687.4_Silent_p.V88V|TBCK_ENST00000394708.2_Silent_p.V88V					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TACAGTACCTCACAGGTTTCC	0.383																																						uc010ilv.2																			0				NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						c.(262-264)gtG>gtA		Homo sapiens TBC1 domain containing kinase (TBCK), transcript variant 1, mRNA.							116.0	116.0	116.0					4																	107216253		2203	4300	6503	SO:0001819	synonymous_variant	93627					intracellular	Rab GTPase activator activity	g.chr4:107216253C>T		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.264G>A	4.37:g.107216253C>T			Somatic				TBCK_uc003hye.2_Silent_p.V88V|TBCK_uc003hyc.2_Silent_p.V88V|TBCK_uc003hyd.2_5'UTR|TBCK_uc003hyf.2_Silent_p.V88V	p.V88V	NM_001163435	NP_001156908	WXS	Illumina GAIIx	Phase_I	Q8TEA7	TBCK_HUMAN			2	629	-			88			Protein kinase.			Silent	SNP	ENST00000273980.5	37	c.264G>A	CCDS54788.1																																																																																				0.383	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		42	71	0	0	0	1	0	42	71				
COL9A2	1298	broad.mit.edu	37	1	40767021	40767021	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr1:40767021C>T	ENST00000372748.3	-	32	1999	c.1903G>A	c.(1903-1905)Ggc>Agc	p.G635S	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	635	Triple-helical region 1 (COL1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	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;2.08e-17)			CCATCCTTGCCGTTGATTGCC	0.637																																						uc001cfh.1																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22						c.(1903-1905)Ggc>Agc		Homo sapiens collagen, type IX, alpha 2 (COL9A2), mRNA.							22.0	28.0	26.0					1																	40767021		2197	4300	6497	SO:0001583	missense	1298				axon guidance|skeletal system development	collagen type IX		g.chr1:40767021C>T	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1903G>A	1.37:g.40767021C>T	ENSP00000361834:p.Gly635Ser		Somatic				COL9A2_uc001cfi.1_Missense_Mutation_p.G454S	p.G635S	NM_001852	NP_001843	WXS	Illumina GAIIx	Phase_I	Q14055	CO9A2_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)		31	2015	-	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)	635			Triple-helical region 1 (COL1).		B2RMP9	Missense_Mutation	SNP	ENST00000372748.3	37	c.1903G>A	CCDS450.1	.	.	.	.	.	.	.	.	.	.	C	33	5.258623	0.95368	.	.	ENSG00000049089	ENST00000372748	D	0.97378	-4.36	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.98661	0.9551	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99433	1.0936	10	0.87932	D	0	.	16.2802	0.82672	0.0:1.0:0.0:0.0	.	635	Q14055	CO9A2_HUMAN	S	635	ENSP00000361834:G635S	ENSP00000361834:G635S	G	-	1	0	COL9A2	40539608	1.000000	0.71417	0.935000	0.37517	0.878000	0.50629	7.033000	0.76504	2.708000	0.92522	0.655000	0.94253	GGC		0.637	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852		7	27	0	0	0	1	0	7	27				
LRP4	4038	broad.mit.edu	37	11	46920980	46920980	+	Missense_Mutation	SNP	C	C	T	rs201585639	byFrequency	TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr11:46920980C>T	ENST00000378623.1	-	5	747	c.505G>A	c.(505-507)Ggt>Agt	p.G169S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	169	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TCGGTGTCACCGTCGCAGTAC	0.582													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		22776	0.0		0.0	False		,,,				2504	0.0					uc001ndn.4																			0				breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70						c.(505-507)Ggt>Agt		Homo sapiens low density lipoprotein receptor-related protein 4 (LRP4), mRNA.		C	SER/GLY	2,4400	4.2+/-10.8	0,2,2199	182.0	141.0	155.0		505	5.6	0.4	11		155	0,8598		0,0,4299	yes	missense	LRP4	NM_002334.3	56	0,2,6498	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	169/1906	46920980	2,12998	2201	4299	6500	SO:0001583	missense	4038				Wnt receptor signaling pathway|endocytosis|negative regulation of canonical Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity	g.chr11:46920980C>T	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.505G>A	11.37:g.46920980C>T	ENSP00000367888:p.Gly169Ser		Somatic				LRP4_uc009ylh.2_Missense_Mutation_p.G120S	p.G169S	NM_002334	NP_002325	WXS	Illumina GAIIx	Phase_I	O75096	LRP4_HUMAN		Lung(87;0.159)	4	748	-			169			LDL-receptor class A 4.		B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	c.505G>A	CCDS31478.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	28.0	4.883292	0.91740	4.54E-4	0.0	ENSG00000134569	ENST00000378623;ENST00000534404	D;D	0.96774	-4.12;-4.12	5.55	5.55	0.83447	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97660	0.9233	M	0.78344	2.41	0.58432	D	0.999999	D;D	0.69078	0.991;0.997	P;P	0.58577	0.651;0.841	D	0.97595	1.0119	10	0.51188	T	0.08	.	19.5068	0.95121	0.0:1.0:0.0:0.0	.	214;169	C9JRN7;O75096	.;LRP4_HUMAN	S	169;120	ENSP00000367888:G169S;ENSP00000434763:G120S	ENSP00000367888:G169S	G	-	1	0	LRP4	46877556	0.960000	0.32886	0.365000	0.25901	0.975000	0.68041	3.816000	0.55658	2.621000	0.88768	0.561000	0.74099	GGT		0.582	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		5	166	0	0	0	1	0	5	166				
