#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
GPR4	2828	broad.mit.edu	37	19	46094655	46094655	+	Missense_Mutation	SNP	T	T	A			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr19:46094655T>A	ENST00000323040.4	-	2	1414	c.470A>T	c.(469-471)gAg>gTg	p.E157V	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	157					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		TCGGAAGAGCTCGTCATGGAA	0.652																																					Esophageal Squamous(117;181 1612 1673 14956 42937)	ENST00000323040.4																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						c.(469-471)gAg>gTg		G protein-coupled receptor 4							59.0	60.0	60.0					19																	46094655		2203	4300	6503	SO:0001583	missense	2828					integral to plasma membrane	G-protein coupled receptor activity	g.chr19:46094655T>A	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.470A>T	19.37:g.46094655T>A	ENSP00000319744:p.Glu157Val					OPA3_ENST00000544371.1_Intron	p.E157V	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)	2	1414	-			157					A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000323040.4	37	c.470A>T	CCDS12669.1	.	.	.	.	.	.	.	.	.	.	T	19.95	3.921780	0.73213	.	.	ENSG00000177464	ENST00000323040	T	0.72282	-0.64	5.23	5.23	0.72850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000004	T	0.76307	0.3969	L	0.45285	1.41	0.42849	D	0.994078	D	0.71674	0.998	D	0.72625	0.978	T	0.77664	-0.2503	10	0.56958	D	0.05	.	9.3319	0.38027	0.0:0.0:0.1807:0.8193	.	157	P46093	GPR4_HUMAN	V	157	ENSP00000319744:E157V	ENSP00000319744:E157V	E	-	2	0	GPR4	50786495	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.994000	0.56994	1.978000	0.57642	0.374000	0.22700	GAG		0.652	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282		11	85	0	0	0	1	0	11	85				
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	lincRNA	SNP	C	C	T	rs367060	byFrequency	TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTCAGCCTTCCGCCGGGCCAG	0.672													.|||	253	0.0505192	0.115	0.0533	5008	,	,		65734	0.0119		0.0437	False		,,,				2504	0.0082					ENST00000412962.1																			0																																																			0							g.chr1:16946434C>T	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946434C>T														0	1085	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		3	15	0	0	0	1	0	3	15				
MLLT4	4301	broad.mit.edu	37	6	168227250	168227250	+	5'Flank	SNP	C	C	T			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr6:168227250C>T	ENST00000447894.2	+	0	0				MLLT4_ENST00000392108.3_5'Flank|MLLT4_ENST00000392112.1_5'Flank|MLLT4_ENST00000344191.4_5'Flank|MLLT4-AS1_ENST00000359760.5_RNA|MLLT4_ENST00000351017.4_5'Flank|MLLT4_ENST00000400822.3_5'Flank|MLLT4_ENST00000366806.2_5'Flank			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4						adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		CCGGACTCTGCACCGCGCGTC	0.667			T	MLL	AL																																	ENST00000359760.5				Dom	yes		6	6q27	4301		"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""			L					0																																																	SO:0001631	upstream_gene_variant	0							g.chr6:168227250C>T	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031		6.37:g.168227250C>T	Exception_encountered							NR_027906.1						0	139	-								O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	RNA	SNP	ENST00000447894.2	37																																																																																						0.667	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		8	29	0	0	0	1	0	8	29				
GPR101	83550	broad.mit.edu	37	X	136112376	136112376	+	Missense_Mutation	SNP	G	G	T			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chrX:136112376G>T	ENST00000298110.1	-	1	1457	c.1458C>A	c.(1456-1458)gaC>gaA	p.D486E		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	486						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					TTCCGGGCAGGTCTGGGTGGC	0.478																																						ENST00000298110.1																			0				autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42						c.(1456-1458)gaC>gaA		G protein-coupled receptor 101							101.0	95.0	97.0					X																	136112376		2203	4300	6503	SO:0001583	missense	83550					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chrX:136112376G>T	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1458C>A	X.37:g.136112376G>T	ENSP00000298110:p.Asp486Glu						p.D486E	NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN			1	1457	-	Acute lymphoblastic leukemia(192;0.000127)		486					Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	c.1458C>A	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	G	5.090	0.202294	0.09652	.	