#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
PGBD2	267002	broad.mit.edu	37	1	249211207	249211207	+	Missense_Mutation	SNP	G	G	T	rs367674534		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr1:249211207G>T	ENST00000329291.5	+	3	571	c.424G>T	c.(424-426)Gtg>Ttg	p.V142L	PGBD2_ENST00000539153.1_Missense_Mutation_p.V139L|PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000355360.4_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	142										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GCTGAGTCCCGTGGGCCTTTT	0.398																																						uc001ifh.3																			0				NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14						c.(424-426)Gtg>Ttg		Homo sapiens piggyBac transposable element derived 2 (PGBD2), transcript variant 1, mRNA.							62.0	70.0	67.0					1																	249211207		2201	4300	6501	SO:0001583	missense	267002							g.chr1:249211207G>T	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.424G>T	1.37:g.249211207G>T	ENSP00000331643:p.Val142Leu		Somatic				PGBD2_uc001ifg.3_Intron|PGBD2_uc009xhd.3_Missense_Mutation_p.V139L|PGBD2_uc021pmh.1_5'Flank	p.V142L	NM_170725	NP_001017434	WXS	Illumina GAIIx	Phase_I	Q6P3X8	PGBD2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		2	571	+	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	142					B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	37	c.424G>T	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951177	0.53186	.	.	ENSG00000185220	ENST00000329291;ENST00000539153	T;T	0.18960	2.18;2.18	4.18	4.18	0.49190	.	0.000000	0.30473	U	0.009559	T	0.33294	0.0858	L	0.49350	1.555	0.24069	N	0.995988	D;D	0.76494	0.982;0.999	P;D	0.85130	0.88;0.997	T	0.14699	-1.0463	10	0.06757	T	0.87	-25.4058	12.2179	0.54416	0.0:0.0:1.0:0.0	.	139;142	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	L	142;139	ENSP00000331643:V142L;ENSP00000439950:V139L	ENSP00000331643:V142L	V	+	1	0	PGBD2	247177830	0.998000	0.40836	0.812000	0.32479	0.721000	0.41392	2.096000	0.41738	2.331000	0.79229	0.655000	0.94253	GTG		0.398	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			13	35	0	0	0	1	0	13	35				
CACNA1A	773	broad.mit.edu	37	19	13565980	13565980	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:13565980C>T	ENST00000360228.5	-	2	339	c.340G>A	c.(340-342)Gtc>Atc	p.V114I	CACNA1A_ENST00000573710.2_Missense_Mutation_p.V114I	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	114					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	AGTGCGAGGACGATGCAATTC	0.453																																						uc010xne.2																			0				breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42						c.(340-342)Gtc>Atc		Homo sapiens calcium channel, voltage-dependent, P/Q type, alpha 1A subunit (CACNA1A), transcript variant 2, mRNA.	Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)						193.0	193.0	193.0					19																	13565980		2042	4220	6262	SO:0001583	missense	773				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding	g.chr19:13565980C>T	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.340G>A	19.37:g.13565980C>T	ENSP00000353362:p.Val114Ile		Somatic				CACNA1A_uc010xnd.2_Missense_Mutation_p.V114I|CACNA1A_uc021ups.1_Missense_Mutation_p.V114I|CACNA1A_uc002mwy.3_Missense_Mutation_p.V114I|CACNA1A_uc010dze.2_Missense_Mutation_p.V114I|CACNA1A_uc021upt.1_Missense_Mutation_p.V114I	p.V114I	NM_023035	NP_075461	WXS	Illumina GAIIx	Phase_I	O00555	CAC1A_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		1	576	-			114					J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	c.340G>A	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112780	0.94339	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	T	0.71222	-0.55	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000009	D	0.84678	0.5525	M	0.80422	2.495	0.53688	D	0.999977	D;D	0.76494	0.999;0.999	D;D	0.72982	0.972;0.979	D	0.86819	0.2003	10	0.72032	D	0.01	.	17.4452	0.87577	0.0:1.0:0.0:0.0	.	114;114	O00555;Q9NS88	CAC1A_HUMAN;.	I	114	ENSP00000353362:V114I	ENSP00000317661:V114I	V	-	1	0	CACNA1A	13426980	1.000000	0.71417	0.996000	0.52242	0.859000	0.49053	7.684000	0.84104	2.489000	0.83994	0.655000	0.94253	GTC		0.453	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		64	185	0	0	0	1	0	64	185				
