#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
HIF3A	64344	broad.mit.edu	37	19	46825036	46825036	+	Missense_Mutation	SNP	C	C	T			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr19:46825036C>T	ENST00000377670.4	+	10	1179	c.1148C>T	c.(1147-1149)aCc>aTc	p.T383I	HIF3A_ENST00000472815.1_Missense_Mutation_p.T314I|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000420102.2_Missense_Mutation_p.T332I|HIF3A_ENST00000600383.1_Missense_Mutation_p.T314I|HIF3A_ENST00000300862.3_Missense_Mutation_p.T381I|HIF3A_ENST00000244303.6_Missense_Mutation_p.T314I|HIF3A_ENST00000339613.2_Missense_Mutation_p.T327I	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	383					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CCTGCAGACACCCCTGGCCCC	0.662																																						ENST00000339613.2																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33						c.(979-981)aCc>aTc		hypoxia inducible factor 3, alpha subunit							55.0	67.0	63.0					19																	46825036		2203	4300	6503	SO:0001583	missense	64344				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity	g.chr19:46825036C>T	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1148C>T	19.37:g.46825036C>T	ENSP00000366898:p.Thr383Ile					HIF3A_ENST00000420102.2_Missense_Mutation_p.T332I|HIF3A_ENST00000244303.6_Missense_Mutation_p.T314I|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000600383.1_Missense_Mutation_p.T314I|HIF3A_ENST00000300862.3_Missense_Mutation_p.T381I|HIF3A_ENST00000377670.4_Missense_Mutation_p.T383I|HIF3A_ENST00000472815.1_Missense_Mutation_p.T314I	p.T327I			Q9Y2N7	HIF3A_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)	10	1235	+		Ovarian(192;0.00965)|all_neural(266;0.0887)	383					B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	c.980C>T	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	C	8.665	0.901495	0.17760	.	.	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.65178	0.61;-0.14;0.48;0.61;-0.14	4.43	2.25	0.28309	.	2.786710	0.01156	N	0.006530	T	0.47619	0.1455	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;B	0.20052	0.023;0.005;0.028;0.002;0.041;0.041;0.017	B;B;B;B;B;B;B	0.18561	0.02;0.004;0.022;0.004;0.01;0.01;0.006	T	0.40496	-0.9560	10	0.56958	D	0.05	.	6.1771	0.20449	0.0:0.708:0.1891:0.1029	.	332;314;381;332;327;383;383	F5H884;B4DNA2;Q9Y2N7-2;B4DSD9;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;.;HIF3A_HUMAN;.	I	383;383;314;327;327;381;332	ENSP00000366898:T383I;ENSP00000244303:T314I;ENSP00000341877:T327I;ENSP00000300862:T381I;ENSP00000407771:T332I	ENSP00000244302:T383I	T	+	2	0	HIF3A	51516876	0.000000	0.05858	0.058000	0.19502	0.025000	0.11179	-0.350000	0.07721	0.603000	0.29913	0.655000	0.94253	ACC		0.662	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			38	93	0	0	0	0.002222	0	38	93				
CUX1	1523	broad.mit.edu	37	7	101847718	101847718	+	Silent	SNP	G	G	A	rs373412162		TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr7:101847718G>A	ENST00000292535.7	+	19	2993	c.2955G>A	c.(2953-2955)ccG>ccA	p.P985P	CUX1_ENST00000550008.2_Silent_p.P929P|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000546411.2_Silent_p.P883P|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Silent_p.P996P|CUX1_ENST00000549414.2_Silent_p.P963P|CUX1_ENST00000556210.1_Silent_p.P827P	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	985					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TGTCCCGACCGAAGCCATGGA	0.622																																						ENST00000360264.3																			0				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						c.(2986-2988)ccG>ccA		cut-like homeobox 1		G	,,,,,,	1,4405	2.1+/-5.4	0,1,2202	105.0	90.0	95.0		2988,,,,,,2955	-2.4	0.9	7		95	0,8600		0,0,4300	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,	996/1517,,,,,,985/1506	101847718	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1523				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:101847718G>A	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2955G>A	7.37:g.101847718G>A						CUX1_ENST00000560541.1_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000556210.1_Silent_p.P827P|CUX1_ENST00000549414.2_Silent_p.P963P|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000546411.2_Silent_p.P883P|CUX1_ENST00000550008.2_Silent_p.P929P|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000292535.7_Silent_p.P985P|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron	p.P996P	NM_001202543.1	NP_001189472.1	P39880	CUX1_HUMAN			19	3008	+			985					B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	c.2988G>A	CCDS5721.1																																																																																				0.622	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		7	108	0	0	0	0.001984	0	7	108				