.	ENSG00000165370	ENST00000298110	T	0.36157	1.27	5.08	-1.35	0.09114	.	.	.	.	.	T	0.16041	0.0386	N	0.14661	0.345	0.20307	N	0.999919	B	0.02656	0.0	B	0.04013	0.001	T	0.32134	-0.9918	9	0.11182	T	0.66	-9.416	5.3993	0.16286	0.3315:0.2257:0.4428:0.0	.	486	Q96P66	GP101_HUMAN	E	486	ENSP00000298110:D486E	ENSP00000298110:D486E	D	-	3	2	GPR101	135940042	1.000000	0.71417	0.158000	0.22627	0.382000	0.30200	1.202000	0.32271	-0.414000	0.07495	0.429000	0.28392	GAC		0.478	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			22	77	1	0	1.87028e-06	1	1.94222e-06	22	77				
AGPAT6	137964	broad.mit.edu	37	8	41470442	41470442	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr8:41470442C>T	ENST00000396987.3	+	8	1801	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	292					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			CTGGTTTGAGCGCTCGGAAGT	0.552											OREG0018739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000396987.3																			0				endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14						c.(874-876)Cgc>Tgc		1-acylglycerol-3-phosphate O-acyltransferase 6							104.0	77.0	86.0					8																	41470442		2203	4300	6503	SO:0001583	missense	137964				acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity	g.chr8:41470442C>T	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20880	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, zeta"""	608143	"""1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"""			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.874C>T	8.37:g.41470442C>T	ENSP00000380184:p.Arg292Cys		OREG0018739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	901	RP11-360L9.8_ENST00000581909.1_RNA	p.R292C	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)		8	1801	+	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	292					Q86V89	Missense_Mutation	SNP	ENST00000396987.3	37	c.874C>T	CCDS6117.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727164	0.89390	.	.	ENSG00000158669	ENST00000396987	D	0.99214	-5.57	5.3	5.3	0.74995	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99569	0.9845	M	0.94142	3.5	0.80722	D	1	D	0.69078	0.997	D	0.66979	0.948	D	0.98154	1.0443	10	0.87932	D	0	.	18.1301	0.89598	0.0:1.0:0.0:0.0	.	292	Q86UL3	GPAT4_HUMAN	C	292	ENSP00000380184:R292C	ENSP00000380184:R292C	R	+	1	0	AGPAT6	41589599	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.793000	0.69060	2.769000	0.95229	0.655000	0.94253	CGC		0.552	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		5	14	0	0	0	1	0	5	14				
KRT9	3857	broad.mit.edu	37	17	39725743	39725743	+	Missense_Mutation	SNP	G	G	A			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr17:39725743G>A	ENST00000246662.4	-	4	1044	c.979C>T	c.(979-981)Cgt>Tgt	p.R327C	KRT9_ENST00000588431.1_Missense_Mutation_p.R94C	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	327	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TACTCCTGACGCATGTCATTG	0.502																																						ENST00000246662.4																			0				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						c.(979-981)Cgt>Tgt		keratin 9							216.0	174.0	188.0					17																	39725743		2203	4300	6503	SO:0001583	missense	3857				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton	g.chr17:39725743G>A		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.979C>T	17.37:g.39725743G>A	ENSP00000246662:p.Arg327Cys					KRT9_ENST00000588431.1_Missense_Mutation_p.R94C	p.R327C	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN			4	1044	-		Breast(137;0.000307)	327			Coil 2.|Rod.		O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	c.979C>T	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.163226	0.38217	.	.	ENSG00000171403	ENST00000246662	D	0.93426	-3.22	4.25	3.25	0.37280	Filament (1);	.	.	.	.	D	0.94248	0.8153	H	0.96996	3.92	0.39645	D	0.970389	D	0.54207	0.965	B	0.40901	0.343	D	0.94494	0.7704	9	0.87932	D	0	.	6.4217	0.21748	0.0984:0.0:0.5989:0.3027	.	327	P35527	K1C9_HUMAN	C	327	ENSP00000246662:R327C	ENSP00000246662:R327C	R	-	1	0	KRT9	36979269	1.000000	0.71417	0.658000	0.29665	0.276000	0.26787	1.819000	0.39022	1.887000	0.54652	0.561000	0.74099	CGT		0.502	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		9	47	0	0	0	1	0	9	47				