TTN	7273	broad.mit.edu	37	2	179402314	179402314	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:179402314T>C	ENST00000591111.1	-	305	94921	c.94697A>G	c.(94696-94698)tAt>tGt	p.Y31566C	TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Y33207C|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Y30639C|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Y24142C|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Y24267C|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Y24334C			Q8WZ42	TITIN_HUMAN	titin	31566					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACAGCTCCATAATATTTCTC	0.458																																						uc021vsy.1																			0				NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448						c.(91915-91917)tAt>tGt		Homo sapiens titin (TTN), transcript variant N2-A, mRNA.							78.0	78.0	78.0					2																	179402314		1878	4108	5986	SO:0001583	missense	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179402314T>C	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.94697A>G	2.37:g.179402314T>C	ENSP00000465570:p.Tyr31566Cys		Somatic				MIR548N_uc021vsx.1_Intron|LOC100506866_uc002umo.3_Non-coding_Transcript|LOC100506866_uc002ump.2_Intron|TTN_uc021vsz.1_Missense_Mutation_p.Y24334C|TTN_uc021vta.1_Missense_Mutation_p.Y24267C|TTN_uc021vtb.1_Missense_Mutation_p.Y24142C	p.Y30639C	NM_133378	NP_596869	WXS	Illumina GAIIx	Phase_I	Q8WZ42	TITIN_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		303	92141	-			31566			Fibronectin type-III 123.		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37	c.91916A>G		.	.	.	.	.	.	.	.	.	.	T	12.55	1.971308	0.34754	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.89	5.89	0.94794	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.20536	0.0494	N	0.03608	-0.345	0.41560	D	0.988627	B;B;B;B	0.20261	0.043;0.043;0.043;0.024	B;B;B;B	0.20577	0.03;0.03;0.03;0.03	T	0.09773	-1.0659	9	0.87932	D	0	.	6.6093	0.22743	0.1376:0.0715:0.0:0.7908	.	24142;24267;24334;31566	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	30639;24142;24334;24267;24139	ENSP00000343764:Y30639C;ENSP00000434586:Y24142C;ENSP00000340554:Y24334C;ENSP00000352154:Y24267C	ENSP00000340554:Y24334C	Y	-	2	0	TTN	179110560	0.987000	0.35691	1.000000	0.80357	0.991000	0.79684	2.114000	0.41911	2.257000	0.74773	0.460000	0.39030	TAT		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		3	37	0	0	0	1	0	3	37				
IRX2	153572	broad.mit.edu	37	5	2748624	2748624	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr5:2748624C>A	ENST00000382611.6	-	3	1446	c.1198G>T	c.(1198-1200)Gcg>Tcg	p.A400S	IRX2_ENST00000502957.1_5'Flank|IRX2_ENST00000302057.5_Missense_Mutation_p.A400S	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	400					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		TGCAGCGCCGCGTTCAAGTTC	0.706																																						uc003jda.3																			0				breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26						c.(1198-1200)Gcg>Tcg		Homo sapiens iroquois homeobox 2 (IRX2), transcript variant 2, mRNA.							37.0	38.0	38.0					5																	2748624		2189	4286	6475	SO:0001583	missense	153572					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr5:2748624C>A	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"""Homeoboxes / TALE class"""	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.1198G>T	5.37:g.2748624C>A	ENSP00000372056:p.Ala400Ser		Somatic				IRX2_uc003jdb.3_Missense_Mutation_p.A400S	p.A400S	NM_001134222	NP_150366	WXS	Illumina GAIIx	Phase_I	Q9BZI1	IRX2_HUMAN		GBM - Glioblastoma multiforme(108;0.204)	2	1440	-			400					Q68A19|Q7Z2I7	Missense_Mutation	SNP	ENST00000382611.6	37	c.1198G>T	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.511595	0.27036	.	.	ENSG00000170561	ENST00000382611;ENST00000302057	T;T	0.64803	-0.12;-0.12	4.43	4.43	0.53597	.	0.067153	0.64402	D	0.000011	T	0.51295	0.1666	L	0.39898	1.24	0.35681	D	0.81406	B	0.31040	0.305	B	0.25884	0.064	T	0.57596	-0.7784	10	0.16420	T	0.52	-19.73	17.4343	0.87547	0.0:1.0:0.0:0.0	.	400	Q9BZI1	IRX2_HUMAN	S	400	ENSP00000372056:A400S;ENSP00000307006:A400S	ENSP00000307006:A400S	A	-	1	0	IRX2	2801624	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.982000	0.70532	2.184000	0.69523	0.561000	0.74099	GCG		0.706	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2			40	78	0	0	0	1	0	40	78				