OR8I2	120586	broad.mit.edu	37	11	55861326	55861326	+	Silent	SNP	A	A	G			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr11:55861326A>G	ENST00000302124.2	+	1	574	c.543A>G	c.(541-543)acA>acG	p.T181T		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GTGACACCACAGCTCTTTTAG	0.433																																						ENST00000302124.2																			0				NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53						c.(541-543)acA>acG		olfactory receptor, family 8, subfamily I, member 2							155.0	145.0	148.0					11																	55861326		2201	4296	6497	SO:0001819	synonymous_variant	120586				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55861326A>G	AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.543A>G	11.37:g.55861326A>G						OR8I2_ENST00000560768.1_Silent_p.T181T	p.T181T			Q8N0Y5	OR8I2_HUMAN			1	574	+	Esophageal squamous(21;0.00693)		181					B2RNN4|Q6IFC0|Q96RC5	Silent	SNP	ENST00000302124.2	37	c.543A>G	CCDS31517.1																																																																																				0.433	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		4	105	0	0	0	0.000602	0	4	105				
FZD3	7976	broad.mit.edu	37	8	28409258	28409258	+	Missense_Mutation	SNP	A	A	G			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr8:28409258A>G	ENST00000240093.3	+	6	2021	c.1543A>G	c.(1543-1545)Agg>Ggg	p.R515G	FZD3_ENST00000537916.1_Missense_Mutation_p.R515G	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	515					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TCATGGTCGTAGGAAAAAAGA	0.358																																						ENST00000240093.3																			0				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41						c.(1543-1545)Agg>Ggg		frizzled family receptor 3							100.0	97.0	98.0					8																	28409258		2203	4300	6503	SO:0001583	missense	7976				canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding	g.chr8:28409258A>G	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1543A>G	8.37:g.28409258A>G	ENSP00000240093:p.Arg515Gly					FZD3_ENST00000537916.1_Missense_Mutation_p.R515G	p.R515G	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)	6	2021	+		Ovarian(32;2.06e-05)	515					A8K615	Missense_Mutation	SNP	ENST00000240093.3	37	c.1543A>G	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.557817	0.45590	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	D;D	0.81908	-1.55;-1.55	5.17	4.01	0.46588	.	0.095624	0.64402	D	0.000002	T	0.79311	0.4424	L	0.46947	1.48	0.42793	D	0.993905	B	0.22683	0.073	B	0.31101	0.124	T	0.76152	-0.3064	10	0.66056	D	0.02	.	11.4143	0.49943	0.8344:0.1656:0.0:0.0	.	515	Q9NPG1	FZD3_HUMAN	G	515	ENSP00000437489:R515G;ENSP00000240093:R515G	ENSP00000240093:R515G	R	+	1	2	FZD3	28465177	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.805000	0.55575	0.910000	0.36722	0.477000	0.44152	AGG		0.358	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		3	43	0	0	0	0.000248	0	3	43				
RBM6	10180	broad.mit.edu	37	3	50005666	50005666	+	Missense_Mutation	SNP	A	A	G			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr3:50005666A>G	ENST00000266022.4	+	3	1067	c.808A>G	c.(808-810)Agg>Ggg	p.R270G	RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.R138G	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	270					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TCAGGATTTTAGGGGCAGAGA	0.453																																						ENST00000443081.1																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33						c.(412-414)Agg>Ggg		RNA binding motif protein 6							76.0	80.0	78.0					3																	50005666		2203	4300	6503	SO:0001583	missense	10180				RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding	g.chr3:50005666A>G	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.808A>G	3.37:g.50005666A>G	ENSP00000266022:p.Arg270Gly					RBM6_ENST00000266022.4_Missense_Mutation_p.R270G|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000441115.1_Intron	p.R138G			P78332	RBM6_HUMAN		BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)	3	1331	+			270					O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	c.412A>G	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.638237	0.47153	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.36878	1.28;1.23	6.04	4.86	0.63082	.	0.056955	0.64402	D	0.000008	T	0.42899	0.1223	L	0.29908	0.895	0.80722	D	1	D	0.63880	0.993	P	0.59948	0.866	T	0.17198	-1.0377	9	.	.	.	-13.914	13.694	0.62567	0.8717:0.1283:0.0:0.0	.	270	P78332	RBM6_HUMAN	G	270;138	ENSP00000266022:R270G;ENSP00000396466:R138G	.	R	+	1	2	RBM6	49980670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.330000	0.59266	1.072000	0.40860	0.459000	0.35465	AGG		0.453	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		3	78	0	0	0	0.000248	0	3	78				