LAIR2	3904	broad.mit.edu	37	19	55020248	55020248	+	Missense_Mutation	SNP	G	G	C	rs12949		TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr19:55020248G>C	ENST00000301202.2	+	4	490	c.368G>C	c.(367-369)aGc>aCc	p.S123T	LAIR2_ENST00000351841.2_Intron	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	123						extracellular region (GO:0005576)		p.S123T(1)		central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		TTTACAGAAAGCTCTGGAGGC	0.627																																						ENST00000301202.2																			1	Substitution - Missense(1)	p.S123T(1)	kidney(1)	central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18						c.(367-369)aGc>aCc		leukocyte-associated immunoglobulin-like receptor 2							54.0	63.0	60.0					19																	55020248		2127	4276	6403	SO:0001583	missense	3904					extracellular region	receptor activity	g.chr19:55020248G>C	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.368G>C	19.37:g.55020248G>C	ENSP00000301202:p.Ser123Thr					LAIR2_ENST00000351841.2_Intron	p.S123T	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN		GBM - Glioblastoma multiforme(193;0.0967)	4	490	+	Ovarian(34;0.19)		123					Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	c.368G>C	CCDS12897.1	97	0.044413919413919416	28	0.056910569105691054	13	0.03591160220994475	7	0.012237762237762238	49	0.06464379947229551	C	0.004	-2.301275	0.00243	.	.	ENSG00000167618	ENST00000301202	T	0.00523	6.83	1.4	-1.19	0.09585	.	.	.	.	.	T	0.00039	0.0001	N	0.02539	-0.55	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	9	0.14252	T	0.57	.	0.4992	0.00576	0.2475:0.3218:0.2448:0.1859	rs3177589;rs17343215	123	Q6ISS4	LAIR2_HUMAN	T	123	ENSP00000301202:S123T	ENSP00000301202:S123T	S	+	2	0	LAIR2	59712060	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.594000	0.02094	-0.745000	0.04772	-0.980000	0.02579	AGC		0.627	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			3	12	0	0	0	1	0	3	12				
SDHAP1	255812	broad.mit.edu	37	3	195717102	195717102	+	RNA	SNP	A	A	G			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr3:195717102A>G	ENST00000427841.1	-	0	48					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		GCGCTTGGCAACCGCGACAGG	0.776																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195717102A>G	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195717102A>G								NR_003264.2						0	48	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.776	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			4	12	0	0	0	1	0	4	12				
MAN1A1	4121	broad.mit.edu	37	6	119569448	119569448	+	Silent	SNP	A	A	C			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr6:119569448A>C	ENST00000368468.3	-	6	1410	c.969T>G	c.(967-969)ccT>ccG	p.P323P	MAN1A1_ENST00000368466.2_Silent_p.P346P	NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	323					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		GCAATGCCCAAGGTATTCCAG	0.343																																					Ovarian(136;8 1825 12608 33541 47587)	ENST00000368468.3																			0				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24						c.(967-969)ccT>ccG		mannosidase, alpha, class 1A, member 1							92.0	89.0	90.0					6																	119569448		2203	4300	6503	SO:0001819	synonymous_variant	4121				post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	g.chr6:119569448A>C	AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	3.2.1.113		6821	protein-coding gene	gene with protein product		604344				8223597	Standard	NM_005907		Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.969T>G	6.37:g.119569448A>C						MAN1A1_ENST00000368466.2_Silent_p.P346P	p.P323P	NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)	6	1410	-		all_epithelial(87;0.173)	323					E7EU32|Q6P052|Q9NU44|Q9UJI3	Silent	SNP	ENST00000368468.3	37	c.969T>G	CCDS5122.1																																																																																				0.343	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	NM_005907		10	29	0	0	0	1	0	10	29				