CLRN3	119467	broad.mit.edu	37	10	129676574	129676575	+	Missense_Mutation	DNP	TC	TC	AA	rs550245323		TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr10:129676574_129676575TC>AA	ENST00000368671.3	-	3	681_682	c.519_520GA>TT	c.(517-522)acGAcc>acTTcc	p.T174S		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	174						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TAACTGTGGGTCGTTCCTTTAC	0.45																																						uc001lka.1																			0				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						c.(517-522)acgacc>acTTcc		Homo sapiens clarin 3 (CLRN3), mRNA.																																				SO:0001583	missense	119467					integral to membrane		g.chr10:129676574_129676575TC>AA	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.519_520delinsAA	10.37:g.129676574_129676575delinsAA	ENSP00000357660:p.Thr174Ser		Somatic				CLRN3_uc001ljz.1_Missense_Mutation_p.T106S	p.T174S	NM_152311	NP_689524	WXS	Illumina GAIIx	Phase_I	Q8NCR9	CLRN3_HUMAN			2	682_683	-		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)	174					Q6MZX8	Missense_Mutation	DNP	ENST00000368671.3	37	c.519_520GA>TT	CCDS7656.1																																																																																				0.450	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		61	96	0	0	0	1	0	61	96				
WDR59	79726	broad.mit.edu	37	16	74919593	74919593	+	Missense_Mutation	SNP	A	A	C			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr16:74919593A>C	ENST00000262144.6	-	25	2777	c.2647T>G	c.(2647-2649)Ttg>Gtg	p.L883V		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	883										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						ACAAACTTCAACACTTCAGCT	0.458																																						uc002fdh.1																			0				breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						c.(2647-2649)Ttg>Gtg		Homo sapiens WD repeat domain 59 (WDR59), mRNA.							123.0	110.0	115.0					16																	74919593		2198	4300	6498	SO:0001583	missense	79726							g.chr16:74919593A>C	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.2647T>G	16.37:g.74919593A>C	ENSP00000262144:p.Leu883Val		Somatic				WDR59_uc002fdf.1_Missense_Mutation_p.L328V|WDR59_uc002fdg.1_Missense_Mutation_p.L475V	p.L883V	NM_030581	NP_085058	WXS	Illumina GAIIx	Phase_I	Q6PJI9	WDR59_HUMAN			24	2749	-			883					B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	c.2647T>G	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.637314	0.47049	.	.	ENSG00000103091	ENST00000262144	T	0.73897	-0.79	5.36	0.973	0.19710	.	0.000000	0.85682	D	0.000000	T	0.81456	0.4826	M	0.72353	2.195	0.58432	D	0.999997	D;D	0.67145	0.993;0.996	D;D	0.75484	0.967;0.986	T	0.78802	-0.2061	10	0.41790	T	0.15	-14.4767	9.1438	0.36919	0.3511:0.0:0.6489:0.0	.	883;328	Q6PJI9;Q6PJI9-4	WDR59_HUMAN;.	V	883	ENSP00000262144:L883V	ENSP00000262144:L883V	L	-	1	2	WDR59	73477094	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	1.998000	0.40796	0.626000	0.30322	-1.145000	0.01858	TTG		0.458	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		27	60	0	0	0	1	0	27	60				
PTPRD	5789	broad.mit.edu	37	9	8501033	8501033	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr9:8501033T>C	ENST00000381196.4	-	21	2392	c.1849A>G	c.(1849-1851)Agt>Ggt	p.S617G	PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.S617G|PTPRD_ENST00000356435.5_Missense_Mutation_p.S617G|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.S604G|PTPRD_ENST00000358503.5_Missense_Mutation_p.S604G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	617	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTGGTGCAACTAATGTCTTGA	0.403										TSP Lung(15;0.13)																												uc003zkk.3																			0				NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168						c.