LAMA4	3910	broad.mit.edu	37	6	112469364	112469364	+	Missense_Mutation	SNP	T	T	A			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr6:112469364T>A	ENST00000230538.7	-	18	2745	c.2348A>T	c.(2347-2349)gAt>gTt	p.D783V	LAMA4_ENST00000424408.2_Missense_Mutation_p.D776V|LAMA4_ENST00000522006.1_Missense_Mutation_p.D776V|LAMA4_ENST00000389463.4_Missense_Mutation_p.D776V	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	783	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GATACCTGCATCCCTAGCAGA	0.393																																						ENST00000230538.7																			0				NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100						c.(2347-2349)gAt>gTt		laminin, alpha 4							95.0	91.0	92.0					6																	112469364		2203	4300	6503	SO:0001583	missense	3910				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding	g.chr6:112469364T>A		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.2348A>T	6.37:g.112469364T>A	ENSP00000230538:p.Asp783Val					LAMA4_ENST00000522006.1_Missense_Mutation_p.D776V|LAMA4_ENST00000424408.2_Missense_Mutation_p.D776V|LAMA4_ENST00000389463.4_Missense_Mutation_p.D776V	p.D783V	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)	18	2745	-		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)	783			Domain II and I.		Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	c.2348A>T	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	T	19.24	3.790281	0.70337	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.18	5.18	0.71444	Laminin II (1);	0.242760	0.48767	D	0.000176	T	0.42854	0.1221	L	0.44542	1.39	0.80722	D	1	P;D	0.67145	0.82;0.996	P;P	0.62298	0.543;0.9	T	0.30031	-0.9992	10	0.40728	T	0.16	.	14.3576	0.66748	0.0:0.0:0.0:1.0	.	783;776	Q16363;Q16363-2	LAMA4_HUMAN;.	V	783;776;776;776	ENSP00000230538:D783V;ENSP00000429488:D776V;ENSP00000374114:D776V;ENSP00000416470:D776V	ENSP00000230538:D783V	D	-	2	0	LAMA4	112576057	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	3.843000	0.55865	2.164000	0.68074	0.533000	0.62120	GAT		0.393	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		17	40	0	0	0	0.004007	0	17	40				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		8	47	0	0	0	0.006214	0	8	47				
INTS3	65123	broad.mit.edu	37	1	153719545	153719545	+	Splice_Site	SNP	A	A	G			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr1:153719545A>G	ENST00000318967.2	+	4	999	c.431A>G	c.(430-432)cAg>cGg	p.Q144R	INTS3_ENST00000456435.1_5'UTR|INTS3_ENST00000435409.2_Splice_Site_p.Q144R|RP11-216N14.8_ENST00000453778.1_RNA	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	144					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGCCGTACTCAGGTAAGGCCA	0.463																																						ENST00000318967.2																			0				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						c.e4+1		integrator complex subunit 3							67.0	68.0	68.0					1																	153719545		2203	4300	6503	SO:0001630	splice_region_variant	65123				DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding	g.chr1:153719545A>G	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.432+1A>G	1.37:g.153719545A>G						INTS3_ENST00000435409.2_Splice_Site_p.Q144_splice|INTS3_ENST00000456435.1_5'UTR|RP11-216N14.8_ENST00000453778.1_RNA	p.Q144_splice	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.151)		4	999	+	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		144					A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Splice_Site	SNP	ENST00000318967.2	37	c.432_splice	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.672040	0.88348	.	.	ENSG00000143624	ENST00000318967;ENST00000435409	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.69895	0.3162	M	0.75615	2.305	0.58432	D	0.999996	P	0.48294	0.908	P	0.61397	0.888	T	0.75082	-0.3443	9	0.87932	D	0	.	12.3981	0.55397	1.0:0.0:0.0:0.0	.	144	Q68E01-2	.	R	144	.	ENSP00000318641:Q144R	Q	+	2	0	INTS3	151986169	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.389000	0.90172	2.029000	0.59856	0.459000	0.35465	CAG		0.463	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	Missense_Mutation	4	76	0	0	0	0.000248	0	4	76				