TACC2	10579	broad.mit.edu	37	10	123842613	123842613	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr10:123842613A>G	ENST00000369005.1	+	4	938	c.598A>G	c.(598-600)Atg>Gtg	p.M200V	TACC2_ENST00000334433.3_Missense_Mutation_p.M200V|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.M200V|TACC2_ENST00000515273.1_Missense_Mutation_p.M200V|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.M200V	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	200					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GTCACCTGGAATGTCGCCAGT	0.582																																						uc001lfv.3																			0				NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83						c.(598-600)Atg>Gtg		Homo sapiens transforming, acidic coiled-coil containing protein 2 (TACC2), transcript variant 1, mRNA.							33.0	31.0	32.0					10																	123842613		2203	4300	6503	SO:0001583	missense	10579					microtubule organizing center|nucleus	nuclear hormone receptor binding	g.chr10:123842613A>G	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.598A>G	10.37:g.123842613A>G	ENSP00000358001:p.Met200Val		Somatic				TACC2_uc001lfw.3_Intron|TACC2_uc009xzx.3_Missense_Mutation_p.M200V|TACC2_uc010qtv.2_Missense_Mutation_p.M200V	p.M200V	NM_206862	NP_996744	WXS	Illumina GAIIx	Phase_I	O95359	TACC2_HUMAN			3	958	+		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)	200					Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	c.598A>G	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	A	6.786	0.514079	0.12944	.	.	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02525	4.26;4.27;4.27;4.26;4.27	5.72	0.706	0.18133	.	0.978077	0.08303	N	0.966559	T	0.01558	0.0050	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.48681	-0.9014	10	0.11182	T	0.66	2.1058	9.2055	0.37287	0.6161:0.0:0.3839:0.0	.	200;200;200	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	V	200;200;200;200;200;190	ENSP00000358001:M200V;ENSP00000424467:M200V;ENSP00000427618:M200V;ENSP00000334280:M200V;ENSP00000395048:M200V	ENSP00000334280:M200V	M	+	1	0	TACC2	123832603	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.130000	0.10498	0.114000	0.18032	0.528000	0.53228	ATG		0.582	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			17	33	0	0	0	1	0	17	33				
COL4A4	1286	broad.mit.edu	37	2	227875182	227875182	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:227875182C>G	ENST00000396625.3	-	46	4576	c.4369G>C	c.(4369-4371)Ggg>Cgg	p.G1457R	COL4A4_ENST00000329662.7_Missense_Mutation_p.G1454R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1457	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GGGCCAAACCCTTTGGGCCCA	0.572																																						uc021vxr.1																			0				breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98						c.(4369-4371)Ggg>Cgg		Homo sapiens collagen, type IV, alpha 4 (COL4A4), mRNA.							25.0	25.0	25.0					2																	227875182		1842	4092	5934	SO:0001583	missense	1286				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding	g.chr2:227875182C>G		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4369G>C	2.37:g.227875182C>G	ENSP00000379866:p.Gly1457Arg		Somatic				COL4A4_uc021vxs.1_Missense_Mutation_p.G1454R	p.G1457R	NM_000092	NP_000083	WXS	Illumina GAIIx	Phase_I	P53420	CO4A4_HUMAN		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)	44	4470	-		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)	1457			Triple-helical region.		A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	c.4369G>C	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165708	0.38217	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.99429	-5.89;-5.89	5.69	5.69	0.88448	.	.	.	.	.	D	0.99619	0.9861	H	0.94183	3.505	0.39561	D	0.969137	D	0.76494	0.999	D	0.75020	0.985	D	0.98200	1.0467	9	0.72032	D	0.01	.	13.0739	0.59077	0.0:0.9268:0.0:0.0732	.	1457	P53420	CO4A4_HUMAN	R	1457;1454	ENSP00000379866:G1457R;ENSP00000328553:G1454R	ENSP00000328553:G1454R	G	-	1	0	COL4A4	227583426	0.996000	0.38824	0.962000	0.40283	0.478000	0.33099	3.291000	0.51764	2.687000	0.91594	0.655000	0.94253	GGG		0.572	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		6	21	0	0	0	1	0	6	21				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	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)	uc003vwc.4	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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(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		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	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		Somatic					p.V600E	NM_004333	NP_004324	WXS	Illumina GAIIx	Phase_I	P15056	BRAF_HUMAN			14	1860	-	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		12	38	0	0	0	1	0	12	38				