(1849-1851)Agt>Ggt		Homo sapiens protein tyrosine phosphatase, receptor type, D (PTPRD), transcript variant 1, mRNA.							102.0	93.0	96.0					9																	8501033		2203	4300	6503	SO:0001583	missense	5789				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr9:8501033T>C	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1849A>G	9.37:g.8501033T>C	ENSP00000370593:p.Ser617Gly	TSP Lung(15;0.13)	Somatic				PTPRD_uc003zkp.3_Intron|PTPRD_uc003zkq.3_Intron|PTPRD_uc003zkr.3_Intron|PTPRD_uc003zks.3_Intron|PTPRD_uc022bdj.1_Intron	p.S617G	NM_002839	NP_002830	WXS	Illumina GAIIx	Phase_I	P23468	PTPRD_HUMAN		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)	23	2592	-		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)	617			Fibronectin type-III 4.		B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	c.1849A>G	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.320125	0.41096	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.76	5.76	0.90799	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.260790	0.44483	D	0.000446	T	0.60932	0.2307	M	0.80847	2.515	0.38099	D	0.937206	P;B;B	0.35033	0.481;0.011;0.082	B;B;B	0.33121	0.138;0.024;0.158	T	0.65977	-0.6037	9	.	.	.	.	16.0668	0.80887	0.0:0.0:0.0:1.0	.	604;617;617	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	G	617;617;604;604;617	ENSP00000370593:S617G;ENSP00000348812:S617G;ENSP00000353187:S604G;ENSP00000351293:S604G;ENSP00000438164:S617G	.	S	-	1	0	PTPRD	8491033	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.889000	0.56212	2.192000	0.70111	0.459000	0.35465	AGT		0.403	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			3	56	0	0	0	1	0	3	56				
COL27A1	85301	broad.mit.edu	37	9	117052336	117052336	+	Splice_Site	SNP	A	A	G			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr9:117052336A>G	ENST00000356083.3	+	46	4597		c.e46-1			NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1						extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.?(2)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TTGATTTTTCAGGGACCAAAG	0.627																																						uc011lxl.2																			2	Unknown(2)	p.?(2)	prostate(1)|kidney(1)	central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						c.e46-2		Homo sapiens collagen, type XXVII, alpha 1 (COL27A1), mRNA.							42.0	48.0	46.0					9																	117052336		2203	4300	6503	SO:0001630	splice_region_variant	85301				cell adhesion		extracellular matrix structural constituent	g.chr9:117052336A>G	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4207-1A>G	9.37:g.117052336A>G			Somatic				COL27A1_uc004bii.3_Splice_Site	p.G1403_splice	NM_032888	NP_116277	WXS	Illumina GAIIx	Phase_I	Q8IZC6	CORA1_HUMAN			46	4207	+			1403			Collagen-like 13.|Pro-rich.|Triple-helical region.		Q66K43|Q96JF7	Splice_Site	SNP	ENST00000356083.3	37	c.4207_splice	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.625794	0.66901	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8826	0.46948	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL27A1	116092157	1.000000	0.71417	0.941000	0.38009	0.929000	0.56500	5.131000	0.64751	1.824000	0.53156	0.402000	0.26972	.		0.627	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	Intron	3	67	0	0	0	1	0	3	67				
EPCAM	4072	broad.mit.edu	37	2	47596655	47596655	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr2:47596655C>T	ENST00000263735.4	+	1	369	c.11C>T	c.(10-12)cCg>cTg	p.P4L	EPCAM_ENST00000405271.1_Intron	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	4					negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						ATGGCGCCCCCGCAGGTCCTC	0.741																																						uc002rvx.3																			3	Whole gene deletion(2)|Unknown(1)	p.0?(2)|p.?(1)	haematopoietic_and_lymphoid_tissue(3)	endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						c.(10-12)cCg>cTg		Homo sapiens epithelial cell adhesion molecule (EPCAM), mRNA.							5.0	6.0	6.0					2																	47596655		2013	4103	6116	SO:0001583	missense	4072				positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding	g.chr2:47596655C>T	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"""CD molecules"""	11529	protein-coding gene	gene with protein product		185535	"""antigen identified by monoclonal antibody AUA1"", ""tumor-associated calcium signal transducer 1"""	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.11C>T	2.37:g.47596655C>T	ENSP00000263735:p.Pro4Leu		Somatic					p.P4L	NM_002354	NP_002345	WXS	Illumina GAIIx	Phase_I	P16422	EPCAM_HUMAN			0	369	+			4					P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Missense_Mutation	SNP	ENST00000263735.4	37	c.11C>T	CCDS1833.1	.	.	.	.	.	.	.	.	.	.	c	7.618	0.676140	0.14841	.	.	ENSG00000119888	ENST00000263735;ENST00000419334	T;D	0.85013	-0.77;-1.93	3.97	1.17	0.20885	.	0.616838	0.15894	N	0.239396	T	0.73938	0.3651	L	0.46157	1.445	0.19300	N	0.999978	B	0.15719	0.014	B	0.06405	0.002	T	0.53669	-0.8406	10	0.07813	T	0.8	.	5.8814	0.18858	0.0:0.6529:0.0:0.3471	.	4	P16422	EPCAM_HUMAN	L	4	ENSP00000263735:P4L;ENSP00000389028:P4L	ENSP00000263735:P4L	P	+	2	0	EPCAM	47450159	0.006000	0.16342	0.214000	0.23707	0.133000	0.20885	0.236000	0.17967	0.042000	0.15717	-0.318000	0.08688	CCG		0.741	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2			2	1	0	0	0	1	0	2	1				