AGPAT6	137964	broad.mit.edu	37	8	41470441	41470441	+	Silent	SNP	G	G	A	rs371903817		TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr8:41470441G>A	ENST00000396987.3	+	8	1800	c.873G>A	c.(871-873)gaG>gaA	p.E291E	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	291					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			TCTGGTTTGAGCGCTCGGAAG	0.547											OREG0018739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000396987.3																			0				endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14						c.(871-873)gaG>gaA		1-acylglycerol-3-phosphate O-acyltransferase 6							105.0	77.0	87.0					8																	41470441		2203	4300	6503	SO:0001819	synonymous_variant	137964				acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity	g.chr8:41470441G>A	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20880	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, zeta"""	608143	"""1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"""			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.873G>A	8.37:g.41470441G>A			OREG0018739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	901	RP11-360L9.8_ENST00000581909.1_RNA	p.E291E	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)		8	1800	+	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	291					Q86V89	Silent	SNP	ENST00000396987.3	37	c.873G>A	CCDS6117.1																																																																																				0.547	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		5	14	0	0	0	1	0	5	14				
TNNT3	7140	broad.mit.edu	37	11	1956128	1956128	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr11:1956128G>C	ENST00000397301.1	+	15	701	c.693G>C	c.(691-693)aaG>aaC	p.K231N	TNNT3_ENST00000397304.2_Missense_Mutation_p.K201N|TNNT3_ENST00000381589.3_Missense_Mutation_p.K218N|TNNT3_ENST00000381561.4_Missense_Mutation_p.K223N|TNNT3_ENST00000381558.1_Missense_Mutation_p.K212N|TNNT3_ENST00000278317.6_Missense_Mutation_p.K220N|TNNT3_ENST00000381549.3_Missense_Mutation_p.K212N|TNNT3_ENST00000446240.1_Missense_Mutation_p.K201N|TNNT3_ENST00000381579.3_Missense_Mutation_p.K212N|TNNT3_ENST00000360603.3_Missense_Mutation_p.K214N|TNNT3_ENST00000381548.3_Missense_Mutation_p.K222N|TNNT3_ENST00000493234.1_3'UTR			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	231					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		TTGGGGAGAAGCTGAAACGCC	0.612																																						ENST00000381558.1																			0				breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19						c.(634-636)aaG>aaC		troponin T type 3 (skeletal, fast)							132.0	136.0	134.0					11																	1956128		2202	4299	6501	SO:0001583	missense	7140				muscle filament sliding|regulation of ATPase activity|regulation of striated muscle contraction|skeletal muscle contraction	cytosol|troponin complex	calcium-dependent protein binding|tropomyosin binding|troponin C binding|troponin I binding	g.chr11:1956128G>C	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"""troponin-T3, skeletal, fast"""	600692	"""troponin T3, skeletal, fast"""			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	ENST00000397301.1:c.693G>C	11.37:g.1956128G>C	ENSP00000380468:p.Lys231Asn					TNNT3_ENST00000360603.3_Missense_Mutation_p.K214N|TNNT3_ENST00000381548.3_Missense_Mutation_p.K222N|TNNT3_ENST00000381561.4_Missense_Mutation_p.K223N|TNNT3_ENST00000446240.1_Missense_Mutation_p.K201N|TNNT3_ENST00000381579.3_Missense_Mutation_p.K212N|TNNT3_ENST00000397301.1_Missense_Mutation_p.K231N|TNNT3_ENST00000278317.6_Missense_Mutation_p.K220N|TNNT3_ENST00000493234.1_3'UTR|TNNT3_ENST00000397304.2_Missense_Mutation_p.K201N|TNNT3_ENST00000381589.3_Missense_Mutation_p.K218N|TNNT3_ENST00000381549.3_Missense_Mutation_p.K212N	p.K212N			P45378	TNNT3_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)	13	915	+		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	231					A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Missense_Mutation	SNP	ENST00000397301.1	37	c.636G>C		.	.	.	.	.	.	.	.	.	.	.	13.21	2.169166	0.38315	.	.	ENSG00000130595	ENST00000278317;ENST00000397309;ENST00000381561;ENST00000381548;ENST00000360603;ENST00000381549;ENST00000381589;ENST00000381579;ENST00000381557;ENST00000453458;ENST00000381563;ENST00000344578;ENST00000381558;ENST00000397301;ENST00000397304;ENST00000446240	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34;-2.34	4.28	1.25	0.21368	.	0.096661	0.64402	D	0.000002	D	0.90665	0.7072	M	0.82517	2.595	0.48288	D	0.999622	D;D;D;D;P	0.56035	0.974;0.974;0.974;0.974;0.956	P;P;P;P;P	0.56700	0.804;0.735;0.804;0.804;0.641	D	0.89491	0.3757	10	0.54805	T	0.06	-12.8892	10.4399	0.44460	0.3021:0.0:0.6979:0.0	.	220;212;218;212;231	P45378-2;P45378-7;P45378-6;P45378-4;P45378	.;.;.;.;TNNT3_HUMAN	N	220;232;223;222;214;212;218;212;206;201;223;207;212;231;201;201	ENSP00000278317:K220N;ENSP00000370973:K223N;ENSP00000370960:K222N;ENSP00000353815:K214N;ENSP00000370961:K212N;ENSP00000371001:K218N;ENSP00000370991:K212N;ENSP00000370969:K206N;ENSP00000415614:K201N;ENSP00000370975:K223N;ENSP00000344870:K207N;ENSP00000370970:K212N;ENSP00000380468:K231N;ENSP00000380471:K201N;ENSP00000413203:K201N	ENSP00000278317:K220N	K	+	3	2	TNNT3	1912704	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	0.737000	0.26144	0.384000	0.24942	0.313000	0.20887	AAG		0.612	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757		31	108	0	0	0	1	0	31	108				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	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		11	56	0	0	0	1	0	11	56				