E2F3	1871	broad.mit.edu	37	6	20486987	20486987	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:20486987G>T	ENST00000346618.3	+	5	1018	c.952G>T	c.(952-954)Gtg>Ttg	p.V318L	E2F3_ENST00000535432.1_Missense_Mutation_p.V187L	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	318	Dimerization. {ECO:0000255}.				mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			TGTTATAGTTGTGAAAGCCCC	0.383																																						uc003nda.2																			0				central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7						c.(952-954)Gtg>Ttg		Homo sapiens E2F transcription factor 3 (E2F3), transcript variant 1, mRNA.							84.0	76.0	79.0					6																	20486987		2203	4300	6503	SO:0001583	missense	1871				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:20486987G>T	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.952G>T	6.37:g.20486987G>T	ENSP00000262904:p.Val318Leu		Somatic				E2F3_uc021ymj.1_Missense_Mutation_p.V187L	p.V318L	NM_001949	NP_001940	WXS	Illumina GAIIx	Phase_I	O00716	E2F3_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)		4	1279	+	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		318			Dimerization (Potential).		Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	c.952G>T	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808216	0.70797	.	.	ENSG00000112242	ENST00000346618;ENST00000535432	D;D	0.90732	-2.72;-2.72	5.93	5.06	0.68205	.	0.119035	0.56097	N	0.000023	D	0.84710	0.5532	L	0.59436	1.845	0.58432	D	0.999999	P	0.45986	0.87	B	0.43194	0.411	D	0.86007	0.1498	10	0.56958	D	0.05	.	10.467	0.44614	0.069:0.1349:0.7961:0.0	.	318	O00716	E2F3_HUMAN	L	318;187	ENSP00000262904:V318L;ENSP00000443418:V187L	ENSP00000262904:V318L	V	+	1	0	E2F3	20594966	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.765000	0.74965	1.495000	0.48549	0.561000	0.74099	GTG		0.383	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			11	39	0	0	0	1	0	11	39				
FAM208B	54906	broad.mit.edu	37	10	5781833	5781833	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr10:5781833A>C	ENST00000328090.5	+	13	2325	c.1700A>C	c.(1699-1701)gAt>gCt	p.D567A	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	567																	CCACAAAATGATGTTTTGCTC	0.378																																						uc001iij.3																			0											c.(1699-1701)gAt>gCt		Homo sapiens family with sequence similarity 208, member B (FAM208B), mRNA.							90.0	84.0	86.0					10																	5781833		1856	4093	5949	SO:0001583	missense	54906							g.chr10:5781833A>C	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.1700A>C	10.37:g.5781833A>C	ENSP00000328426:p.Asp567Ala		Somatic				FAM208B_uc001iik.3_Intron	p.D567A	NM_017782	NP_060252	WXS	Illumina GAIIx	Phase_I	Q5VWN6	CJ018_HUMAN			12	2325	+			567					Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	c.1700A>C	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	A	8.339	0.828256	0.16749	.	.	ENSG00000108021	ENST00000328090	D	0.96940	-4.18	5.7	4.57	0.56435	.	0.698059	0.14004	N	0.347915	D	0.93867	0.8038	L	0.44542	1.39	0.09310	N	1	P	0.39352	0.669	B	0.41374	0.355	D	0.88174	0.2866	10	0.62326	D	0.03	.	8.4131	0.32655	0.8433:0.0:0.1567:0.0	.	567	Q5VWN6	F208B_HUMAN	A	567	ENSP00000328426:D567A	ENSP00000328426:D567A	D	+	2	0	C10orf18	5821839	0.017000	0.18338	0.010000	0.14722	0.063000	0.16089	0.631000	0.24568	0.993000	0.38866	0.402000	0.26972	GAT		0.378	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		21	43	0	0	0	1	0	21	43				
AGR2	10551	broad.mit.edu	37	7	16839390	16839390	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr7:16839390T>C	ENST00000419304.2	-	5	460	c.308A>G	c.(307-309)cAg>cGg	p.Q103R	AGR2_ENST00000419572.2_Missense_Mutation_p.Q123R|AGR2_ENST00000401412.1_Missense_Mutation_p.Q103R	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	103					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GAGGACAAACTGCTCTGCCAA	0.308																																						uc003str.3																			0				endometrium(2)|lung(1)|prostate(1)|skin(2)	6						c.