DNAH9	1770	broad.mit.edu	37	17	11607602	11607602	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr17:11607602C>T	ENST00000262442.4	+	25	5302	c.5234C>T	c.(5233-5235)gCc>gTc	p.A1745V	DNAH9_ENST00000454412.2_Missense_Mutation_p.A1745V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1745	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.A1745V(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TATGAGAGTGCCATGAAGGAC	0.522																																						uc002gne.3																			1	Substitution - Missense(1)	p.A1745V(2)|p.S1744N(1)	central_nervous_system(1)	NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290						c.(5233-5235)gCc>gTc		Homo sapiens dynein, axonemal, heavy chain 9 (DNAH9), transcript variant 2, mRNA.							119.0	112.0	114.0					17																	11607602		2203	4300	6503	SO:0001583	missense	1770				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:11607602C>T	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.5234C>T	17.37:g.11607602C>T	ENSP00000262442:p.Ala1745Val		Somatic				DNAH9_uc010coo.3_Missense_Mutation_p.A1039V	p.A1745V	NM_001372	NP_001363	WXS	Illumina GAIIx	Phase_I	Q9NYC9	DYH9_HUMAN		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	24	5302	+		Breast(5;0.0122)|all_epithelial(5;0.131)	1745			Stem (By similarity).		A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	c.5234C>T	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.649581	0.87958	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.30714	1.56;1.52	5.91	5.91	0.95273	.	0.062515	0.64402	D	0.000006	T	0.64505	0.2604	H	0.96080	3.765	0.80722	D	1	D	0.57899	0.981	P	0.58454	0.839	T	0.73729	-0.3891	10	0.48119	T	0.1	.	15.7416	0.77901	0.0:0.8642:0.1358:0.0	.	1745	Q9NYC9	DYH9_HUMAN	V	1745;1745;327	ENSP00000262442:A1745V;ENSP00000414874:A1745V	ENSP00000262442:A1745V	A	+	2	0	DNAH9	11548327	1.000000	0.71417	0.997000	0.53966	0.919000	0.55068	5.634000	0.67833	2.813000	0.96785	0.655000	0.94253	GCC		0.522	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		7	105	0	0	0	1	0	7	105				
SPON2	10417	broad.mit.edu	37	4	1165191	1165191	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr4:1165191C>T	ENST00000290902.5	-	3	636	c.304G>A	c.(304-306)Gag>Aag	p.E102K	SPON2_ENST00000431380.1_Missense_Mutation_p.E102K	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	102	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		GCCCAGGCCTCGCCGCGCTCC	0.701																																						uc021xkj.1																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9						c.(304-306)Gag>Aag		Homo sapiens spondin 2, extracellular matrix protein (SPON2), transcript variant 3, mRNA.							24.0	27.0	26.0					4																	1165191		2183	4267	6450	SO:0001583	missense	10417				axon guidance|cell adhesion|innate immune response	proteinaceous extracellular matrix	metal ion binding	g.chr4:1165191C>T	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.304G>A	4.37:g.1165191C>T	ENSP00000290902:p.Glu102Lys		Somatic				SPON2_uc003gco.4_Missense_Mutation_p.E102K|SPON2_uc010ibr.3_Missense_Mutation_p.E102K|SPON2_uc003gcm.1_Missense_Mutation_p.E20K	p.E102K	NM_001199021	NP_001185950	WXS	Illumina GAIIx	Phase_I	Q9BUD6	SPON2_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)	4	929	-			102			Spondin.		D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	c.304G>A	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.847839	0.51164	.	.	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765	T;T;T	0.43294	0.95;0.95;0.95	4.5	4.5	0.54988	Spondin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	L	0.51422	1.61	0.80722	D	1	P;D;D	0.67145	0.726;0.993;0.996	B;B;P	0.49597	0.223;0.365;0.616	T	0.32640	-0.9899	10	0.16420	T	0.52	.	16.7743	0.85547	0.0:1.0:0.0:0.0	.	102;102;102	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	K	102	ENSP00000290902:E102K;ENSP00000394832:E102K;ENSP00000424542:E102K	ENSP00000290902:E102K	E	-	1	0	SPON2	1155191	1.000000	0.71417	0.974000	0.42286	0.111000	0.19643	7.011000	0.76359	2.053000	0.61076	0.511000	0.50034	GAG		0.701	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			16	74	0	0	0	1	0	16	74				