ISG20L2	81875	broad.mit.edu	37	1	156694023	156694023	+	Frame_Shift_Del	DEL	G	G	-			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr1:156694023delG	ENST00000313146.6	-	2	1647	c.865delC	c.(865-867)ctcfs	p.L289fs	ISG20L2_ENST00000368219.1_Frame_Shift_Del_p.L289fs|ISG20L2_ENST00000472824.2_5'UTR	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	289	Exonuclease.				ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCCGGTTGAGGGGGGGGATA	0.557																																						ENST00000313146.6																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16						c.(865-867)tcfs		interferon stimulated exonuclease gene 20kDa-like 2							82.0	86.0	85.0					1																	156694023		2203	4300	6503	SO:0001589	frameshift_variant	81875				ribosome biogenesis	nucleolus	exonuclease activity|nucleic acid binding|protein binding	g.chr1:156694023delG	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.865delC	1.37:g.156694023delG	ENSP00000323424:p.Leu289fs					ISG20L2_ENST00000472824.1_5'UTR|ISG20L2_ENST00000368219.1_Frame_Shift_Del_p.L289fs	p.L289fs	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN			2	1647	-	all_hematologic(923;0.088)|Hepatocellular(266;0.158)		289			Exonuclease.		D3DVC6|Q64KA2	Frame_Shift_Del	DEL	ENST00000313146.6	37	c.865delC	CCDS1153.1																																																																																				0.557	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		7	186						7	186	---	---	---	---
CEP68	23177	broad.mit.edu	37	2	65301473	65301476	+	Frame_Shift_Del	DEL	ACTG	ACTG	-			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr2:65301473_65301476delACTG	ENST00000377990.2	+	4	2145_2148	c.1942_1945delACTG	c.(1942-1947)actgacfs	p.TD648fs	CEP68_ENST00000260569.4_Frame_Shift_Del_p.TD511fs|CEP68_ENST00000537589.1_3'UTR|CEP68_ENST00000546106.1_Frame_Shift_Del_p.TD648fs|CEP68_ENST00000497039.1_3'UTR|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	648					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TGCAGATGTTACTGACCACGGGAC	0.48																																						ENST00000377990.2																			0				breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						c.(1942-1947)acfs		centrosomal protein 68kDa																																				SO:0001589	frameshift_variant	23177				centrosome organization	centrosome		g.chr2:65301473_65301476delACTG	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.1942_1945delACTG	2.37:g.65301473_65301476delACTG	ENSP00000367229:p.Thr648fs					CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Frame_Shift_Del_p.TD511fs|CEP68_ENST00000546106.1_Frame_Shift_Del_p.TD648fs|CEP68_ENST00000537589.1_3'UTR|RAB1A_ENST00000494188.1_Intron	p.TD648fs	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN			4	2145_2148	+			648					B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Frame_Shift_Del	DEL	ENST00000377990.2	37	c.1942_1945delACTG	CCDS1880.2																																																																																				0.480	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		20	77						20	77	---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241696841	241696843	+	Intron	DEL	TCC	TCC	-	rs537608637|rs10594016|rs533559120		TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr2:241696841_241696843delTCC	ENST00000320389.7	-	25	2714				KIF1A_ENST00000498729.2_In_Frame_Del_p.E917del	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A						anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		ctcctcctcatcctcctcctcct	0.675																																						ENST00000498729.2																			0				NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66						c.(2749-2754)gat>ga		kinesin family member 1A																																				SO:0001627	intron_variant	547				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity	g.chr2:241696841_241696843delTCC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2555+933GGA>-	2.37:g.241696850_241696852delTCC						KIF1A_ENST00000320389.7_Intron	p.ED917del	NM_001244008.1	NP_001230937.1	Q12756	KIF1A_HUMAN		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)	27	2997_2999	-		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)	697					B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	In_Frame_Del	DEL	ENST00000320389.7	37	c.2751_2753delGGA	CCDS46561.1																																																																																				0.675	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		2	4						2	4	---	---	---	---