(307-309)cAg>cGg		Homo sapiens anterior gradient 2 homolog (Xenopus laevis) (AGR2), mRNA.							164.0	166.0	165.0					7																	16839390		2203	4299	6502	SO:0001583	missense	10551				mucus secretion	endoplasmic reticulum|extracellular region	protein binding	g.chr7:16839390T>C	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"""Protein disulfide isomerases"""	328	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 17"""	606358	"""anterior gradient 2 homolog (Xenopus laevis)"""			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.308A>G	7.37:g.16839390T>C	ENSP00000391490:p.Gln103Arg		Somatic					p.Q103R	NM_006408	NP_006399	WXS	Illumina GAIIx	Phase_I	O95994	AGR2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.184)	4	495	-	Lung NSC(10;0.0376)|all_lung(11;0.0855)		103						Missense_Mutation	SNP	ENST00000419304.2	37	c.308A>G	CCDS5364.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.703253	0.48412	.	.	ENSG00000106541	ENST00000419304;ENST00000450569;ENST00000419572;ENST00000401412;ENST00000412973	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.1	5.1	0.69264	Thioredoxin-like fold (2);	0.121273	0.56097	D	0.000027	T	0.29355	0.0731	N	0.11927	0.2	0.33620	D	0.604711	B	0.09022	0.002	B	0.23150	0.044	T	0.40232	-0.9574	10	0.87932	D	0	-16.1632	14.5894	0.68354	0.0:0.0:0.0:1.0	.	103	O95994	AGR2_HUMAN	R	103;33;123;103;103	ENSP00000391490:Q103R;ENSP00000388342:Q123R;ENSP00000386025:Q103R;ENSP00000411969:Q103R	ENSP00000386025:Q103R	Q	-	2	0	AGR2	16805915	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.906000	0.56340	1.931000	0.55961	0.454000	0.30748	CAG		0.308	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408		6	18	0	0	0	1	0	6	18				
CD3D	915	broad.mit.edu	37	11	118209888	118209888	+	Missense_Mutation	SNP	G	G	A	rs367800432		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr11:118209888G>A	ENST00000300692.4	-	5	641	c.505C>T	c.(505-507)Cgg>Tgg	p.R169W	CD3D_ENST00000529594.1_Missense_Mutation_p.R96W|CD3D_ENST00000392884.2_Missense_Mutation_p.R125W	NM_000732.4	NP_000723.1	P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	169					cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	CACTTGTTCCGAGCCCAGTTT	0.502																																						uc001pss.1																			0				large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9						c.(505-507)Cgg>Tgg		Homo sapiens CD3d molecule, delta (CD3-TCR complex) (CD3D), transcript variant 1, mRNA.		G	TRP/ARG,TRP/ARG	1,4399	2.1+/-5.4	0,1,2199	119.0	110.0	113.0		505,373	1.0	0.1	11		113	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	CD3D	NM_000732.4,NM_001040651.1	101,101	0,2,6494	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	169/172,125/128	118209888	2,12990	2200	4296	6496	SO:0001583	missense	915				T cell costimulation|T cell receptor signaling pathway|positive thymic T cell selection	cytoplasm|integral to membrane	protein heterodimerization activity	g.chr11:118209888G>A	X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286		"""CD molecules"""	1673	protein-coding gene	gene with protein product		186790	"""CD3d antigen, delta polypeptide (TiT3 complex)"""	T3D			Standard	NM_000732		Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000300692.4:c.505C>T	11.37:g.118209888G>A	ENSP00000300692:p.Arg169Trp		Somatic				CD3D_uc001pst.1_Missense_Mutation_p.R125W|CD3D_uc021qrf.1_Missense_Mutation_p.R96W	p.R169W	NM_000732	NP_000723	WXS	Illumina GAIIx	Phase_I	P04234	CD3D_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	4	642	-	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)	169					A8MVP6	Missense_Mutation	SNP	ENST00000300692.4	37	c.505C>T	CCDS8394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.94|15.94	2.981355|2.981355	0.53827|0.53827	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000167286|ENSG00000167286	ENST00000300692;ENST00000529594;ENST00000392884|ENST00000534687	T;T;T|.	0.71817|.	-0.6;-0.45;0.48|.	5.18|5.18	1.03|1.03	0.20045|0.20045	.|.	0.361176|.	0.23660|.	N|.	0.045834|.	T|T	0.48804|0.48804	0.1520|0.1520	M|M	0.81802|0.81802	2.56|2.56	0.18873|0.18873	N|N	0.999986|0.999986	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.81914|.	0.995;0.995|.	T|T	0.44283|0.44283	-0.9338|-0.9338	10|5	0.87932|.	D|.	0|.	-4.8893|-4.8893	4.0466|4.0466	0.09776|0.09776	0.177:0.0:0.4972:0.3257|0.177:0.0:0.4972:0.3257	.|.	125;169|.	A8MVP6;P04234|.	.;CD3D_HUMAN|.	W|L	169;96;125|129	ENSP00000300692:R169W;ENSP00000437335:R96W;ENSP00000376622:R125W|.	ENSP00000300692:R169W|.	R|S	-|-	1|2	2|0	CD3D|CD3D	117715098|117715098	0.353000|0.353000	0.24904|0.24904	0.060000|0.060000	0.19600|0.19600	0.787000|0.787000	0.44495|0.44495	1.147000|1.147000	0.31602|0.31602	0.353000|0.353000	0.24079|0.24079	-0.188000|-0.188000	0.12872|0.12872	CGG|TCG		0.502	CD3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392128.1	NM_000732		31	112	0	0	0	1	0	31	112				