ALG3	10195	broad.mit.edu	37	3	183963511	183963511	+	Missense_Mutation	SNP	C	C	T	rs367679074		TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr3:183963511C>T	ENST00000397676.3	-	2	316	c.286G>A	c.(286-288)Gga>Aga	p.G96R	ALG3_ENST00000445626.2_Missense_Mutation_p.G48R|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000455059.1_Missense_Mutation_p.G56R|ALG3_ENST00000418734.2_Intron|EIF2B5_ENST00000444495.1_Intron	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	96					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACAAGTGGTCCGGTGTCACCC	0.522																																						uc003fne.2																			0				kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						c.(286-288)Gga>Aga		Homo sapiens asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae) (ALG3), transcript variant 1, mRNA.		C	ARG/GLY,ARG/GLY	0,4158		0,0,2079	96.0	97.0	96.0		142,286	4.9	1.0	3		96	1,8401		0,1,4200	no	missense,missense	ALG3	NM_001006941.2,NM_005787.5	125,125	0,1,6279	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging,probably-damaging	48/391,96/439	183963511	1,12559	2079	4201	6280	SO:0001583	missense	10195				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity	g.chr3:183963511C>T	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.286G>A	3.37:g.183963511C>T	ENSP00000380793:p.Gly96Arg		Somatic				ALG3_uc011brc.1_Missense_Mutation_p.G61R|ALG3_uc011brd.1_Intron|ALG3_uc011bre.1_Missense_Mutation_p.G48R|ALG3_uc011brf.1_Intron	p.G96R	NM_005787	NP_005778	WXS	Illumina GAIIx	Phase_I	Q92685	ALG3_HUMAN	Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		1	317	-	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		96					A8JZZ6|Q9BT71	Missense_Mutation	SNP	ENST00000397676.3	37	c.286G>A	CCDS46968.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.458059	0.84317	0.0	1.19E-4	ENSG00000214160	ENST00000397676;ENST00000445626;ENST00000455059	D;D;D	0.94000	-3.33;-3.33;-3.33	4.93	4.93	0.64822	.	0.000000	0.85682	U	0.000000	D	0.97711	0.9249	H	0.95224	3.64	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.81914	0.942;0.995;0.983	D	0.98821	1.0747	10	0.87932	D	0	-2.1164	16.8688	0.86036	0.0:1.0:0.0:0.0	.	48;56;96	A8JZZ6;C9J7S5;Q92685	.;.;ALG3_HUMAN	R	96;48;56	ENSP00000380793:G96R;ENSP00000402744:G48R;ENSP00000397613:G56R	ENSP00000380793:G96R	G	-	1	0	ALG3	185446205	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	7.531000	0.81973	2.562000	0.86427	0.462000	0.41574	GGA		0.522	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787		19	24	0	0	0	1	0	19	24				
MPDZ	8777	broad.mit.edu	37	9	13138104	13138104	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr9:13138104A>G	ENST00000319217.7	-	29	4299	c.4052T>C	c.(4051-4053)aTt>aCt	p.I1351T	MPDZ_ENST00000538841.1_Missense_Mutation_p.I210T|MPDZ_ENST00000381015.4_Missense_Mutation_p.I1351T|MPDZ_ENST00000381022.2_Missense_Mutation_p.I1351T|MPDZ_ENST00000540202.1_5'UTR|MPDZ_ENST00000546205.1_Missense_Mutation_p.I1365T|MPDZ_ENST00000447879.1_Missense_Mutation_p.I1318T|MPDZ_ENST00000541093.1_5'Flank|MPDZ_ENST00000541718.1_Missense_Mutation_p.I1351T|MPDZ_ENST00000536827.1_Missense_Mutation_p.I1318T	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1351	PDZ 8. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CTCCAGTTCAATCATATGCAG	0.403																																						uc010mhy.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61						c.(4051-4053)aTt>aCt		Homo sapiens multiple PDZ domain protein (MPDZ), mRNA.							73.0	69.0	70.0					9																	13138104		1891	4121	6012	SO:0001583	missense	8777				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding	g.chr9:13138104A>G	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.4052T>C	9.37:g.13138104A>G	ENSP00000320006:p.Ile1351Thr		Somatic				MPDZ_uc003zky.4_5'Flank|MPDZ_uc010mib.3_Missense_Mutation_p.I56T|MPDZ_uc010mhx.3_Missense_Mutation_p.I173T|MPDZ_uc011lmm.2_Missense_Mutation_p.I210T|MPDZ_uc003zkz.4_Missense_Mutation_p.I44T|MPDZ_uc010mhz.3_Missense_Mutation_p.I1318T|MPDZ_uc011lmn.2_Missense_Mutation_p.I1318T|MPDZ_uc003zlb.4_Missense_Mutation_p.I1351T|MPDZ_uc010mia.1_Missense_Mutation_p.I1351T	p.I1351T	NM_003829	NP_003820	WXS	Illumina GAIIx	Phase_I	O75970	MPDZ_HUMAN		GBM - Glioblastoma multiforme(50;2.03e-06)	27	4109	-			1351			PDZ 8.		A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37	c.4052T>C		.	.	.	.	.	.	.	.	.	.	