PHKA2	5256	broad.mit.edu	37	X	18913268	18913268	+	Silent	SNP	C	C	T			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chrX:18913268C>T	ENST00000379942.4	-	31	3989	c.3324G>A	c.(3322-3324)tcG>tcA	p.S1108S	PHKA2-AS1_ENST00000439295.1_RNA|PHKA2-AS1_ENST00000452900.1_RNA|PHKA2_ENST00000481718.1_5'UTR	NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1108					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CTCGGGTCGTCGAGGATGGGA	0.527																																						ENST00000379942.4																			0				NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61						c.(3322-3324)tcG>tcA		phosphorylase kinase, alpha 2 (liver)							173.0	147.0	156.0					X																	18913268		2203	4300	6503	SO:0001819	synonymous_variant	5256				glucose metabolic process|glycogen catabolic process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity	g.chrX:18913268C>T		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.3324G>A	X.37:g.18913268C>T						PHKA2_ENST00000481718.1_5'UTR	p.S1108S	NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN			31	3989	-	Hepatocellular(33;0.183)		1108					A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Silent	SNP	ENST00000379942.4	37	c.3324G>A	CCDS14190.1																																																																																				0.527	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		25	89	0	0	0	1	0	25	89				
PELI1	57162	broad.mit.edu	37	2	64323399	64323399	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr2:64323399T>C	ENST00000358912.4	-	6	992	c.550A>G	c.(550-552)Acc>Gcc	p.T184A		NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	184					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						CCATTAGTGGTCAAGCCATCC	0.428																																						ENST00000358912.4																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						c.(550-552)Acc>Gcc		pellino E3 ubiquitin protein ligase 1							145.0	132.0	137.0					2																	64323399		2203	4300	6503	SO:0001583	missense	57162				innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol		g.chr2:64323399T>C		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.550A>G	2.37:g.64323399T>C	ENSP00000351789:p.Thr184Ala						p.T184A	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN			6	992	-			184					Q96SM0|Q9GZY5|Q9HCX0	Missense_Mutation	SNP	ENST00000358912.4	37	c.550A>G	CCDS1876.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.627442	0.87560	.	.	ENSG00000197329	ENST00000358912	T	0.57436	0.4	5.65	5.65	0.86999	.	0.134439	0.64402	D	0.000002	T	0.75961	0.3921	M	0.89095	3.005	0.58432	D	0.999999	D	0.65815	0.995	D	0.66497	0.944	T	0.80353	-0.1418	10	0.56958	D	0.05	-11.7071	16.1778	0.81874	0.0:0.0:0.0:1.0	.	184	Q96FA3	PELI1_HUMAN	A	184	ENSP00000351789:T184A	ENSP00000351789:T184A	T	-	1	0	PELI1	64176903	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.279000	0.76181	0.533000	0.62120	ACC		0.428	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651		5	66	0	0	0	1	0	5	66				
SDHAP1	255812	broad.mit.edu	37	3	195717098	195717098	+	RNA	SNP	G	G	A			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr3:195717098G>A	ENST00000427841.1	-	0	52					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		CCGAGCGCTTGGCAACCGCGA	0.781																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195717098G>A	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195717098G>A								NR_003264.2						0	52	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.781	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			4	12	0	0	0	1	0	4	12				