PPP1R35	221908	broad.mit.edu	37	7	100033362	100033362	+	Silent	SNP	G	G	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr7:100033362G>C	ENST00000292330.2	-	3	670	c.480C>G	c.(478-480)ctC>ctG	p.L160L	RP11-758P17.3_ENST00000475250.1_RNA|PPP1R35_ENST00000476185.1_Intron|RP11-758P17.2_ENST00000492523.1_RNA	NM_145030.2	NP_659467.1	Q8TAP8	PPR35_HUMAN	protein phosphatase 1, regulatory subunit 35	160					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGTCCCGGAAGAGCCGCTTGG	0.721																																						uc003uuy.1																			0											c.(478-480)ctC>ctG		Homo sapiens protein phosphatase 1, regulatory subunit 35 (PPP1R35), mRNA.							13.0	15.0	14.0					7																	100033362		2194	4292	6486	SO:0001819	synonymous_variant	221908							g.chr7:100033362G>C	BC026269	CCDS5694.1	7q22.1	2012-04-17	2011-10-11	2011-10-11	ENSG00000160813	ENSG00000160813		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28320	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 47"""	C7orf47		12477932	Standard	NM_145030		Approved	MGC22793	uc003uuy.1	Q8TAP8	OTTHUMG00000159540	ENST00000292330.2:c.480C>G	7.37:g.100033362G>C			Somatic					p.L160L	NM_145030	NP_659467	WXS	Illumina GAIIx	Phase_I	Q8TAP8	CG047_HUMAN			2	577	-			160					A4D2C5	Silent	SNP	ENST00000292330.2	37	c.480C>G	CCDS5694.1																																																																																				0.721	PPP1R35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356095.2	NM_145030		3	8	0	0	0	1	0	3	8				
CDH11	1009	broad.mit.edu	37	16	64984728	64984728	+	Silent	SNP	G	G	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr16:64984728G>A	ENST00000268603.4	-	12	2451	c.1836C>T	c.(1834-1836)aaC>aaT	p.N612N	CDH11_ENST00000566827.1_Silent_p.N486N|CDH11_ENST00000394156.3_Silent_p.N612N	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	612	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TCAGGCCGGCGTTCAGAATGT	0.632			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																												uc002eoi.3				Dom	yes		16	16q22.1	1009	T	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""			M	USP6		aneurysmal bone cysts		0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88						c.(1834-1836)aaC>aaT		Homo sapiens cadherin 11, type 2, OB-cadherin (osteoblast) (CDH11), mRNA.							91.0	69.0	77.0					16																	64984728		2203	4300	6503	SO:0001819	synonymous_variant	1009				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding	g.chr16:64984728G>A	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1836C>T	16.37:g.64984728G>A		TSP Lung(24;0.17)	Somatic				CDH11_uc010cdn.3_Non-coding_Transcript|CDH11_uc002eoj.3_Silent_p.N612N|CDH11_uc010vin.2_Silent_p.N486N	p.N612N	NM_001797	NP_001788	WXS	Illumina GAIIx	Phase_I	P55287	CAD11_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.205)	11	2270	-		Ovarian(137;0.0973)	612			Cadherin 5.		A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	c.1836C>T	CCDS10803.1																																																																																				0.632	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		27	61	0	0	0	1	0	27	61				
PITX2	5308	broad.mit.edu	37	4	111539506	111539506	+	Missense_Mutation	SNP	A	A	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:111539506A>T	ENST00000354925.2	-	7	2434	c.729T>A	c.(727-729)aaT>aaA	p.N243K	PITX2_ENST00000556049.1_5'Flank|PITX2_ENST00000394595.3_Nonstop_Mutation_p.*175K|PITX2_ENST00000394598.2_Missense_Mutation_p.N243K|PITX2_ENST00000306732.3_Missense_Mutation_p.N250K|RP11-380D23.2_ENST00000503456.1_lincRNA|PITX2_ENST00000355080.5_Missense_Mutation_p.N197K	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	243					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		TGTTCAAGTTATTCAGGCTGT	0.582																																						uc003iac.3																			0				breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10						c.