A	26.6	4.753081	0.89753	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359	T;T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.72	5.72	0.89469	.	0.000000	0.47455	D	0.000223	T	0.69611	0.3130	M	0.87097	2.86	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.976;0.998;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.967;0.995;0.999;1.0;0.999	T	0.74777	-0.3550	10	0.56958	D	0.05	.	15.999	0.80275	1.0:0.0:0.0:0.0	.	1318;210;56;1318;1231;1351	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2	.;.;.;.;.;.	T	1351;1351;1351;287;210;1318;1318;1351;1231;1365;173	ENSP00000320006:I1351T;ENSP00000439807:I1351T;ENSP00000370410:I1351T;ENSP00000444230:I287T;ENSP00000444717:I210T;ENSP00000444151:I1318T;ENSP00000415208:I1318T;ENSP00000370403:I1351T;ENSP00000446358:I1365T;ENSP00000389705:I173T	ENSP00000320006:I1351T	I	-	2	0	MPDZ	13128104	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.300000	0.96151	2.176000	0.68965	0.528000	0.53228	ATT		0.403	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		13	16	0	0	0	1	0	13	16				
CCNT1	904	broad.mit.edu	37	12	49087252	49087252	+	Missense_Mutation	SNP	C	C	A			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr12:49087252C>A	ENST00000261900.3	-	9	1967	c.1745G>T	c.(1744-1746)gGg>gTg	p.G582V		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	582	Ser-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AAACACAGCCCCTCCAGTCTC	0.458																																						uc001rsd.4																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						c.(1744-1746)gGg>gTg		Homo sapiens cyclin T1 (CCNT1), mRNA.							76.0	79.0	78.0					12																	49087252		2203	4300	6503	SO:0001583	missense	904				cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding	g.chr12:49087252C>A	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1745G>T	12.37:g.49087252C>A	ENSP00000261900:p.Gly582Val		Somatic				CCNT1_uc009zkz.2_Missense_Mutation_p.G297V|CCNT1_uc021qxk.1_5'Flank	p.G582V	NM_001240	NP_001231	WXS	Illumina GAIIx	Phase_I	O60563	CCNT1_HUMAN			8	2068	-			582			Ser-rich.		A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	c.1745G>T	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	C	8.877	0.950606	0.18431	.	.	ENSG00000129315	ENST00000261900	T	0.17854	2.25	4.53	2.57	0.30868	.	0.624514	0.15089	N	0.281179	T	0.09512	0.0234	N	0.08118	0	0.27924	N	0.938125	B	0.15141	0.012	B	0.16289	0.015	T	0.24476	-1.0159	10	0.23302	T	0.38	-0.4412	14.1178	0.65167	0.0:0.5547:0.4453:0.0	.	582	O60563	CCNT1_HUMAN	V	582	ENSP00000261900:G582V	ENSP00000261900:G582V	G	-	2	0	CCNT1	47373519	0.019000	0.18553	0.770000	0.31555	0.882000	0.50991	1.089000	0.30890	0.542000	0.28846	0.561000	0.74099	GGG		0.458	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		41	46	0	0	0	1	0	41	46				
F2RL2	2151	broad.mit.edu	37	5	75914398	75914398	+	Missense_Mutation	SNP	G	G	T	rs140813985		TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr5:75914398G>T	ENST00000296641.4	-	2	337	c.134C>A	c.(133-135)cCa>cAa	p.P45Q	IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000379730.3_Intron|IQGAP2_ENST00000502745.1_Intron|IQGAP2_ENST00000396234.3_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.P23Q	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	45					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		AAAAGAATTTGGGGGAGCTCC	0.413																																						uc003kem.3																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32						c.(133-135)cCa>cAa		Homo sapiens coagulation factor II (thrombin) receptor-like 2 (F2RL2), mRNA.							85.0	95.0	92.0					5																	75914398		2196	4299	6495	SO:0001583	missense	2151				platelet activation	extracellular region|integral to plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|thrombin receptor activity	g.chr5:75914398G>T	U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"""GPCR / Class A : Protease activated receptors"""	3539	protein-coding gene	gene with protein product	"""proteinase-activated receptor-3"""	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.134C>A	5.37:g.75914398G>T	ENSP00000296641:p.Pro45Gln		Somatic				IQGAP2_uc003kek.3_Intron|IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.2_Intron|IQGAP2_uc003kel.3_Intron|F2RL2_uc011csw.2_Missense_Mutation_p.P23Q	p.P45Q	NM_004101	NP_004092	WXS	Illumina GAIIx	Phase_I	O00254	PAR3_HUMAN		all cancers(79;4.43e-43)	1	319	-		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)	45					B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	37	c.134C>A	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.949273	0.00475	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.62364	0.05;0.03	4.65	-5.18	0.02840	.	2.240730	0.02110	N	0.054707	T	0.30696	0.0773	N	0.01109	-1.01	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.32587	-0.9901	10	0.14656	T	0.56	12.5948	12.6713	0.56868	0.0666:0.0:0.2001:0.7333	.	45	O00254	PAR3_HUMAN	Q	45;23	ENSP00000296641:P45Q;ENSP00000426703:P23Q	ENSP00000296641:P45Q	P	-	2	0	F2RL2	75950154	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-1.921000	0.01569	-0.587000	0.05890	0.563000	0.77884	CCA		0.413	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			4	139	0	0	0	1	0	4	139				