SYF2	25949	broad.mit.edu	37	1	25553932	25553934	+	Splice_Site	DEL	CTG	CTG	-			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr1:25553932_25553934delCTG	ENST00000236273.4	-	5	491_493	c.466_468delCAG	c.(466-468)cagdel	p.Q156del	SYF2_ENST00000354361.3_Splice_Site_p.Q114del|SYF2_ENST00000476231.1_5'Flank	NM_015484.4	NP_056299.1	O95926	SYF2_HUMAN	SYF2 pre-mRNA-splicing factor	156					embryonic organ development (GO:0048568)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|mitotic G2 DNA damage checkpoint (GO:0007095)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(4)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)		AAAGGACTTACTGTTTTTCTCTC	0.384																																						ENST00000236273.4																			0				kidney(1)|large_intestine(1)|lung(4)	6						c.e5+1		SYF2 pre-mRNA-splicing factor																																				SO:0001630	splice_region_variant	25949					catalytic step 2 spliceosome		g.chr1:25553932_25553934delCTG	AF273089	CCDS258.1, CCDS259.1	1p36.11	2013-08-21	2013-08-21	2005-09-14	ENSG00000117614	ENSG00000117614			19824	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 29"""	607090	"""CCNDBP1 interactor"", ""SYF2 homolog, RNA splicing factor (S. cerevisiae)"""	CBPIN		11118353	Standard	NM_207170		Approved	p29, DKFZp564O2082, NTC31, fSAP29	uc001bjt.1	O95926	OTTHUMG00000043610	ENST00000236273.4:c.467+1CAG>-	1.37:g.25553932_25553934delCTG						SYF2_ENST00000354361.3_Splice_Site_p.114_splice	p.156_splice	NM_015484.4	NP_056299.1	O95926	SYF2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201)	5	491_493	-		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)	156					Q5TH73	Splice_Site	DEL	ENST00000236273.4	37	c.467_splice	CCDS259.1																																																																																				0.384	SYF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101962.1	NM_015484	In_Frame_Del	9	98						9	98	---	---	---	---
GJA3	2700	broad.mit.edu	37	13	20716349	20716349	+	Frame_Shift_Del	DEL	G	G	-			TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr13:20716349delG	ENST00000241125.3	-	2	1255	c.1079delC	c.(1078-1080)ccgfs	p.P361fs		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	361					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		CGCGAGTGGCGGGGAGCTGCT	0.766																																						ENST00000241125.3																			0				NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						c.(1078-1080)cgfs		gap junction protein, alpha 3, 46kDa							2.0	4.0	3.0					13																	20716349		1618	3343	4961	SO:0001589	frameshift_variant	2700				cell-cell signaling|visual perception	connexon complex|integral to membrane		g.chr13:20716349delG	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"""Ion channels / Gap junction proteins (connexins)"""	4277	protein-coding gene	gene with protein product	"""connexin 46"""	121015	"""gap junction protein, alpha 3, 46kD (connexin 46)"", ""gap junction protein, alpha 3, 46kDa (connexin 46)"""	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.1079delC	13.37:g.20716349delG	ENSP00000241125:p.Pro361fs						p.P361fs	NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)	2	1255	-		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)	361					Q0VAB7|Q9H537	Frame_Shift_Del	DEL	ENST00000241125.3	37	c.1079delC	CCDS9289.1																																																																																				0.766	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954		2	4						2	4	---	---	---	---
TMEM199	147007	broad.mit.edu	37	17	26684394	26684395	+	5'Flank	INS	-	-	G	rs202089331|rs17856014	byFrequency	TCGA-EL-A4JX-01A-12D-A257-08	TCGA-EL-A4JX-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8fc9f8a6-5a37-4f2b-b160-6e1f06a433dd	7edd3289-ff98-4237-a5bf-a3ece719e294	g.chr17:26684394_26684395insG	ENST00000292114.3	+	0	0				TMEM199_ENST00000509083.1_5'Flank|POLDIP2_ENST00000540200.1_Splice_Site|TMEM199_ENST00000395404.3_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|POLDIP2_ENST00000003607.4_5'UTR	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		AGAGCGGCTTTGCCACCGGGCC	0.762																																						ENST00000540200.1																			0											c.e1+1		polymerase (DNA-directed), delta interacting protein 2				2770,50		1380,10,20						0.4	0.1		dbSNP_130	4	6440,112		3203,34,39	no	frameshift	POLDIP2	NM_015584.3		4583,44,59	A1A1,A1R,RR		1.7094,1.773,1.7286				9210,162				SO:0001631	upstream_gene_variant	26073					mitochondrial nucleoid|nucleus		g.chr17:26684394_26684395insG	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26684395_26684395dupG	Exception_encountered					POLDIP2_ENST00000003607.4_5'UTR		NM_015584.3	NP_056399.1	Q9Y2S7	PDIP2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	1	78	-	all_lung(13;0.000354)|Lung NSC(42;0.00115)								Splice_Site	INS	ENST00000292114.3	37		CCDS11228.1																																																																																				0.762	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464		2	4						2	4	---	---	---	---