(748-750)aaT>aaA		Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 3, mRNA.							56.0	59.0	58.0					4																	111539506		2203	4300	6503	SO:0001583	missense	5308				determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding	g.chr4:111539506A>T	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.729T>A	4.37:g.111539506A>T	ENSP00000347004:p.Asn243Lys		Somatic				PITX2_uc003iaf.3_Missense_Mutation_p.N243K|PITX2_uc003iad.3_Missense_Mutation_p.N243K|PITX2_uc021xqr.1_Missense_Mutation_p.N243K|PITX2_uc003iae.3_Missense_Mutation_p.N197K|PITX2_uc021xqs.1_Missense_Mutation_p.N197K	p.N250K	NM_000325	NP_000316	WXS	Illumina GAIIx	Phase_I	Q99697	PITX2_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00222)	2	1388	-		Hepatocellular(203;0.217)	243					A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	37	c.750T>A	CCDS3692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.34|13.34	2.208825|2.208825	0.39003|0.39003	.|.	.|.	ENSG00000164093|ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837|ENST00000394595	D;D;D;D;D|.	0.92699|.	-2.74;-2.86;-3.0;-2.86;-3.09|.	5.68|5.68	1.91|1.91	0.25777|0.25777	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.52533|.	0.1740|.	M|M	0.68952|0.68952	2.095|2.095	0.09310|0.09310	N|N	1|1	B;D;P;P|.	0.61080|.	0.349;0.989;0.695;0.481|.	B;D;B;B|.	0.70487|.	0.108;0.969;0.114;0.217|.	T|.	0.42916|.	-0.9423|.	10|.	0.29301|.	T|.	0.29|.	.|.	9.9959|9.9959	0.41898|0.41898	0.6677:0.0:0.3323:0.0|0.6677:0.0:0.3323:0.0	.|.	197;197;243;250|.	A8K6C6;Q99697-3;Q99697;Q99697-2|.	.;.;PITX2_HUMAN;.|.	K|K	250;243;197;243;243|175	ENSP00000304169:N250K;ENSP00000378097:N243K;ENSP00000347192:N197K;ENSP00000347004:N243K;ENSP00000421454:N243K|.	ENSP00000304169:N250K|.	N|X	-|-	3|1	2|0	PITX2|PITX2	111758955|111758955	.|.	.|.	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	.|.	.|.	0.111000|0.111000	0.17947|0.17947	0.533000|0.533000	0.62120|0.62120	AAT|TAA		0.582	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2			28	68	0	0	0	1	0	28	68				
FAM120B	84498	broad.mit.edu	37	6	170628184	170628184	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:170628184C>T	ENST00000476287.1	+	2	1814	c.1706C>T	c.(1705-1707)aCc>aTc	p.T569I	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000537664.1_Missense_Mutation_p.T592I|FAM120B_ENST00000540480.1_Missense_Mutation_p.T581I	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	569					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		CAACAAGTAACCATGGTTTCA	0.388																																						uc003qxp.3																			0		p.V568L(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44						c.(1705-1707)aCc>aTc		Homo sapiens family with sequence similarity 120B (FAM120B), mRNA.							47.0	51.0	49.0					6																	170628184		2200	4297	6497	SO:0001583	missense	84498				cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr6:170628184C>T	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1706C>T	6.37:g.170628184C>T	ENSP00000417970:p.Thr569Ile		Somatic				FAM120B_uc003qxo.1_Missense_Mutation_p.T569I|FAM120B_uc011ehd.2_Intron	p.T569I	NM_032448	NP_115824	WXS	Illumina GAIIx	Phase_I	Q96EK7	F120B_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)	1	1814	+		Breast(66;0.000338)|Esophageal squamous(34;0.241)	569					B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	c.1706C>T	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241785	0.58995	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.10005	2.93;2.92;2.94	4.0	4.0	0.46444	.	0.979946	0.08367	N	0.956701	T	0.09512	0.0234	L	0.48642	1.525	0.80722	D	1	P;P	0.50528	0.936;0.922	P;P	0.52189	0.692;0.614	T	0.30822	-0.9965	10	0.18710	T	0.47	-4.1795	11.9003	0.52680	0.0:1.0:0.0:0.0	.	569;569	Q96EK7;F2Z2E1	F120B_HUMAN;.	I	581;592;569	ENSP00000444125:T581I;ENSP00000440125:T592I;ENSP00000417970:T569I	ENSP00000436640:T569I	T	+	2	0	FAM120B	170470109	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.156000	0.50708	2.536000	0.85505	0.561000	0.74099	ACC		0.388	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		10	27	0	0	0	1	0	10	27				
HYPK	25764	broad.mit.edu	37	15	44093364	44093364	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr15:44093364A>G	ENST00000406925.1	+	3	4332	c.221A>G	c.(220-222)gAg>gGg	p.E74G	SERINC4_ENST00000249714.3_5'Flank|SERINC4_ENST00000319327.6_5'Flank|HYPK_ENST00000442995.2_Missense_Mutation_p.E74G|SERF2_ENST00000600633.1_Missense_Mutation_p.E74G|RP11-296A16.1_ENST00000417761.2_5'Flank|SERF2_ENST00000594896.1_Missense_Mutation_p.E120G|HYPK_ENST00000498605.1_3'UTR|HYPK_ENST00000458412.1_Intron|SERINC4_ENST00000299969.6_5'Flank			Q9NX55	HYPK_HUMAN	huntingtin interacting protein K	74						cytoplasm (GO:0005737)|nucleus (GO:0005634)							all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;8.1e-07)		AGGTCCCGGGAGCAGAAAGCC	0.493																																						uc001ztb.3																			0				endometrium(1)|large_intestine(1)|ovary(1)	3						c.