FGD4	121512	broad.mit.edu	37	12	32793220	32793220	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr12:32793220C>T	ENST00000427716.2	+	17	2478	c.2054C>T	c.(2053-2055)gCc>gTc	p.A685V	FGD4_ENST00000534526.2_Missense_Mutation_p.A822V|FGD4_ENST00000525053.1_Missense_Mutation_p.A797V|FGD4_ENST00000546442.1_Missense_Mutation_p.A592V|FGD4_ENST00000531134.1_Missense_Mutation_p.A770V	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	685	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GACGTCAGAGCCCAGGCCACC	0.493																																						uc010ske.2																			0				breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27						c.(2389-2391)gCc>gTc		Homo sapiens FYVE, RhoGEF and PH domain containing 4 (FGD4), mRNA.							137.0	133.0	135.0					12																	32793220		2203	4300	6503	SO:0001583	missense	121512				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	Golgi apparatus|cytoskeleton|cytosol|filopodium|lamellipodium|ruffle	Rho guanyl-nucleotide exchange factor activity|metal ion binding|small GTPase binding	g.chr12:32793220C>T	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.2054C>T	12.37:g.32793220C>T	ENSP00000394487:p.Ala685Val		Somatic				FGD4_uc001rlc.3_Missense_Mutation_p.A770V|FGD4_uc001rkz.3_Missense_Mutation_p.A685V|FGD4_uc001rla.3_Missense_Mutation_p.A341V|FGD4_uc001rlb.1_Non-coding_Transcript	p.A797V	NM_139241	NP_640334	WXS	Illumina GAIIx	Phase_I	Q96M96	FGD4_HUMAN			16	2474	+	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		685					Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	37	c.2390C>T	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661138	0.88154	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000427716;ENST00000546442;ENST00000525053	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	5.31	5.31	0.75309	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.51477	D	0.000086	T	0.43411	0.1246	M	0.84219	2.685	0.80722	D	1	P;P;D	0.89917	0.933;0.933;1.0	P;P;D	0.75484	0.897;0.897;0.986	T	0.43572	-0.9383	10	0.59425	D	0.04	-11.148	18.9773	0.92742	0.0:1.0:0.0:0.0	.	797;770;685	E9PJX4;B7Z493;Q96M96	.;.;FGD4_HUMAN	V	822;770;685;592;797	ENSP00000449273:A822V;ENSP00000431323:A770V;ENSP00000394487:A685V;ENSP00000446695:A592V;ENSP00000433666:A797V	ENSP00000394487:A685V	A	+	2	0	FGD4	32684487	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.288000	0.78691	2.470000	0.83445	0.563000	0.77884	GCC		0.493	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		60	111	0	0	0	1	0	60	111				
BRAF	673	broad.mit.edu	37	7	140477832	140477846	+	In_Frame_Del	DEL	AGGTGTAGGTGCTGT	AGGTGTAGGTGCTGT	-	rs375520366		TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr7:140477832_140477846delAGGTGTAGGTGCTGT	ENST00000288602.6	-	12	1522_1536	c.1462_1476delACAGCACCTACACCT	c.(1462-1476)acagcacctacacctdel	p.TAPTP488del		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	488	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.L485_P490>Y(2)|p.N486_P490del(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)	GTAACTGCTGAGGTGTAGGTGCTGTCACATTCAAC	0.358		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)	uc003vwc.4		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)	3	Complex - deletion inframe(2)|Deletion - In frame(1)	p.L485_P490>Y(4)|p.N486_P490del(3)	lung(2)|ovary(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.(1462-1476)acagcacctacacctdel		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)																																			SO:0001651	inframe_deletion	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.chr7:140477832_140477846delAGGTGTAGGTGCTGT	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.1462_1476delACAGCACCTACACCT	7.37:g.140477832_140477846delAGGTGTAGGTGCTGT	ENSP00000288602:p.Thr488_Pro492del		Somatic					p.TAPTP488del	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			11	1523_1537	-	Melanoma(164;0.00956)		488			Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	In_Frame_Del	DEL	ENST00000288602.6	37	c.1462_1476delACAGCACCTACACCT	CCDS5863.1																																																																																				0.358	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		19	26						19	26	---	---	---	---