POU4F2	5458	broad.mit.edu	37	4	147560457	147560458	+	In_Frame_Ins	INS	-	-	GGC	rs530695040|rs72269802|rs5862765		TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr4:147560457_147560458insGGC	ENST00000281321.3	+	1	413_414	c.165_166insGGC	c.(166-168)ggc>GGCggc	p.56_56G>GG	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	56	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					ACGCTggtggtggcggcggcgg	0.762																																						ENST00000281321.3																			0				NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33						c.(163-168)gggcgg>ggGGCgcgg		POU class 4 homeobox 2																																				SO:0001652	inframe_insertion	5458				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	g.chr4:147560457_147560458insGGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.196_198dupGGC	4.37:g.147560464_147560466dupGGC	ENSP00000281321:p.Gly68dup					AC093887.1_ENST00000584185.1_RNA	p.55_56GR>GAR	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN			1	413_414	+	all_hematologic(180;0.151)		55			Poly-Gly.		B1PJR6|B2RC84|Q13883|Q14987	In_Frame_Ins	INS	ENST00000281321.3	37	c.165_166insGGC	CCDS34074.1																																																																																				0.762	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		8	17						8	17	---	---	---	---
MS4A2	2206	broad.mit.edu	37	11	59863096	59863096	+	Frame_Shift_Del	DEL	C	C	-			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr11:59863096delC	ENST00000278888.3	+	7	804	c.702delC	c.(700-702)gacfs	p.D234fs		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	234					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	AGTTGGAAGACCCAGGGGAAA	0.413																																						ENST00000278888.3																			0				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17						c.(700-702)gafs		membrane-spanning 4-domains, subfamily A, member 2	Omalizumab(DB00043)						121.0	119.0	119.0					11																	59863096		2201	4295	6496	SO:0001589	frameshift_variant	2206				cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity	g.chr11:59863096delC	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"""Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"""	147138	"""IgE responsiveness (atopic)"", ""membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"""	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.702delC	11.37:g.59863096delC	ENSP00000278888:p.Asp234fs						p.D234fs	NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN			7	804	+		all_epithelial(135;0.245)	234					Q54A81	Frame_Shift_Del	DEL	ENST00000278888.3	37	c.702delC	CCDS7980.1																																																																																				0.413	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1			10	53						10	53	---	---	---	---
ACTN3	89	broad.mit.edu	37	11	66321928	66321928	+	RNA	DEL	A	A	-			TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr11:66321928delA	ENST00000502692.1	+	0	714				ACTN3_ENST00000513398.1_RNA	NM_001258371.1	NP_001245300.1	Q08043	ACTN3_HUMAN	actinin, alpha 3 (gene/pseudogene)						focal adhesion assembly (GO:0048041)|muscle filament sliding (GO:0030049)|regulation of apoptotic process (GO:0042981)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)	10						accctgtctcaaaaaaaaaaa	0.537																																						ENST00000513398.1																			0				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)	10								actinin, alpha 3 (gene/pseudogene)																																						89				focal adhesion assembly|muscle filament sliding|regulation of apoptosis	actin filament|cytosol|focal adhesion|pseudopodium	actin binding|calcium ion binding|integrin binding|protein homodimerization activity|structural constituent of muscle	g.chr11:66321928delA	M86407		11q13.2	2013-10-02	2012-10-05		ENSG00000248746	ENSG00000248746			165	protein-coding gene	gene with protein product		102574	"""actinin, alpha 3"""			1339456	Standard	NM_001104		Approved		uc031qbp.1	Q08043	OTTHUMG00000160815		11.37:g.66321928delA						ACTN3_ENST00000502692.1_RNA		NM_001104.2	NP_001095.1	Q08043	ACTN3_HUMAN			0	566	+								A6NP77|Q4KKV2	RNA	DEL	ENST00000502692.1	37																																																																																						0.537	ACTN3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000362465.1	NM_001104		2	4						2	4	---	---	---	---
FRG2KP	102724018	broad.mit.edu	37	16	31576130	31576131	+	RNA	DEL	TC	TC	-	rs72374895|rs398058199|rs34385075	byFrequency	TCGA-H2-A26U-01A-11D-A16O-08	TCGA-H2-A26U-10A-01D-A16O-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a84193e-84f1-4729-b467-480c8b73e0e7	539571d0-752a-4bc0-ad14-71dbbe052642	g.chr16:31576130_31576131delTC	ENST00000565692.1	-	0	343																											TGAAAGGTGATCTCTCTCTCTC	0.515														3584	0.715655	0.9448	0.4827	5008	,	,		20755	0.5327		0.6491	False		,,,				2504	0.8282					ENST00000565692.1																			0																																																			0							g.chr16:31576130_31576131delTC																													16.37:g.31576140_31576141delTC														0	343	-									RNA	DEL	ENST00000565692.1	37																																																																																						0.515	CTD-2014E2.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432903.1			7	3						7	3	---	---	---	---