(358-360)gAg>gGg		Homo sapiens chromosome 15 open reading frame 63 (C15orf63), transcript variant 1, mRNA.							87.0	79.0	82.0					15																	44093364		2198	4298	6496	SO:0001583	missense	25764							g.chr15:44093364A>G	AF049613	CCDS10104.1	15q14	2012-10-08	2012-10-08	2012-10-08	ENSG00000242028	ENSG00000242028			18418	protein-coding gene	gene with protein product	"""Huntingtin yeast partner K"""	612784	"""chromosome 15 open reading frame 63"""	C15orf63		9700202, 20154145	Standard	NM_016400		Approved	HSPC136, FLJ20431	uc001ztf.3	Q9NX55	OTTHUMG00000060146	ENST00000406925.1:c.221A>G	15.37:g.44093364A>G	ENSP00000384474:p.Glu74Gly		Somatic				ELL3_uc001zsx.1_5'Flank|SERINC4_uc001ztc.1_5'Flank|SERINC4_uc010bds.1_5'Flank|SERINC4_uc001zte.1_5'Flank|C15orf63_uc001ztf.3_Missense_Mutation_p.E74G|C15orf63_uc021skf.1_Intron|C15orf63_uc001ztg.1_Intron	p.E120G	NM_016400	NP_057484	WXS	Illumina GAIIx	Phase_I	Q9NX55	HYPK_HUMAN			3	842	+			74					C9JKJ0|O75408|Q8WUW8|Q9P024	Missense_Mutation	SNP	ENST00000406925.1	37	c.359A>G	CCDS10104.1	.	.	.	.	.	.	.	.	.	.	A	32	5.165387	0.94768	.	.	ENSG00000242028	ENST00000406925;ENST00000442995	T;T	0.50813	0.73;0.73	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.65780	0.2724	M	0.79123	2.44	0.80722	D	1	D	0.69078	0.997	P	0.58721	0.844	T	0.70795	-0.4775	10	0.72032	D	0.01	-21.5167	15.4975	0.75666	1.0:0.0:0.0:0.0	.	74	Q9NX55	HYPK_HUMAN	G	74	ENSP00000384474:E74G;ENSP00000401155:E74G	ENSP00000384474:E74G	E	+	2	0	C15orf63	41880656	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.847000	0.92166	2.324000	0.78689	0.533000	0.62120	GAG		0.493	HYPK-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133876.3	NM_016400		16	83	0	0	0	1	0	16	83				
TNIP2	79155	broad.mit.edu	37	4	2757866	2757866	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:2757866delG	ENST00000315423.7	-	1	237	c.151delC	c.(151-153)cgcfs	p.R51fs	TNIP2_ENST00000503235.1_Frame_Shift_Del_p.R51fs|TNIP2_ENST00000510267.1_5'UTR	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCGGCCAGGCGGGCGCGGAGG	0.761																																						uc003gfg.2																			0				breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14						c.(151-153)cgcfs		Homo sapiens TNFAIP3 interacting protein 2 (TNIP2), transcript variant 1, mRNA.							2.0	2.0	2.0					4																	2757866		1279	2739	4018	SO:0001589	frameshift_variant	79155					cytosol	protein binding	g.chr4:2757866delG	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.151delC	4.37:g.2757866delG	ENSP00000321203:p.Arg51fs		Somatic				TNIP2_uc003gff.2_5'Flank	p.R51fs	NM_024309	NP_001154999	WXS	Illumina GAIIx	Phase_I	Q8NFZ5	TNIP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	0	238	-			51						Frame_Shift_Del	DEL	ENST00000315423.7	37	c.151delC	CCDS3362.1																																																																																				0.761	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		2	4						2	4	---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41043681	41043682	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chrX:41043681_41043682insA	ENST00000324545.8	+	23	3944_3945	c.3311_3312insA	c.(3310-3315)gcacctfs	p.P1105fs	USP9X_ENST00000378308.2_Frame_Shift_Ins_p.P1105fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1105					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CCTGCTGGTGCACCTCTGGCTG	0.401																																					Ovarian(172;1807 2695 35459 49286)	uc004dfb.3																			0				NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						c.(3310-3312)gcafs		Homo sapiens ubiquitin specific peptidase 9, X-linked (USP9X), transcript variant 3, mRNA.																																				SO:0001589	frameshift_variant	8239				BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity	g.chrX:41043681_41043682insA	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3312dupA	X.37:g.41043682_41043682dupA	ENSP00000316357:p.Pro1105fs		Somatic				USP9X_uc004dfc.3_Frame_Shift_Ins_p.A1104fs	p.A1104fs	NM_001039590	NP_001034679	WXS	Illumina GAIIx	Phase_I	Q93008	USP9X_HUMAN			22	3944_3945	+			1104					O75550|Q8WWT3|Q8WX12	Frame_Shift_Ins	INS	ENST00000324545.8	37	c.3311_3312insA	CCDS43930.1																																																																																				0.401	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		20	41						20	41	---	---	---	---