TNN	63923	broad.mit.edu	37	1	175048656	175048656	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr1:175048656delC	ENST00000239462.4	+	3	710	c.597delC	c.(595-597)tacfs	p.Y199fs		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	199	EGF-like 2.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ACTGCGGCTACCCGGCCTGCC	0.716																																						uc001gkl.1																			0				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156						c.(595-597)tacfs		Homo sapiens tenascin N (TNN), mRNA.							11.0	11.0	11.0					1																	175048656		2136	4205	6341	SO:0001589	frameshift_variant	63923				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix		g.chr1:175048656delC	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.597delC	1.37:g.175048656delC	ENSP00000239462:p.Tyr199fs		Somatic				TNN_uc010pmx.1_Frame_Shift_Del_p.Y199fs	p.Y199fs	NM_022093	NP_071376	WXS	Illumina GAIIx	Phase_I	Q9UQP3	TENN_HUMAN		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)	2	710	+		Breast(1374;0.000962)	199			EGF-like 2.		B9EGP3|Q5R360	Frame_Shift_Del	DEL	ENST00000239462.4	37	c.597delC	CCDS30943.1																																																																																				0.716	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		2	4						2	4	---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111160356	111160356	+	Frame_Shift_Del	DEL	T	T	-			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr13:111160356delT	ENST00000360467.5	+	47	4975	c.4669delT	c.(4669-4671)tatfs	p.Y1557fs	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1557	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TGTCTGCTACTATGCCAGCCG	0.622																																						uc001vqx.3																			0				NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						c.(4669-4671)tatfs		Homo sapiens collagen, type IV, alpha 2 (COL4A2), mRNA.							78.0	87.0	84.0					13																	111160356		2179	4284	6463	SO:0001589	frameshift_variant	1284				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding	g.chr13:111160356delT	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.4669delT	13.37:g.111160356delT	ENSP00000353654:p.Tyr1557fs		Somatic					p.Y1557fs	NM_001846	NP_001837	WXS	Illumina GAIIx	Phase_I	P08572	CO4A2_HUMAN	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)		46	4958	+	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	1557			Collagen IV NC1.		Q14052|Q548C3|Q5VZA9|Q66K23	Frame_Shift_Del	DEL	ENST00000360467.5	37	c.4669delT	CCDS41907.1																																																																																				0.622	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		57	103						57	103	---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43270075	43270076	+	Intron	INS	-	-	A			TCGA-EM-A2P2-01A-11D-A202-08	TCGA-EM-A2P2-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ffffff5c-9797-4c83-b841-120e142e999e	d44f44bd-cfb5-4d3a-8793-9c1085fff05b	g.chr15:43270075_43270076insA	ENST00000290650.4	-	38	4297				UBR1_ENST00000382177.2_Intron	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1						cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACTGAACACTTACCAAAACATG	0.287																																						uc001zqq.3																			0				NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58						c.e38+1		Homo sapiens ubiquitin protein ligase E3 component n-recognin 1 (UBR1), mRNA.																																				SO:0001627	intron_variant	197131				cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding	g.chr15:43270075_43270076insA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4218+1->T	15.37:g.43270076_43270076dupA			Somatic					p.L1406_splice	NM_174916	NP_777576	WXS	Illumina GAIIx	Phase_I	Q8IWV7	UBR1_HUMAN		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)	38	4284	-		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)	1406					O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Splice_Site	INS	ENST00000290650.4	37	c.4218_splice	CCDS10091.1																																																																																				0.287	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		42	53						42	53	---	---	---	---
